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The Multinational Science Steering Committee:
Committee Chair: Gerd Jürgens, University of Tübingen, Germany
Michael
Bevan, John Innes Centre, Norwich, United Kingdom
Michel Caboche, Lab. Biol.
Cellulaire, INRA, Versailles, France
Daphne Preuss, University of Chicago,
Chicago, IL, USA
Joseph Ecker, University of Pennsylvania, Philadelphia, PA
USA
Fernando Migliaccio, CNR, Monterotondo, Italy
Kiyotaka Okada, Kyoto
University, Kyoto, Japan
David Smyth, Monash University, Clayton, Australia
Marc Van Montagu, University of Ghent, Belgium
Preface
Overview of Genome
Analysis
Stock
Center Resources and Data Bases
National and
Transnational Projects
Appendix 1: NSF Arabidopsis
Genome Meeting Report
Appendix 2: Summary of
December 1998 AGI Meeting at CSHL
Appendix 3: Database
Workshop (Madison, WI 1998) Report
Appendix 4: "Arabidopsis
thaliana Information Resource Project" Announcment
The "Multinational Coordinated Arabidopsis thaliana Genome Research Project"
was established in 1990 to promote international cooperation in basic and
applied research with Arabidopsis, a model plant species amenable to
experimental manipulation in the laboratory. The primary objective of this
project has been to understand the molecular basis of plant growth and
development and to address fundamental questions in plant genetics, physiology,
biochemistry, cell biology, and pathology. Initial plans were outlined in a
publication (NSF #90-80) drafted nine years ago by an ad hoc committee of nine
scientists from the United States, Europe, Japan, and Australia. In recent
years, this project has become a model for widespread participation and
effective coordination of multinational research efforts in modern biology.
Arabidopsis thaliana, a small plant in the mustard family, was chosen for
this large-scale research effort because it offers many advantages for detailed
genetic and molecular studies. Among these features are its small size, short
life cycle, small genome, ability to be transformed, availability of numerous
mutations, and prolific seed production. By concentrating research efforts on a
single model organism, detailed information on specific genes and cellular
processes can be readily obtained and rapidly applied to a wide range of plants
relevant to agriculture, health, energy, manufacturing, and the environment.
Each year since 1990, the scientific steering committee for the Arabidopsis
Genome Project has prepared a progress report summarizing recent advances in
Arabidopsis research. This is the seventh annual progress report published by
the steering committee in conjunction with the U.S. National Science Foundation.
Three years ago the report was a color brochure designed to explain the value
and significance of Arabidopsis research to a wide audience. Two years ago the
report presented a detailed overview of recent advances in research with
Arabidopsis, along with technical information for use by members of the
Arabidopsis community. The sixth report presented an updated vision statement
for the future to stimulate further advances in the use of Arabidopsis as a
model system for the analysis of complex organisms.
This report covers progress for the seventh and eighth years of the project.
It is focused on the large-scale analysis of the Arabidopsis genome.
Specifically, this report is designed to make the available information
accessible to the scientific community in a hands-on format. At the current rate
of progress, the genome sequencing project can be expected to be completed
within two years. The 1998 genome issue of Science (Meinke et al. 1998) featured
Arabidopsis prominently.
Multinational cooperation and communication continue to be an important feature of the Arabidopsis genome project. A brief overview of Arabidopsis research efforts in a number of participating countries is therefore included in this report. Additional information can be obtained through recent publications, electronic news groups and databases, and biological resource centers devoted to Arabidopsis research. As with any document that attempts to summarize the contributions of many individuals, this report may fail to include or misrepresent some significant achievements. The steering committee hopes that members of the Arabidopsis community will overlook such shortcomings and will communicate any concerns to committee members so that future reports will be as accurate as possible. We thank all members of the Arabidopsis community for their many contributions to the success of the initial phase of the Multinational Coordinated Arabidopsis thaliana Genome Research Project.
| 1983 | Publication of first genetic map |
| 1988-89 | Publication of RFLP maps |
| 1990 | Multinational Coordinated Arabidopsis thaliana Genome Research Project initiated |
| 1991 | Arabidopsis Stock Centers at Ohio State (USA) and Nottingham (UK), as well as the Arabidopsis Data Base (AtDB), were established |
| 1991 | First YAC libraries and anchoring of YAC clones to RFLP map |
| 1992 | Publication of first chromosome walk (local contig) |
| 1993 | Recombinant inbred (RI) map |
| 1994-8 | Collections of cDNA (EST) clones sequenced linking up genetic and cytogenetic with physical maps |
| 1995-6 | CIC-YACs, TAMU-BACs, IGF-BACs, Mitsui-P1, Kazusa-P1 libraries |
| 1995-8 | Physical map of all 5 chromosomes delineated |
| Jan 98 | Publication of 1.9 Mb of contiguous DNA sequence from chromosome 4 |
| June 98 | 29 Mb of genomic DNA sequenced |
| Oct. 98 | Arabidopsis featured in genome issue of "Science" |
| Dec 98 | >46 Mb of genomic DNA sequenced and annotated 90 Mb of genomic DNA in edited BAC contigs >41,000 (of 44,000) BAC ends sequenced >11,000 non-redundant (of >37,000) EST clones |
| 2000 | Completion of genome sequencing (expected
date) |
Two genetic maps were independently developed: a classic map of mutations
(Koornneef et al., 1983) and a recombinant inbred (RI) map of molecular markers
(Lister and Dean, 1993). As an increasing number of genes originally identified
by mutation has been cloned and converted to molecular markers mapped onto the
RI map, the two maps are beginning to merge into a unified genetic map. Map
distances differ between the two maps, presumably because of the different
genetic backgrounds. In addition, map distances are calculated with the Mapmaker
program, resulting in local inaccuracies, such as relative order of closely
linked markers. These problems will eventually be resolved by physical
mapping.
The RI map is now commonly used as the standard reference, enabling new genes
identified by mutation to be easily mapped by PCR markers (SSLP, CAPS). The
current RI map (November 1998) contains ca. 800 markers which fall into 3
different categories: "framework" (fixed reference location), "unique" (defined
location on the map) and "multiple" (several possible locations). RI markers
were also used to map a collection of YAC, BAC and P1 clones from which physical
maps of the 5 chromosomes were initiated, thus linking genetic and physical maps
from the very beginning.
Several physical maps have been established for all 5 chromosomes. Initially,
contigs of large YAC clones were assembled and anchored to RI markers (e.g.
Schmidt et al., 1997; Bouchez et al., 1998). Corresponding BAC and P1 clones
were identified by hybridisation with YAC clones. For chromosome 5, a
nearly complete physical map was established by P1 and TAC clone contigs (Kazusa
homepage; Kotani et al., 1997). BAC contigs have also been established at the
global scale by fingerprinting and by hybridisation with BAC endprobes.
For example, 9 Mb constituting the bottom arm of chromosome 3 have been covered
by a single BAC contig (see http://www.genoscope.cns.fr/externe/English/Projets/projetsindex.html).
In addition to whole-chromosome physical mapping with YAC, BAC and P1 clones,
chromosome walks in several chromosome regions have yielded local contigs up to
2 Mb long (e.g. Hardtke & Berleth, 1996; Wang et al., 1997; Thorlby et al.,
1997), and several hundred EST clones have been PCR-mapped onto YAC clones
(Agyare et al., 1997).
Fingerprinting data of BAC clones were used to assemble contigs with FPC
software, followed by manual editing to join the initial contigs. At present,
ca. 70 BAC contigs encompass ca. 90 Mb of estimated 121 Mb total sequence (M.
Marra & M. Sekhon, Washington University, St. Louis; M.A. Marra et
al.,1997). High throughput BAC-endprobe hybridization was used as a
complementary approach to assemble contigs (Mozo et al., 1998). Information
gathered from 2995 hybridization data (including 272 mapped markers) was
manually edited after application of the probeorder computer program and
integrated with the fingerprint data to generate a complete BAC-based physical
map consisting of 27 contigs distributed over the 10 chromosome arms that covers
approximately 124 Mb (see: http://www.mpimp-golm.mpg.de/101/bac.html).
As the genome sequencing project is progressing, many RI markers are mapped
physically, resulting in an excellent alignment of genetic and physical maps
(see AtDB; see also integrated contig tables by Daphne Preuss and colleagues at
the CSHL website). This integration will undoubtedly facilitate gene isolation
by map-based cloning.
In addition to the unique-sequence regions of the chromosome arms, both rDNA
repeats (NORs on chromosomes 2 and 4) and centromeric regions have been mapped
genetically and physically. The centromeric regions were mapped by tetrad
analysis (Copenhaver et al., 1998) and localized by in situ hybridization
(Brandes et al., 1997). Thus, an outline of the physical organisation of the
nuclear genome has emerged.
Agyare FD, Lashkari DA, Lagos A, Namath AF, Lagos G, Davis RW, Lemieux B
(1997) Mapping expressed sequence tag sites on yeast artificial chromosome
clones of Arabidopsis thaliana DNA. Genome Res. 7: 1-9.
Brandes A, Thompson H, Dean C, Heslop-Harrison JS (1997) Multiple repetitive
DNA sequences in the paracentromeric regions of Arabidopsis thaliana L.
Chromosome Res. 5: 238-246.
Camilleri C, Lafleuriel J, Macadre C, Varoquaux F, Parmentier Y, Picard G,
Caboche M, Bouchez D (1998) A YAC contig map of Arabidopsis thaliana chromosome
3. Plant J. 14:633-642.
Copenhaver GP, Browne WE, Preuss D (1998) Assaying genome-wide recombination
and centromere functions with Arabidopsis tetrads. Proc. Natl. Acad. Sci. USA
95: 247-252.
Hardtke CS, Berleth T (1996) Genetic and contig map of a 2200-kb region
encompassing 5.5 cM on chromosome 1 of Arabidopsis thaliana. Genome 39:
1086-1092.
Kotani H, Sato S, Fukami M, Hosouchi T, Nakazaki N, Okumura S, Wada T, Liu
YG, Shibata D, Tabata S (1997) A fine physical map of Arabidopsis thaliana
chromosome 5: construction of a sequence-ready contig map. DNA Res.
4:371-378.
Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW,
McPherson JD, Waterston RH (1997) High throughput fingerprint analysis of
large-insert clones. Genome Res. 7: 1072-1084.
Meinke, DW, Cherry JC, Dean C, Rounsley SD, Koornneef M (1998) Arabidopsis
thaliana: A model plant for genome analysis. Science 282: 662-682.
McPherson JD, Waterston RH (1997) High throughput fingerprint analysis of
large-insert clones. Genome Res. 7:1072-1084.
Mozo T, Fischer S, Maier-Ewert S, Lehrach H, Altmann T (1998) Use of the IGF
BAC library for physical mapping of the Arabidopsis thaliana genome. Plant J.
16, 377-384.
Round EK, Flowers SK, Richards EJ (1997) Arabidopsis thaliana centromere
regions: genetic map positions and repetitive DNA structure. Genome Res 1997
Nov;7(11):1045-53
Sato S, Kotani H, Hayashi R, Liu YG, Shibata D, Tabata S (1998) A physical
map of Arabidopsis thaliana chromosome 3 represented by two contigs of CIC YAC,
P1, TAC and BAC clones. DNA Res.5:163-168.
Schmidt R, Love K, West J, Lenehan Z, Dean C (1997) Description of 31 YAC
contigs spanning the majority of Arabidopsis thaliana chromosome 5. Plant J. 11:
563-572.
Thorlby GJ, Shlumukov L, Vizir IY, Yang CY, Mulligan BJ, Wilson ZA (1997)
Fine-scale molecular genetic (RFLP) and physical mapping of a 8.9 cM region on
the top arm of Arabidopsis chromosome 5 encompassing the male sterility gene,
ms1. Plant J. 12: 471-479.
Wang ML, Huang L, Bongard-Pierce DK, Belmonte S, Zachgo EA, Morris JW, Dolan
M, Goodman HM (1997) Construction of an approximately 2 Mb contig in the region
around 80 cM of Arabidopsis thaliana chromosome 2. Plant J. 12: 711-730.
More than 37,000 partial cDNA (EST) sequences have been deposited in the
public databases while the total number of genes is most likely about 20,000.
Building EST "contigs", i.e. larger cDNA sequences from overlapping ESTs,
reduces the number of ESTs to those representing different genomic sequences
(Rounsley et al., 1996; Cooke et al., 1997). The current estimate of
non-redundant ESTs is about 11,000 or approximately half the total number of
genes.
Large-scale high-throughput genomic sequencing makes use of the physical maps
and the available BAC (TAMU, IGF), P1 and TAC (Mitsui, Kazusa) libraries (see
AGI). BAC, TAC and P1 clones are mapped onto YAC, and their ends are sequenced
to determine minimum tiling paths for sequencing large regions. More than 41,000
BAC ends (of a total of 22,000 BAC clones) have been sequenced, yielding
stretches of ca. 400 bp every 4 kb on average (total sequence ca. 14 Mb). The
largest contiguous region sequenced to date is nearly 1.9 Mb long (Bevan et al.,
1998). This region around FCA on chromosome 4 contains 389 genes of which
46% could not be assigned a putative function by sequence comparisons with the
databases. On average, one gene (ORF) was found every 4.8 kb, and similar values
were observed for other genomic regions (Quigley et al., 1996; Sato et al.,
1997; Kotani et al., 1997). For many ORFs no corresponding EST was found in the
databases. To identify expressed genes within contig regions, a novel cDNA
selection method has been proposed (Seki et al., 1997).
Bevan M et al. (1998) Analysis of 1.9 Mb of contiguous sequence from
chromosome 4 of Arabidopsis thaliana. Nature 391: 485-488.
Cooke R, Raynal M, Laudie M, Delseny M (1997) Identification of members of
gene families in Arabidopsis thaliana by contig construction from partial cDNA
sequences: 106 genes encoding 50 cytoplasmic ribosomal proteins. Plant J.
11: 1127-1140.
Kotani H, Nakamura Y, Sato S, Kaneko T, Asamizu E, Miyajima N, Tabata S
(1997) Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
features of the regions of 1,044,062 bp covered by thirteen physically assigned
P1 clones. DNA Res. 4: 291-300.
Quigley F, Dao P, Cottet A, Mache R (1996) Sequence analysis of an 81 kb
contig from Arabidopsis thaliana chromosome III. Nucl. Acids Res. 24:
4313-4318.
Rounsley SD, Glodek A, Sutton G, Adams MD, Somerville CR, Venter JC (1996)
The construction of Arabidopsis expressed sequence tag assemblies. Plant Phys.
112: 1177-1183.
Sato S, Kotani H, Nakamura Y, Kaneko T, Asamizu E, Fukami M, Miyajima N,
Tabata S (1997) Structural analysis of Arabidopsis thaliana chromosome 5. I.
Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1
clones. DNA Res. 4:215-230
Seki M, Hayashida N, Kato N, Yohda M, Shinozaki K (1997) Rapid construction
of a transcription map for a cosmid contig of Arabidopsis thaliana genome using
a novel cDNA selection method. Plant J. 12: 481-487.
The AGI was established on August 20-21, 1996 when representatives of six
research groups (3 from USA and one each from EU, Japan and France) committed to
sequencing the Arabidopsis genome met in Arlington, VA to discuss strategies for
facilitating international cooperation in completing the genome project. In
order to avoid duplication of efforts, the six groups of the Arabidopsis Genome
Initiative (AGI) agreed to focus on different regions of the genome (Bevan et
al., 1997, Plant Cell 9:476-487). In July 1998, the members of the AGI met again
in Arlington, VA to discuss progress to date, to anticipate barriers to timely
completion, and to establish an oversight committee for the U.S.-based labs
(see Appendix).
At present, the major sequencing domains of the AGI groups have been assigned
as follows:
| Chromosome 1 (30 Mb) | SPP group (Stanford, PennU, PGEC) |
|---|---|
| Chromosome 2 (14 Mb) | TIGR group |
| Chromosome 3 (top - 13.5 Mb) | Kazusa group |
| Chromosome 3 (top - 5 Mb) | TIGR group* |
| Chromosome 3 (bottom - 9 Mb) | EU project chrom3 (coordinated by Genoscope) |
| Chromosome 4 (top - 4 Mb) | CSHSC (CSH-WU-ABI group) |
| Chromosome 4 (bottom - 13 Mb) | EU group (ESSA I, II, III) |
| Chromosome 5 (top - 9 Mb) | EU group (ESSA III) |
| Chromosome 5 (top + middle - 4 Mb) | CSHSC (CSH-WU-ABI group) |
| Chromosome 5 (top + bottom - 17 Mb) | Kazusa group |
Sequencing is being done on BAC and P1 clones. Two different strategies are
pursued. Both the SPP group and the TIGR group have selected nucleating sites
("seed BACs") around which BAC contigs have been established by using BAC end
sequences to select adjacent clones with minimum overlap. This sequential
sequencing procedures involves 32 and 16 starting points on chromosomes 1 and 2,
respectively. The other sequencing strategy adopted by CSHSC, ESSA and Kazusa
involves building of BAC or P1/TAC tiling paths with minimum overlap of adjacent
clones ("sequence ready maps"). This procedure requires more preparative work
but once established, large regions can be sequenced in parallel, e.g. by the
several sequencing groups within the ESSA group.
Lists of clones selected for sequencing can be found on the web sites of the
sequencing groups. Start dates for sequencing are indicated and it is agreed
that the finished sequences will be released within 4-6 month after the start of
sequencing (for details, see Appendix). The current state of genome sequencing
is as follows (for overview by chromosome region, see AtDB / Arabidopsis
Sequencing View and the homepages of the AGI groups):
| Chr. | Est. Size | Completed |
|
|
| |||||
| (Target) | Clones | Mb | Clones | Mb | Clones | Mb | Clones | Mb | ||
| 1 | 30 Mb | 52 | 5.52 | 16 | 2.02 | 16 | 1.7 | 84 | 9.25 | |
| 2 | 17 Mb | 107 | 10.29 | 45 | 4.32 | 27 | 2.64 | 179 | 17.25 | |
| 3 | 22.2 Mb | 13 | 1.09 | 29 | 2.5 | 27 | 1.2 | 69 | 5.8 | |
| 4 | 18.5 Mb | 153 | 11.71 | 51 | 5.2 | 28 | 2.6 | 231 | 19.4 | |
| 5 | 29.2 Mb | 208 | 14.62 | 15 | 1.2 | 38 | 2.7 | 261 | 18.54 | |
| Total | 120 Mb | 534 | 43.32 | 156 | 15.2 | 136 | 11.8 | 826 | 70.3 | |
Note that the total sequence entered into AtDB and summarised above includes overlaps between adjacent clones (except for those submitted by ESSA and WashU, which have overlaps almost all removed). For this reason the total number of clones sequenced is a better estimate of progress. With 10% overlap, 120 Mb will require 1,390 BAC clones. On 31 December 1998 the following finished clones had been deposited in Genbank:
SPP 50 BAC clones
TIGR 105 BAC clones
CSHSC 60 BAC clones
ESSA
117 BAC and cosmid clones
Kazusa 202 P1, TAC and BAC clones
Total 534
clones (approx. 39% of the total genome)
As of 31 December 1998, the AtDB Sequencing View displays 46 Mb (39% of
estimated 120 Mb genome size) of complete sequence. This figure is 17 Mb higher
than that given at the end of June 1998, indicating that the current rate of
sequencing is close to 3 Mb per month for the entire AGI project. Taking into
account the sequences that have not been released, the actual amount of sequence
information is close to 55 Mb (almost 50% of the unique sequences). It is thus a
realistic goal to finish the sequence of the Arabidopsis genome (excluding
telomeric and centromeric regions as well as NORs) by the end of the year 2000.
Completion of the sequence is defined as each chromosome arm between
subtelomeric repeats and centromeric repeats consisting of a single fully
sequenced contig. This excludes the rDNA repeats (NORs on chromosomes 2 and 4
each of which accounts for ca. 3.5 Mb) and other internal tandem repeat regions.
For these regions, it will be sufficient to sequence one repeat unit and to
estimate the repeat number at each site. By these criteria, sequencing of
chromosomes 2 (14 Mb) and 4 (17 Mb) can be expected to be complete before the
end of 1999.
As sequencing is reaching the closing phase, boundaries between sequencing
domains have to be defined precisely to avoid duplication of efforts by
different sequencing groups. This difficulty has already been encountered by all
the sequencing groups, resulting in duplication of sequences and mismapped
clones (see table). For example, on chromosome 4 both CSHSC and ESSA sequenced
two different but overlapping clones and had to reassign remaining projects in a
common region of ca. 900 kb. TIGR and SPP have abandoned or mismapped at least 4
BACs and a chimaeric YAC, while Kazusa has sequenced several duplicate clones on
chromosome 5. Depending on different rates of progress, it may seem advisable,
in the interest of the Arabidopsis community, to reallocate genomic regions
between the sequencing groups (see Appendix 1 and 2). The fingerprint map
constructed at Washington University and the hybridisation-based map constructed
by T. Altmann have the potential for delineating these regions before they are
sequenced, and will probably be used for this purpose.
| chromosome 1: | http://pgec-genome.pw.usda.gov/ http://cbil.humgen.upenn.edu/~atgc/ATGCUP.html |
|---|---|
| chromosome 2: | http://www.tigr.org/tigr_home/tdb/at/atgenome/atgenome.html |
| chromosome 3: | http://www.genoscope.cns.fr/ http://www.inra.fr/Versailles/BIOCEL/CHR3-INRA/chromosome3.html |
| chromosome 3,4&5: | http://websvr.mips.biochem.mpg.de/proj/thal/ |
| chromosome 3&5: | http://www.kazusa.or.jp/arabi/ |
| entire genome: | http://genome-www3.stanford.edu/cgi-bin/AtDB/Schromosomes |
The seed stocks currently available from the two centers include mutant lines
(600), T-DNA lines and pools (30,000+), mapping strains, the G. P. Rédei
collection of mutants and research lines (300+), the A. R. Kranz collection of
mutants and ecotypes (700+), transposon/transposase lines (100+), RI lines (3
populations), ecotypes (400+), transgene lines and related species. The genetic
mapping resources of the centers and the T-DNA and transposon resources
complement the AGI sequencing efforts and the current research focus on
functional genomics.
DNA stocks of ABRC include cloned genes (200), RFLP mapping clones (300+),
expressed sequence tagged (EST) clones (30,000+), cDNA libraries (7), a phage
genomic library, YAC libraries (6), BAC and P1 libraries used in genome
sequencing (3) and two-hybrid libraries (2). In addition, filters of BACs, P1s
and YACs for hybridization and isolated DNA from T-DNA populations (12,000
lines) are available.
The EST collection has been organized so that a set of 11,000, non-redundant
based on the sequences available to TIGR, is being used by AGI. The 3' sequences
of these clones are being analyzed by the MSU EST project to further eliminate
redundancy. Copies of BAC and P1 clones, for which sequences have been
published, are being sent to many research laboratories. In this connection,
ABRC requests that all sequencing projects adhere, if at all possible, to the
agreed clone-naming conventions when publishing sequences so that researchers
can identify, without confusion, the proper clones to obtain.
NASC and ABRC are working to enlarge the collections of characterized mutants
and clones. In addition, it is expected that large numbers of T-DNA lines will
be received so that, within the next year, the available T-DNA lines will
represent essential saturation of the genome. In connection with the
accumulating genomic and cDNA sequence information, these resources will prove
invaluable to the research community. In addition, new transposon-tagged
populations, recombinant inbred mapping populations, a tetrad mapping
populations and GFP lines are being incorporated into the collections.
The Nottingham Arabidopsis Stock Centre (NASC) curates the Lister and Dean RI
maps that were originally developed and maintained by Clare Lister and Caroline
Dean (JIC, Norwich). NASC also offers a weekly community mapping service. Anyone
can submit data to NASC for mapping using the specially designed data submission
form. The positions of all markers mapped at NASC are made publicly available
through the NASC WWW server, the Arabidopsis Genome Resource and AtDB. For
private mapping, all the marker scores are available from NASC. However, the aim
for the community is to have as many markers as possible placed on the canonical
map and so the submission of mapping data for inclusion on the RI map is
appreciated.
The Arabidopsis node of the BBSRC funded UK-Crop Plant Bioinformatics Network (UK-CropNet) based at NASC has established the Arabidopsis Genome Resource (AGR). AGR is being developed as a repository of Arabidopis data of value in the comparative analysis of plant genomes and as an essential tool to aid in the cloning of homeologous genes of agronomic importance.
Comparative analysis in plants relies upon genetic and physical mapping of common probes between species. To this end AGR has made available the YAC physical maps of chromosomes IV and V (from C.Dean, R.Schmidt, M. Stammers). AGR also includes the Recombinant Inbred Maps from NASC integrated with the AGI sequence template clones (locations provided through AtDB). Arabidopsis nucleotide sequences are also included within AGR.
Integrating these data sets is the next key step in the development of AGR.
Sequence overlap between completed AGI clones define contigs of BACs and P1s.
These contigs will be fixed to the YAC physical maps using the results of
BAC-YAC hybridisations. Contigs may be anchored on the RI maps through the
nearest marker information from individual clones. RI maps and YAC physical maps
are to some extent integrated through the use of some RI markers as probes in
YAC physical mapping.
In collaboration with Martin Trick (John Innes Center), these data will be
used to generate comparative map displays between Arabidopsis and the
Brassicas.
Contact Persons
Randy Scholl, ABRC email: scholl.1@osu.edu
Mary Anderson, NASC email:
arabidopsis@nottingham.ac.uk
Web sites
| ABRC: | http://aims.cps.msu.edu/aims/ |
|---|---|
| NASC: | http://nasc.nott.ac.uk/ |
The Arabidopsis Data Base (AtDB) is, at this time, located at Stanford University, Mike Cherry, P.I. The explosion of data, both genomic and biological, makes it clear that the data base as it now exists is operating at a minimal, not an optimal, level. The recognition that the community had to express its needs in a more concrete way resulted in two workshops addressing the issues of database composition and management. One was held in 1993 in Dallas, TX.
However, a more recent workshop on the same topic was held at the
international meeting at Madison, WI in 1998 and that report is attached as an
appendix. The needs are for a central database with links to other useful
databases and information which is organized in a user-friendly fashion.
Recognition of the needs of the Arabiopsis community as well as other interested
communities has resulted in a call for proposals to the NSF titled "Arabidopsis
thaliana Information Resource Project (AtIR)" The deadline date is March 22,
1999 and a copy of that announcement is attached to this report as an
appendix.
Recommendation on information management
Large-scale genomic sequencing has reached a critical stage, with about half
the genome in hand. Although the AGI sequencing groups provide information for
specific regions of chromosomes, it is difficult and time-consuming for the
Arabidopsis community to retrieve the relevant information. To take full
advantage of all the progress that has been made in the analysis of the
Arabidopsis genome, it will be necessary to establish a well-funded unified
genome database that displays sequence and related features together with
biological information in a user-friendly way.
Australia
Arabidopsis research in Australia is focused on building an understanding of
fundamental aspects of plant biology. There is no direct commitment to large
scale genome sequencing at this stage.
Among recent highlights, Liz Dennis, Jim Peacock and colleagues from CSIRO
Division of Plant Industry in Canberra have discovered a second nonsymbiotic
leghemoglobin gene from Arabidopsis (Proc. Nat. Acad. Sci. US 94, 12230-12234,
1997). They propose that all plants have two classes of leghemoglobins, as
exemplified by the two genes in Arabidopsis. In the evolution of symbiosis, the
product of one or other of the genes has been recruited on different occasions
to play a new role in association with the symbiont. In most cases class 1 gene
products have been involved, but the newly discovered class 2 proteins are also
potentially symbiotic.
Another highlight has been the discovery of a gene encoding the catalytic
subunit of cellulose synthase (Science 279, 717-720, 1998). Tony Arioli and
colleagues in Richard Williamson's research group in the Research School of
Biological Sciences at ANU in Canberra have walked to the locus of a temperature
sensitive mutant that leads to root swelling (RSW1). The gene that complements
the mutant phenotype is related to a cellulose synthase subunit gene from
cotton. In the mutant there is widespread accumulation of beta-1,4-glucan but it
is not crystallised into microfibrils, suggesting such assembly is a role of the
RSW1 gene product.
Other active programs include studies of various aspects of flowering, from
induction through floral organ morphogenesis to fertilisation and seed
development. Also topics as diverse as aspects of photosynthesis, analysis of
effects of abiotic stresses including heavy metals and UV, epigenetic effects of
cytosine methylation, and the roles of the MYB gene family are being actively
investigated.
A major commitment is being made to host the 10th International Conference on
Arabidopsis Research in Melbourne from 4-8 July 1999. A Regional Advisory
Committee, with colleagues from Japan, South Korea, Singapore and New Zealand,
has been set up to give the meeeting a Western Pacific focus. This will be the
first time the Arabidopsis community has met outside Europe and North America,
and we look forward to welcoming scientists and students to Australia where
plant science continues to thrive.
Contact Person: David Smyth, Monash University, Melbourne
E-mail Address: David.Smyth@sci.monash.edu.au
Belgium
As Belgium is a federal country we have both federal and Flemish initiatives to support research using Arabidopsis thaliana as the experimental organism.
A Flemisch project is running on the isolation and characterization of new ethylene mutants in Arabidopsis thaliana. This project aims at the isolation of a new series of mutants in the ethylene signal transduction pathway. A combined morphological, physiological and molecular-genetical approach will elucidate a number of previously unknown elements and will provide a better insight in the control of plant development by this hormone.
Belgian governement also stimulates interactions between the different
universities. In this frame a project is running between the universities of
Gent, Antwerp, Brussels and Liège on the growth and development of higher
plants. Many external factors such as light intensity, light quality,
temperature, the availability of nutrients and the interaction with pathogenic
organisms influence to a great extent, growth and development of higher plants.
The current knowledge on the molecular processes that control growth and
development is still very limited. The national network aims at making a
contribution to developmental biology by studying a limited number of aspects of
plant development. Wherever possible, Arabidopsis thaliana will be used
as a model plant. Keyprojects include the identification and cloning of key
regulatory genes involved in leaf morphogenesis, the molecular analysis of the
formation of syncytia (=large feeding cells) in nematode infected Arabidopsis
roots. The Flemish community also supports these projects.
Contact Person: Nancy Terryn /Marc Van Montagu, University of Ghent
E-mail Address: nater@gengenp.rug.ac.be
China
Research using Arabidopsis as a model system was further established
in China at national research institutes and universities in the past year. The
research areas mainly include biosynthesis of amino acids, signal transduction
and metabolism of plant hormones, cell wall formation, seed storage proteins,
response to environmental stresses, isolation of various mutants affecting
growth and development, and characterization of transposable elements. Interests
in reverse genetics and functional genomics are also greatly increased with the
focuses on gene-targeting, constructing a large transgenic population with
mapped Ds randomly distributed at a high density, developing an expression
library to transform in planta and establishing cDNA array to monitor gene
expression and identify functional genes. Grants to support the research
projects mentioned above are mainly from National Natural Science Foundation of
China, Chinese Academy of Sciences and Hong Kong Research Grant Council/UPGC
Grant HKU.
Contact Person: Jiayang Li, Institute of Genetics, Chinese Academy of Sciences
E-mail Address: jyli@ss10.igtp.ac.cn
Genome sequencing
During the last year, three French laboratories (M. Delseny/Perpignan, M.
Kreis/Orsay and R. Mache/Grenoble) have systematically sequenced three BACS (300
kb) as part of the EU-ESSA II Program. Delseny's group has also continued to
sequence cDNA clones corresponding to the 60kbp locus, Em1, on chromosome 3. A
French sequencing center, Genoscope CNS has been created and part of its
activity is devoted to sequencing the Arabidopsis genome. In collaboration with
TIGR and Upenn, Genoscope is generating end sequences from all 23,000 BAC clones
from the TAMU and IGF libraries to expedite the selection of clones with minimal
overlap with those already sequenced. They are also coordinating a new EU
project aimed at sequencing the lower arm of chromosome 3 (9Mb). This project
involves 16 sequencing groups. The goal for Genoscope and three academic French
laboratories is about 2 Mb.
Synteny with other genomes
A program was developed between INRA Rennes and Versailles groups to identify
consensus markers between rapeseed and Arabidopsis for a number of agronomically
relevant genes. A collaboration between laboratories in Perpignan, Davis and
Poznan has found synteny between five adjacent genes in the chromosome 3 Em
locus of Arabidopsis and genes in B. oleracea, B. nigra and B. rapa. The EU
program EuDicotMap has started to select highly conserved ESTs of rice and
Arabidopsis and to map them in Arabidopsis as well as important European crops
in order to identify synteny blocks between different families.
Generation of insertion lines and reverse genetics screenings
INRA-Versailles has now generated more than 38,000 T-DNA mutant lines.
Screening of the collection is being done via a coordinated effort between INRA,
CNRS and various European laboratories. Out of approximately a hundred target
genes selected for the screen insertions were identified in 50% of them. The
systematic characterization of flanking sequences tags of insertions in over a
thousand mutants has now begun. About 11,000 lines will be donated to NASC by
the beginning of next year.
A summary of Arabidopsis genes under study
Research in many areas of plant genetics and biology is being actively
pursued in French laboratories. Plant hormone and signal transduction, cell
wall, secreted and membrane proteins, metabolism, development, and plant
pathogen interactions are being investigated in laboratories throughout
France.
Contact Person: Michel Caboche, INRA Versailles
E-mail Address: caboche@tournesol.versailles.inra.fr
Germany
Arabidopsis research is still increasing in scope at universities and
research institutions. The national research program on "Arabidopsis as a
model for analysing plant development" is in its final two-year funding period.
Because its tremendous success, an initiative has been made by Arabidopsis
researchers to establish a new program focusing on plant cell biology. Another
six-year national research program on plant hormones to start in 1999 includes
several groups working on Arabidopsis. Beside these programs,
Arabidopsis research is funded within European projects and by DFG grants
on an individual basis or as part of local research programs.
Several Arabidopsis projects are related to genome research. ZIGIA, a
program operated at the Max-Planck-Institut in Cologne, aims at the functional
analysis through gene inactivation by transposon insertion. High throughput
endprobe hybridization of BAC clones from the IGF library was done at the
Max-Planck-Institut in Golm. These data were integrated with information made
available by other groups to assemble a complete BAC-based physical map of the
Arabidopsis genome. Projects on transcript profiling have been
initiated at the DKFZ in Heidelberg, the MPI in Golm and the IPK in
Gatersleben. The Federal Ministery of Education and Science (BMBF) has
made a call for proposals within a newly-established Plant Genome Analysis
program (GABI). A joint Arabidopsis proposal involving 32 projects from 27
different institutions has been submitted, aiming at a functional analysis of
the genome.
An EMBO (European Molecular Biology Organisation) Course held at the
Max-Planck-Institut in Cologne in May 1998 entitled "Molecular and Biochemical
Analysis of Arabidopsis" was attended by 16 participants representing 13
European countries. The course covered the theoretical and practical aspects of
forward and reverse genetics, genetic and physical mapping, transformation,
transient gene expression, in situ hybridisation, cell biology, physiology, the
yeast two-hybrid system, complementation of yeast mutants and bioinformatics
over an eleven-day period. EMBO Course seminars from ten invited speakers were
integrated with a two-day meeting of the national Arabidopsis research
program.
Contact Person: Gerd Jürgens, Universität Tübingen
E-mail Address: gerd.juergens@uni-tuebingen.de
Italy
Research in Italy with Arabidopsis is growing. About twenty
laboratories are presently attending to researches regarding this model system.
Investigations cover: plant pathogen relationships, expression of PG and PGIF
genes, role of rolB and rolD in plant differentiation, HD-ZIP transcription
factors in plant morphogenesis, complementation of yeast by Arabidopsis genes,
selection of Ca2+ and K+ transport mutants, genes involved in heat and cold
resistance, myb transcription factors, genes of the polyamine pathway, induction
of noduline genes in plants by Rhizobium, use of antisense RNA to inhibit
nitrogen transport, study of agravitropic mutants in earth and micro g
conditions (ESA-ASI projects). Financial support for the researches is coming
from different sources, e.g. the National Research Council, the Ministry of
Agriculture, the European IV Frame Programs, the ESA-ASI Space Programs, and a
few other National Agencies. Research groups are located both in universities
and in National Institutes (National Research Council, ENEA, National Institute
of Nutrition). The Italian association of researchers interested in Arabidopsis
(ARABITALIA) met for the first time in September 1997 in Abbadia di Fiastra
(Macerata, central Italy). In this occasion the scientists present to the
meeting furnished a report of their Arabidopsis investigations and projects, and
a booklet carrying the information about research on Arabidopsis in Italy was
also distributed. In this occasion some young Italian researchers, who are
working in foreign countries (USA, and UK) also reported about their recent
investigations. The 1998 annual Meeting was held at the end of September in
Viterbo (central Italy) in the occasion of the EUCARPIA Symposium on plant
breeding. A document is in preparation about the state of Arabidopsis research
in Italy, and about the actions that can be started to obtain the financial
support that is needed to foster it.
Contact Person: Fernando Migliaccio, CNR (Monterotondo)
E-mail Address: miglia@nserv.icmat.mlib.cnr.it
Japan
Arabidopsis research is well-established in Japan. The number of
laboratories using the model plant for research and education is still
increasing gradually in universities, national institutes, and private
companies. Areas of research are widely spread from developmental biology,
metabolic regulation, gene expression, environmental stress signaling, and DNA
methylation, to large scale DNA sequencing. The results of the researches were
reported in international meetings such as the " International Congress of
Arabidopsis Research" in Madison, WI, the "Joint Meeting of Japanese and
American Societies of Plant Physiologists" in Vancouver, BC and in national
meetings, especially in the "Workshop on Arabidopsis Studies", an annual
meeting. The 8th workshop was organized by Kazuo Shinozaki, Minami Matsui, Yuji
Kamiya, and Richard E. Kendrick from October 11 to 13, 1997, at Riken Institute
at Wako city, Saitama. The workshop was joined with Frontier Research Forum,
"Recent Progress of Plant Hormone Research in Arabidopsis". We had nearly 250
participants, 20 poster presentations, and 37 speakers including 7 guest
speakers from abroad. The 9th workshop was held in Kazusa Academia Center from
Nov. 19 to 20, 1998. The workshop organized by Satoshi Tabata had nearly 300
participants, 40 poster presentations and 11 presentations. Topics of the
presentations included systemic genome analyses, patent, and postgenome tactics,
as well as mutant analyses, gene cloning, and newly-developed techniques.
The Japanese Arabidopsis communication network, nazuna-net, started in
January 1995, now includes 442 members (Sept. 1998) from 99 organizations
including 17 private companies (contact: Dr. Takayuki Kohchi:
kouchi@bs.aist-nara.ac.jp). A large-scale genome sequencing project showed
extensive progress at Kazusa DNA Research Institute in coordination with the
Multinational Arabidopsis Genome Initiative (contact: Dr. Satoshi Tabata:
tabata@kazusa.or.jp). Nearly 12.5 Mb covering 174 P1 clones have been sequenced
and reported in the journal "DNA Research" (contact: http://www.uap.co.jp/), on a homepage ( http://www.kazusa.or.jp/arabi/). The
Sendai Seed Stock Center (SASSC) is operated by Dr. Nobuharu Goto
(n-goto@ipc.miyakyo-u.ac.jp) since 1993.
Contact Person: Kiyotaka Okada, Kyoto University
E-mail Address: kiyo@ok-lab.bot.kyoto-u.ac.jp
The Netherlands
The Dutch Arabidopsis groups organized their annual meeting in Utrecht on
February 19, which was attended by approximately 80 participants. Arabidopsis
groups are located at the Universities of Leiden, Utrecht and Wageningen and at
CPRO-DLO in Wageningen. Important research topics are in Leiden (Hooykaas)
recombination, auxin action and apoptosis, in Utrecht sugar sensing (Smeekens),
root development (Scheres) and acquired resistance (van Loon), in Wageningen
embryogenesis (de Vries, van Lammeren) and flowering and seed- development
(Koornneef), transposons, genome sequencing, plant disease resistance genes and
developmental biology (Stiekema, Pereira, Angenent, Groot all CPRO-DLO). The
groups collaborate through their involvement in graduate schools and EU
programs.
Contact Person: Maarten Koornneef, Agricultural University Wageningen
E-mail Address: Maarten.Koornneef@BOTGEN.EL.WAU.NL
Spain
No special funding programme supports Arabidopsis research in Spain.
However, more than 20 research groups are currently active in research with this
organism, mainly funded by the National Biotechnology Programme, Basic Research
Programmes, and the European Union BIOTECH Programme. Some of these groups are
involved in large-scale genome sequencing and function search, specially in the
case of the Myb family of transcriptional factors. Spanish groups interested in
Arabidopsis development are mainly focused on seed, leaf and flower
development, and flowering induction. This area is seing the incorporation of
new groups of Arabidopsis users, some of them also interested in cell
differentiation. In the area of plant physiology and metabolism some topics that
have seen significant contributions during the year are the study of secondary
metabolism, the identification of new elements in the signal transduction
pathways involved in different environmental stress responses, and the analysis
of sulfur and phosphate assimilation. Arabidopsis has also being
increasingly used for studies in plant pathogen interactions to identify new
elements in the response signal transduction pathways.
The Spanish Arabidopsis network, funded by the National Biotechnology
Programme, generated a collection of 10000 T-DNA lines that is being actively
used in mutant screenings at both the phenotypic and DNA levels, in many
laboratories. This network that includes all the Spanish laboratories working
with Arabidopsis is now discussing future join activities. Many more
Spanish scientists are currently involved in Arabidopsis research in
other laboratories around the world. Their succesful integration in the Spanish
R&D system would strongly contribute to steer the field and increase the
contribution of our country.
Contact Person: José Martinez Zapater, Centro Nacional de Biotecnología (Madrid)
E-mail Address: zapater@cnb.uam.es
United Kingdom
There are over 190 projects at present in the UK involving
Arabidopsis. The European Commission continues to be a major source of
funding and the newly announced Framework V programme is due to begin calls for
proposals. Although there are no longer any special initiatives aimed
specifically at Arabidopsis research, The Biotechnology and Biological Sciences
Research Council (BBSRC) funds projects through competitive grants and special
initiatives, contributing approximately £ 6.8m to Arabidopsis research in
the UK.
An Arabidopsis Gene Function Search Network is currently under development by
Mike Bevan at the John Innes Centre. This is a network of consortia, groups of
labs with a common goal, being brought together with the aim of doing large
scale screening programmes to reveal the functions of very large numbers of
genes being revealed by the genome project.
The Genetical Society of Great Britain chose Arabidopsis as the subject area for their annual autumn meeting in 1997. The Mendel Lecture was given by Elliott Meyerowitz who was preceded during the day by Mike Bevan, Rob Martienssen, Joe Ecker, Ben Scheres, Caroline Dean, Gerd Jurgens and Brain Staskawicz."Arabidopsis thaliana: Big Ideas from a Small Plant" was such a success that the Society has decided to host a biennial conference on Arabidopsis.
An EMBO (European Molecular Biology Organisation) Course held at the John
Innes Centre in May 1997 entitled "Arabidopsis as an Experimental
Organism" was attended by 12 participants representing seven European countries.
The course covered the theoretical and practical aspects of mutant screening,
genetic and physical mapping, plant pathology, microscopy, biolistics, the yeast
two-hybrid system, and sequence fragment and data analysis over a ten day period
which also included seminars from ten invited speakers.
The Chelsea Flower Show judges awarded a prestigious Silver Medal to the John
Innes Centre Science Communication and Education Department exhibit, entitled
"Arabidopsis - a Wonderful Weed". The exhibit demonstrated how
Arabidopsis is used to recognise genes of agronomic importance in
agricultural crops. The public exposure and media coverage the display attracted
in the UK and abroad has helped to increase awareness of the importance of plant
molecular biology.
In the last year the Nottingham Arabidopsis Stock Centre (NASC) in
collaboration with the Arabidopsis Biological Resource Center (ABRC) has
continued to accumulate the broadest possible range of stocks to provide the
best platform of genetic diversity and genetic tools for the investigation of
this model system. Currently NASC maintains and distributes over 20,000
accessions of Arabidopsis to the research community. New stocks generated within
the UK and shortly to be made available include the first 10,000 of the
Sainsbury Laboratory Arabidopsis transposants (SLAT) lines (Jonathan
Jones, Sainsbury Lab, UK), 100 GFP lines (Jim Haseloff, Cambridge, UK) and a
Recombinant Inbred population of Nd (Niederzenz) x Columbia generated by Eric
Holub, Jim Beynon and Ian Crute (HRI Wellsbourne, UK).
Contact Person: Caroline Dean, John Innes Centre, Norwich
E-mail Address: caroline.dean@bbsrc.ac.uk
United States
Arabidopsis research continues to flourish in both academic and corporate
laboratories in the United States. One of the most obvious indicators of the
value of information that can be gleaned from Arabidopsis research has
been the establishment of several genomics companies that are exploiting
Arabidopsis genetics. Thanks to continued support from the National
Science Foundation (NSF), the Department of Energy (DOE) and the U.S. Department
of Agriculture (USDA), the Arabidopsis genome is on track for being
completely sequenced by the end of 2000. A total of 46 Mb of finished sequence
had been deposited in public databases as of January 1999, of which the US
sequencing groups contributed more than 24 Mb. Importantly, the groups in the US
Arabidopsis Genome Initiative (AGI) finished the first phase of their sequencing
effort in less than the original 3 year time allowed, and could thus begin
during 1998 with the second phase of sequencing ahead of time. In addition to
its value for database mining and other more traditional genomic approaches, the
availability of large amounts of genome sequence together with physical maps
that cover almost the entire genome have begun to eliminate positional cloning
as a bottleneck in Arabidopsis genetics. Much of this information is
conveniently accessed through the Arabidopsis thaliana database (AtDB) at
Stanford University. The growing importance of Arabidopsis research has
also been evident in the increasing number of participants at the Eight and
Ninth International Conferences on Arabidopsis Research, which were held
in Madison, WI, and drew 817 and 998 participants, respectively.
Apart from the genome sequencing efforts, important tools are being developed
for reverse genetics and functional genomics. A significant advance in this area
has been an $8.7M award from the NSF Plant Genome Research Program for a
cooperative effort to provide high-throughput gene expression profiling as well
as gene knock out services to the Arabidopsis community. The identification of
gene knock outs has been made possible through the availability of large numbers
of T-DNA insertion lines, of which 48,500 have already been deposited with the
Arabidopsis Biological Resource Center (ABRC) at Ohio State University. This
number can be expected to at least double in 1999. The ABRC continues to be an
important resource for the Arabidopsis community. It shipped 29,500 seed and
13,000 DNA stocks in 1997; and 46,500 seed and 16,000 DNA stocks in 1998.
As a direct consequence of the improvements in scientific infrastructure,
significant scientific advances have been made in every area of Arabidopsis
research, including hormone and light signaling, circadian clock, responses
to biotic and abiotic stress and developmental biology. Some of the most
noteworthy discoveries in 1998 included the discovery of master regulatory genes
that protect Arabidopsis from cold damage and the identification of
proteins that transport auxins.
Contact Person: Detlef Weigel
E-mail Address: detlef_weigel@gm.salk.edu
Contact Person: Jeff Dangle
E-mail Address:dangle@email.unc.edu
NSF ARABIDOPSIS GENOME MEETING REPORT
INTRODUCTION
In 1990, a report entitled "A Long-range Plan for the Multinational
Coordinated Arabidopsis thaliana Genome Research Project" was published
by the National Science Foundation (NSF 90-80). The report detailed plans made
by members of the Arabidopsis research community in the U.S. and abroad,
to collaborate in the sequencing of the genome of this model plant, and to
characterize the structure, function and regulation of all Arabidopsis
genes. In 1998 it became possible to set a realistic goal of finishing the
sequence by the end of the year 2000.
Since then, a multinational genome sequencing project involving laboratories
in the United States, in Europe, and in Japan, has been engaged in achieving
this goal. This report is the proceedings of a meeting held to discuss progress
to date, to anticipate barriers to timely completion, and to establish an
oversight committee for the U.S. -based labs. The meeting was held at the
National Science Foundation in Arlington, Virginia on July 9 and 10, 1998.
Participants Representing
Elliot Meyerowitz, California Institute of Technology Chair
Ian Bancroft, John Innes Centre ESSA
Michael Bevan, John Innes Centre ESSA
Ellson Chen, Perkin-Elmer Applied Biosystems CSHSC
Ronald Davis, Stanford University SPP
Nancy Federspiel, Stanford University SPP
Gerd Jürgens, University of Tübingen MSC
Richard McCombie, Cold Spring Harbor Laboratory CSHSC
Rob Martienssen, Cold Spring Harbor Laboratory CSHSC
David Meinke Arabidopsis community
Xiaoying Lin, TIGR TIGR
Curtis Palm, Stanford University SPP
Daphne Preuss, University of Chicago Arabidopsis community
Francis Quetier, Genoscope Genoscope
Steven Rounsley, TIGR TIGR
Marcel Salanoubat, Genoscope Genoscope
Satoshi Tabata, Kazusa Kazusa
Athanasios Theologis, USDA Plant Gene Expression Ctr. SPP
Richard Wilson, Washington University CSHSC
Mary Clutter NSF
Machi Dilworth NSF
DeLill Nasser NSF
James Tavares DOE
Jane Peterson NIH
Adam Felsenfeld NIH
Peter Bretting USDA
Liang-Shiou Lin USDA
STRUCTURE AND PROGRESS
There are six different sequencing consortia participating in the sequencing
phase of the Arabidopsis genome project, three from the United States,
two from the European Community, and one from Japan. Each is sequencing a
different region of the genome, and each has its own model for distribution of
the necessary work among consortium members. The progress of each follows,
taking them in turn.
TIGR (The Institute for Genome Research, http://www.tigr.org/tdb/at/at.html)
TIGR has taken on two aspects of the sequencing project. The first is BAC end
sequencing (along with SPP and Genoscope), to provide one-pass sequences of both
ends of the 22,000 BAC clones that are one type of clone being used for
sequencing in the genome project. The purpose of this is to allow sequential
progression from a single sequenced BAC to the two adjacent genomic regions with
minimal overlap. TIGR has sequenced 16,392 BAC ends from a total of 9,572 BAC
clones, providing a total of 7.34 Mb of BAC end sequence. The total BAC end
sequence from all three groups is 36,574 BAC ends from 18,746 clones,
representing 13.64 Mb.
The second TIGR project is the sequencing of chromosome 2. They have chosen
16 well-spaced starting points (by use of the Goodman lab chromosome 2 contig
map), and are sequencing BAC clones in parallel, starting with the original
clone in each location, and proceeding by use of BAC end sequences to adjacent
clones with minimal overlap. The average overlap between adjacent BAC clones has
been 8.2 kb, with a range from 150 bp to 30 kb. At present 4.83 Mb is complete
and annotated, 3.25 Mb has shotgun sequencing or annotation in progress, and
1.38 Mb of BAC clones are in preparation for sequencing, for a total of 9.46 Mb.
The only problem encountered so far is a gap with no clones to cross it in
present BAC collections, in the m336 large contig. Fiber FISH done at the
University of Wisconsin indicates a gap size of 500 kb, and the sequence at
either side of the gap shows no special features. There has also been a BAC
difficult to close due to long tandem dinucleotide repeats, but there is no
theoretical barrier to completion of such clones.
The total estimated length of chromosome 2 is less than 14 Mb, not including
an estimated 3.5 Mb of ribosomal DNA tandem repeats at one end of the
chromosome. The current rate of sequencing in this phase of the project at TIGR
is presently 8 Mb per year, and there is an existing proposal to increase that
to 12 Mb per year. It is estimated that, barring unforeseen problems, chromosome
two, excluding highly repetitive centromeric regions and the rDNA repeats, will
be completed by the end of 1999; if the full capacity is to be used, clones on
other chromosomes will have to be started by the end of 1998.
SPP (Stanford University, Plant Gene Expression Center, University of
Pennsylvania; http://pgec-genome.pw.usda.gov/; http://cbil.humgen.upenn.edu/~atgc/ATGCUP.html;
http://sequence-www.stanford.edu/ara/ArabidopsisSeqStanford.html)
These three groups have as a goal completing the sequence of chromosome 1.
They have divided some of the preparative tasks, with Stanford providing
automated template preparation, Penn mapping chromosome 1 BACs and providing BAC
end sequences to the project, and PGEC making the sequencing libraries. All
groups are involved in sequencing. The strategy is similar to that of TIGR,
whereby seed BAC clones chosen by the Penn laboratory are used a sequencing
origins, and progress made by use both of BAC end sequences and BAC
fingerprints, to provide minimal overlap. Initially 20 starting points were
used, there are plans to add an additional 20 soon.
SPP has provided 8,936 BAC end sequences to the 36,574 BAC end total.
The chromosome 1 sequencing done or in progress has so far totaled 5.64 Mb,
which is the sequence of 55 BACs and 1 YAC clone. Excluding overlap between
adjacent clones leaves a total unique sequence in progress or finished of 5.36
Mb. Of this 4.02 Mb are complete, 0.65 Mb in finishing and 0.97 Mb in shotgun
phase. Overlap between adjacent clones has been 2 to 38 kb, with an average less
than 7 kb; there has as yet been no failure to find the adjacent clone from any
sequenced BAC.
The total estimated length of chromosome 1 is 30 Mb. Capacity exists to
finish it by the end of 2000, given sufficient funding - completion will require
sequencing approximately 300 BAC clones in the next 3 years, or 33 BACs per year
per participating site.
CSHSC (Cold Spring Harbor Sequencing Consortium;
This consortium includes Cold Spring Harbor Laboratories, Washington
University and Perkin-Elmer Applied Biosystems. They are taking a different
approach to choosing the BAC clones to sequence, which involves HindIII and
EcoRI fingerprinting of BAC clones, and from the clone overlaps inferred from
fingerprint identity, producing deep contigs of overlapping clones. Each contig
is then to be anchored to known chromosomal positions by use of the abundant
public information on BAC clone map positions, or by cross-hybridization with
the YAC contigs already established for chromosomes 4 and 5 at the John Innes
Centre in the U.K. Once a genome-wide set of BAC contigs is available, a minimal
tiling path can be calculated and many clones can be sequenced in parallel. This
approach requires the same degree of preparative work as BAC end sequencing for
a comparable cost, but has the advantages of providing a physical map to the
Arabidopsis community prior to the completion of the genomic sequence,
and also will allow parallel sequencing of clones rather than the necessarily
sequential sequencing using BAC end sequences. In addition, this method will
allow gaps to be identified in advance of sequencing in the gapped region, and
thus may allow a longer time to close gaps before they become a critical problem
with sequence completion.
So far an estimated 71 MB of the perhaps 120 Mb nuclear genome is contained
in 66 BAC contigs, which contain 10,840 BAC clones. The chromosome totals
are:
Chromosome Mb Contigs
1 22.5 13
2 >4 7
3 17.0 11
4 15.3 8
5 13.4 8
The current rate of BAC clone fingerprinting and editing is 15 Mb per month.
It is expected that all 22,000 available BAC clone will be added to this map by
the end of 1998. Concentration at present is on chromosome 5, where the CSHSC is
sequencing, and chromosome 3, where Genoscope plans to sequence using the CSHSC
contigs.
The CSHSC is committed to sequencing the top of chromosome 4 and a region of
approximately 4 Mb around the centromere and on the north arm of chromosome 5.
Sequence data has been contributed by all three collaborating partners. Totals
finished so far are 690 kb from ABI, 1.22 Mb from CSH and 1.64 Mb from
Washington University, adding up to 3.54 Mb (with overlap subtracted). In
addition to this, approximately 3 Mb of sequencing is in progress, making a
total of more than 6.0 Mb in 61 BAC clones and 1 YAC. If this rate were to be
continued, the proposed chromosome 4 region could be completed by the end of
1998, with chromosome 5 region completion either 1998 or early 1999.
ESSA (European Scientists Sequencing Arabidopsis; http://muntjac.mips.biochem.mpg.de/arabi/index.html)
The ESSA project is in three phases. Phase I, which is complete, was to
sequence two contiguous regions on chromosome 4. One, surrounding the FCA
genetic marker, is 1.92 Mb (Bevan et al. 1998, Nature 391:485), the other,
around the genetic marker AP2, is 0.41 Mb, for a total completed ESSA I sequence
of 2.33 Mb. ESSA II, which is to be completed in October 1998, has the goal of
completing a 5 Mb region on the long arm of chromosome 4. So far 3.16 Mb is
completed and annotated, an additional 1.73 Mb completed and in annotation
phase, for a total of 4.89 Mb sequenced. Another 0.24 Mb is nearly complete, for
an overall total of ESSA II complete and nearly complete contiguous sequence of
5.13 Mb. The ESSA I and ESSA II total of completed and nearly completed sequence
is thus 7.46 Mb.
The two-year ESSA III project begins in August, 1998. Its goal is to complete
the sequence of the long arm of chromosome 4 (estimated to total 13 to 13.5 Mb)
and to sequence two regions of the north arm of chromosome 5 (with others to be
done by CSHSC and Kazusa), with a total goal of sequencing 9 Mb.
The ESSA procedure is to use the existing YAC contig maps of chromosomes 4
and 5 to group BAC clones in bins according to their YAC cross-hybridization,
then to use SalI digestions and pulsed-field gel electrophoresis followed by
blotting and iterative hybridization with BAC clones to establish both BAC
contigs and an overall SalI restriction map of both chromosomes. A minimal BAC
tiling path is then defined and called the "sequence ready map,", the clones
from this map are then sent to one of 9 collaborating sequencing laboratories
for nucleotide sequencing. The data are collected and annotated at MIPS, the
Munich Information Center for Protein Sequences.
The only problems encountered so far have been two difficult clones, one with
a large hairpin and the other with a large region of tandem repeats. Both have
been nearly completed, with the tandem repeats solved by long PCR as a
supplement to the shotgun sequencing.
Kazusa DNA Research Institute ( http://www.kazusa.or.jp/arabi/)
The Kazusa Institute is engaged in sequencing the long arm of chromosome 5
and along with ESSA and CSHSC, portions of the short arm of this chromosome
(totaling 17.2 Mb when complete), and they are beginning the sequencing of the
long (13.2 Mb) arm of chromosome 3.
The clone libraries used are from the Mitsui Plant Biotechnology Research
Institute, and consist of P1 and TAC clones. Clones from these libraries are
initially selected by cross-hybridization to mapped clone markers. The clones
are then anchored on the YAC contig (for chromosome 5 clones), and fingerprinted
as an integrity check. They are then shotgun sequenced, assembled, and
annotated. A collection of YAC, TAC and P1 clone end sequences has been made for
tiling the chromosome 5 clones, it includes 1254 sequences from 690 CIC YAC
clones and 706 sequences from 389 P1 or TAC clones on chromosome 5. Similar
methods for chromosome 3 are starting, using the YAC contig map of that
chromosome produced by D. Bouchez and collaborators at INRA. At present, two
large contigs for chromosome 3 exist, one of 13.6 Mb for the long arm, and one
of 9.2 Mb for the bottom arm.
Progress to date has been the release of 8.89 Mb of completed, annotated
sequence, with release of an additional 1.60 Mb scheduled by August 1. Thus by
August 1, 1998, 10.49 Mb will have been completed and released. 10.15 Mb of this
is on chromosome 5, 0.34 Mb on chromosome 3. An additional 2 Mb of chromosome 5
sequencing is in progress. At current rates of 700 to 800 kb per month, it is
expected that 27 months will be required for completion of this part of the
project, which is estimated to include (in addition to the 10.49 Mb to be
completed by August 1) 7.05 Mb of chromosome 5 and 13.3 Mb of chromosome 3.
Genoscope has proposed to do 5 Mb of the long arm of chromosome 3 (see below),
if they are able to take this on (a matter now being considered there, and
dependent upon the demand for their resources by human genome sequencing) the
total sequence proposed by Kazusa will be reduced, and completion will be
expected within 2 years.
Genoscope (Centre Nationale de Sequencage; http://www.genoscope.cns.fr/externe/arabidopsis/Arabidopsis.html)
Genoscope is involved in the second European project. They have already
provided BAC end sequences totaling approximately 11,500 completed end
sequences, with plans to provide 2,000 more. Once this is complete 91% of the
22,000 BAC clones used in the sequencing project (from the IGF and the TAMU
collections) will have available end sequences.
Their sequencing plan is to use the Bouchez chromosome 3 YAC contigs to make
a minimal BAC tiling path by use of fingerprints done at Genoscope and at CSHSC,
then to sequence the bottom (9 Mb) arm of chromosome 3. Complete contigs for
this region have been supplied by CSHSC. 16 different European sequencing groups
are receiving the BAC clones from Genoscope, and the data are returned to MIPS
for annotation and entry into a public database. The sending out of clones is to
begin within weeks, and completion of the 9 Mb region is expected by the end of
2000.
Genoscope has in addition explored with Kazusa the possibility of sequencing
an additional 5 Mb on the top arm of chromosome 3; their ability to do this will
depend upon the amount of their sequencing capacity that will be required to do
their part of human chromosome 14, and their ability to generate extra
sequencing capacity. A decision on whether Genoscope or Kazusa will sequence
this 5 Mb is planned for September, 1998.
Summary of Progress
Chromosome Est. Size (Mb) Complete (Mb) Group
1 ~30 4.02 SPP
2 14 (+rDNA) 4.83 TIGR
3 23 0.34 Kazusa & Genoscope
4 17 (+rDNA) 9.02 ESSA & CSHSC
5 ~30 10.15 Kazusa, CSHSC, ESSA
TOTAL ~114 Mb +rDNA 28.36
In addition, shotgun sequencing libraries are in preparation for an
additional 2.80 Mb, and sequencing is in progress but not yet complete for an
additional 2.98 Mb. Furthermore, 36,574 BAC ends from 18,746 clones,
representing 13.64 Mb, provided by TIGR, SPP and Genoscope are completed, as are
1254 end sequences from 690 CIC YAC clones and 706 sequences from 389 P1 or TAC
clones, provided by Kazusa.
COMPLETING THE SEQUENCE
Defining completion
In addition to the gene-rich and highly informative regions of the genome
(with one gene every 4-5 kb), there are regions of repetitive DNA, and perhaps
of lower gene density.
One instance is the ribosomal DNA repeats, which are arranged in two
uninterrupted tandem arrays. Each repeat unit contains a gene for 18S, 5.8S and
25S structural ribosomal RNAs and is 10-10.5 kb in length. The large tandem
arrays of repeat units are found at the top arms of chromosomes 2 (NOR2) and 4
(NOR4). Each is on the order of 3-3.5 Mb, or 300-350 repeat units.
Centromeric regions are only beginning to be defined at the molecular level
in Arabidopsis, but cloning and chromosome in situ hybridization
studies have shown that these regions contain multiple tandem repeats of short
sequences, a major element of which is 180 bp repeats and related repeats. In
one case (chromosome 1) an estimate of the repeat length is 950 kb. For
chromosome 4 the functional centromere is probably on one side of a 180 bp
repeat region, and so far does not seem to be unclonable. There is some
indication that BAC clones from this region may have a higher amount of
repetitive sequence in tandem arrays than other BAC clones sequenced to date,
and one BAC clone from the chromosome 2 centromere region has only 3 genes, a
much lower density than the typical 1 gene per 4-5 kb found elsewhere. Another
BAC from the centromere region of chromosome 4 has a more typical density.
Telomeres and subtelomeric regions in Arabidopsis have been
characterized and appear to be small (totaling perhaps 100 to 200 kb in the
genome) and not difficult to sequence so far.
There are also small regions of simple tandem repeats, as for example as
described above in the ESSA project progress report. This clone, BAC F9F13,
contained 10 tandem copies of a 3.5 kb repeat, as well as 2 additional copies of
the same repeat.
Because the exact sequence and number of tandem repeats is not thought to be
consequential for any functional analysis, and in fact is quite polymorphic
between ecotypes, it was decided that a sufficient characterization of these
repeats would be a sequence of one subunit, and an estimation from blotting or
long-range PCR of the number of tandem copies at each site.
Given this, the complete sequence of the nuclear genome will be considered to
be in hand when each chromosome arm is fully sequenced as a single contig from
subtelomeric repeat to "centromeric" tandem repeats, with internal tandem repeat
regions (including rDNA repeats) characterized only as far as demonstrating that
they are pure tandem repeats, with the sequence of one repeat unit determined,
and an estimate of repeat number at each site provided. This characterization
already exists for the rDNA repeats (Copenhaver et al. (1995) Plant J.
7:273-286). This definition may have to change if unclonable regions are found,
or if non-tandemly organized but nonetheless impossible to sequence (with
available relevant technology) clones are found. To date there is no indication
of either unclonable regions or of clones impossible to sequence for reasons
other than large numbers of small tandem repeats.
Other sequence parameters
Accuracy
All of the participants have agreed before, and continue to agree, that the
standard for sequence accuracy should be one error in 10,000 nucleotides or
better, and the projects so far seem to be achieving this goal. The U.S. groups
agreed to a common pair of tests to monitor sequence accuracy. The first would
be using base calling programs such as Phred (Ewing et al. (1998) Genome Res.
8:175-185) or TIGR Assembler to assess sequence accuracy in each sequencing run.
The second is to independently determine the sequence of all regions of overlap
between adjacent clones, and only after sequence finishing to compare them for
mismatches. This serves as an independent method to determine sequence accuracy,
and since all mismatches are to be resolved by further analysis, this test will
in addition indicate the degree of sequence change due to mutation in the clones
being used for sequencing.
The European and Japanese groups have different methods to measure sequence
accuracy, but have the same goal of less than one error in 10,000 bases.
Annotation
Proper annotation of sequences to indicate the position, structure and nature
of each of the coded genes is a critical component, and in fact the primary
product, of the genome project. It is clear, though, that initial annotation of
sequences is not fully (or even very) accurate, as the software and algorithms
used for gene recognition can miss exons and introns, and can also indicate the
presence of exons or introns where there are none. This is as true in animal
genome projects as in plant projects. Thus, annotation will have to be done in
stages, with initial annotations that can be useful, but that must be
acknowledged to be flawed.
Each of the sequence groups performs its own annotation, as this is not only
an interesting part of the work, but also helps with continued sequencing. It
was agreed that, to provide the highest quality initial annotation, each group
would use multiple software programs for gene recognition, and would indicate in
its output the product of each of the programs (something that GenBank cannot
do; thus this requires output to be in a form other than that sent to GenBank or
equivalent public databases). It should be emphasized that doing this does not
remove the requirement for inclusion of the output in public databases like
GenBank or DDBJ. In addition, experimental means of annotation are to be used by
each group - that is, sequences must be compared with the EST sequences that are
available and that indicate actual RNA sequences, and must be compared with the
genes of known structure that have been individually studied. Furthermore,
feedback from the community of Arabidopsis researchers should be invited
by each group, to allow correction or improvement of each group's annotations.
As the genome project proceeds, it is important to consider additional
experimental methods for gene recognition, and the application of such methods
should be considered important goals for the project. Among the experimental
methods to be considered is sequencing of related genomes (such as those of
Arabis lyrata or Cardaminopsis petraea, see http://www.arabis.net/wild.htm).
Because exonic sequences change more slowly than intronic or intergenic
sequences, this could serve as a very useful indicator of gene location and exon
boundaries. Additional experimental means for improving annotations include RNA
blots and RT-PCR to find if suggested genic sequences in fact correspond to
RNAs, and full-length sequencing of large numbers of cDNA clones for comparison
to genomic sequences.
Maintenance of summary lists of identified genes according to the type of
protein coded (see Bevan et al. 1998, Nature 391:485) is also an important
aspect of annotation.
Because annotation methods and the experimental information on which they are
based is subject to continual improvement, frequent reannotation is worthwhile.
Both the Kazusa and TIGR groups have plans for systematic reannotation of
sequences from all groups. To facilitate this and, especially, to facilitate
community access to annotations, it was agreed that all groups would work toward
a standardized format for data presentation, and that groups doing large-scale
reannotation would make their data freely available for mirroring on the web
sites of all groups that wish to display them.
Data release
Each of the U.S. groups sends sequence out unannotated and in small fragments
as soon as it reaches either approximate 2 kb contigs or 7x average coverage.
The sequences from two of the three groups are sent at this stage to the high
throughput genome sequence (HTGS) part of GenBank, the third group has agreed to
start doing this as well. The sequences are now sent to each group's own web
page, each of which supports BLAST searches, and are also sent at short
intervals to AtDB, the public Arabidopsis database, where they are also
BLAST searchable (
http://genome-www2.stanford.edu/cgi-bin/AtDB/nph-blast2atdb).
The structure of the European projects, where sequence-ready clones are
allocated to many groups, and each group has some discretion (and rules from
their own national government) in how to sequence and when to submit completed
sequence, does not lend itself to identical release methods or policies.
Nonetheless, the groups agree to collect and distribute through MIPS and AtDB
all sequences as soon as practicable, at latest after completion and before
annotation.
The Japanese group also has its own policies and level of funding for
informatics, which so far have dictated that sequence be released only after
both completion and annotation, and then posted to DDBJ (DNA Database of Japan)
and GenBank. This entails a delay in public access relative to other groups, as
the time from completion to annotation is about a month, and the time from
acquisition of the earliest data to completion is also appreciable. The Japanese
group will consider mechanisms for earlier release, within the constraints of
policy and of funding for this aspect of the project.
Clone registration (intention to sequence)
One critical aspect of the project is coordination between groups on the
clones to be sequenced, as without tight coordination, duplication of effort
will occur, especially in the closing phases of the project. In addition, as
different groups complete their assigned regions, reallocation of regions may
become necessary so that groups ahead of their predicted rate can help by
sequencing clones originally assigned to other groups. At present this
coordination has been supplied by direct communication between the groups, and
by the function of an international coordinating committee of the
Arabidopsis Genome Initiative (AGI: see http://genome-www3.stanford.edu/cgi-bin/Webdriver?MIval=atdb_registry_info.html).
This committee will remain the arbitrator of international sequencing efforts,
but will be supplemented with a new committee that will allow for closer
coordination of the U.S. groups. This new committee has been mandated by the
U.S. funding agencies, as a replacement for the three separate advisory groups
that now exist, one for each group.
One of the tasks of the U.S. committee will be clone reallocation, and in
addition frequent communication with the members of the international AGI
committee, as a way of stimulating continued discussion among all groups. As
representatives of all groups will be invited to the meetings of the U.S.
committee, these meetings may also be able to serve as a forum for discussion
and decisions of the AGI committee. This may help the AGI by increasing the
frequency of its considerations.
NEW U.S. STEERING COMMITTEE
Given the important new role of the mandated U.S. Steering Committee as
arbitrator and communication facilitator between the U.S. groups, and as aid to
the AGI committee on the international front, the role a responsibilities of the
committee were discussed and agreed upon.
The U.S. Steering Committee will have the following responsibilities:
1) Setting boundaries between the U.S. sequencing groups (ideally, to be
defined by sequenced clones) to avoid duplication of effort in chromosomes where
more than one group is working
2) Reallocation of clones or chromosome regions from one group to another to
fit sequencing capabilities to the remaining work.
3) Monitoring and enforcement of the common agreements described earlier in
this report, namely the agreement to work toward a common annotation format, to
provide quality control information both from base calling programs and from
clone overlap regions, and to monitor sequence release compliance.
4) Providing annual progress reports to the Arabidopsis community and
to the U.S. funding agencies, separate from the progress reports of each of the
individual sequencing groups. These reports will include a careful consideration
not only of amount of sequence provided by each group, but of progress in all
respects, balanced so that groups taking on difficult clones to sequence, or who
are in closing phase and thus must devote time to closing gaps, are given full
credit for such efforts. In addition, these reports are to detail progress in
the informatics aspects of the project, including a summary of the progress and
needs of the Arabidopsis database - as an interface between the database
and its advisory committee, the sequencing groups, and the Arabidopsis
community.
5) Provide an interface between the U.S. groups and the international AGI
committee, and act to facilitate the setting of boundaries and clone
reallocation at an international level.
6) The committee should endeavor to meet in person at least once a year, and
have regularly scheduled meetings by electronic mail or conference call.
The composition of the committee is as follows:
Members:
Ex officio:
The actual members of the committee who have so far agreed to serve:
Elliot Meyerowitz, chair (U.S. Arabidopsis community)
Daphne Preuss (U.S. Arabidopsis community)
Gerd Jürgens (international Arabidopsis community)
Ex officio:
Joe Ecker, SPP
Dick McCombie, CSHSC
Steve Rounsley, TIGR
Ian Bancroft, ESSA III
Francis Quetier, Genoscope
Satoshi Tabata, Kazusa
Recommendations for the other members were:
Joanne Chory, Pam Green or Detlef Weigel (U.S. Arabidopsis community)
Mark Johnson, Richard Gibbs, John Sulston, Maynard Olsen (sequencing experts)
Mark Boguski (database expert)
Mike Cherry (AtDB representative)
FINAL PROSPECT
Given sufficient funding, which seems very likely, there is no technical
obstacle to the completion of the Arabidopsis nuclear genome sequence by
December 31, 2000. Although the efforts of the project members must be focused
tightly on finishing the sequencing, it is not too early to begin considering
the next steps, among them experimental methods for annotation, and functional
analyses of genes and gene families.
submitted by:
Elliot M. Meyerowitz July 15, 1998
Summary of December 1998 AGI Meeting at CSHL
1. Daphne Preuss summarized her work on centromeric regions and presented
detailed information on approximate map locations of BAC contigs and sequenced
BACS based on hybridization (Altmann) and fingerprint (WashU) data. She agreed
to make this information available to the community. Rob Martienssen stressed
that individual clones would need to be compared closely with fingerprint
contigs constructed at WashU because some hybridization data were unreliable.
2. Each group discussed their estimated sequencing capacity and assigned
chromosomal regions for the coming year. Kazusa expects to finish their assigned
regions on III and V by the end of 1999. ESSA and CSHL/WashU may also complete
their assignments on IV and V at about the same time. SPP is continuing with
chromosome I and was encouraged to avoid starting many additional nucleation
points in order to focus on the same closure issues being addressed by the other
groups. Genoscope has begun sequencing the bottom arm of III and will continue
with this region through 2000. TIGR expects to finish chromosome II by summer
1999 and will therefore be the first funded group to run out of an assigned
region to sequence.
3. AGI members discussed the importance of finishing difficult areas within
assigned regions of the genome while also continuing to make rapid progress on
other regions to maximize release of information to the community.
4. Both TIGR and Kazusa proposed to begin sequencing the "unassigned" top 5-6
Mb of chromosome III during 1999. After considerable discussion, both at the AGI
meeting and later in the conference when Satoshi Tabata arrived, a consensus was
reached to have TIGR begin sequencing this region of chromosome III during the
spring of 1999 with the aim of finishing this region by January 2000.
5. Starting in January 2000, TIGR, Kazusa, CSHL, and ESSA will likely have residual sequencing capacity ready to shift to centromeric regions and portions of chromosome 1 that have not yet been completed. By this time a minimal tiling path based on fingerprint data should be available to facilitate assignment of remaining BACs to AGI members. SPP has funding to complete most or all of chromosome I but recognizes that the entire genome
may be completed more rapidly if other groups contribute in the year 2000 to
sequencing portions of this chromosome (or possibly part of the bottom of
chromosome III depending on progress made by Genoscope) after their own assigned
regions have been essentially completed.
6. Marcel Salanoubat and Francis Quetier led a discussion of the Genoscope
policy for sequence release. While it was clear that the informatics
capabilities of the individual laboratories in their program varied
significantly, there was a general agreement that the group should strive for
immediate release of sequences (at least for the bigger laboratories within
their program).
7 . Rob Martienssen and David Meinke discussed the status of the CSHL/WashU
consortium plans to continue sequencing and fingerprinting efforts. NSF has now
received all of the necessary paperwork for continued funding of this consortium
and expects to make an award at a level sufficient to enable sequencing another
2.4 Mb per year starting early in 1999. In addition, NSF has recommended funding
an informatics person at WashU to finish editing of fingerprinted contigs and
establishment of an interactive version of the BAC physical map that can be
accessed via the Internet. This person will work closely with AtDB to avoid
duplication of effort.
8. The CSHL/WashU group has agreed to release to other sequencing groups all
of their edited contig information and fingerprint database through their ftp
site no later than the end of January, 1999. The SPP and TIGR groups are
particularly anxious to make use of this information in order to avoid repeating
the contig-building steps that have already been completed elsewhere. Rob
Martienssen agreed to provide as soon as possible a minimal BAC tiling path for
regions of the genome that may require coordination during the final year of the
project..
9. Joe Ecker and David Meinke discussed a proposal by Hiroaki Shizuya at
Caltech to fingerprint and end-sequence a new BAC library with large inserts
(180 kb average). The general consensus was that although this library might be
very useful in regions of the genome with minimal coverage and could reduce the
overall cost of sequencing other regions by reducing overlaps, it was unlikely
that many AGI participants would immediate move away from using TAMU and IGF
clones for the bulk of their sequencing efforts. NSF is willing to discuss
further the potential value of this library with interested AGI members.
10. Rob Martienssen agreed to serve as the next AGI chairperson. There was
general agreement that AGI members should meet again in summer 1999, perhaps at
the next Arabidopsis meeting in Australia, to assess progress and make specific
plans for the future.
Joe Ecker, AGI chairperson
I. VENUE AND PARTICIPANTS
To assess the current and future database needs of the Arabidopsis community,
an NSF-supported workshop on this topic was convened in Madison Wisconsin on
June 28, 1998. The workshop participants included the following individuals:
Rick Amasino, University of Wisconsin
Mary Anderson, Nottingham
University
Mike Cherry, Stanford University
Joanne Chory, Salk
Institute
Maarten Chrispeels, University of California San Diego
Jeff
Dangl, University of North Carolina
Keith Davis, Ohio State
University
Allan Dickerman, National Center for Genome Research
David
Flanders, Stanford University
Pam Green, Michigan State
University
Bertrand Lemieux, University of Delaware
David Meinke, Oklahoma
State University
Larry Parnell, Cold Spring Harbor Laboratory
Daphne
Preuss, University of Chicago
Ralph Quatrano, Washington University
Ernie
Retzel, University of Minnesota
Steve Rounsley, The Institute for Genomic
Research
Randy Scholl, Ohio State University
Chris Somerville, Carnegie
Institution of Washington and Stanford University (chair)
Desh Pal Verma,
Ohio State University
The following individuals provided valuable written comments prior to the
meeting (Appendix I):
Jean Greenberg, University of Chicago
Katie Krolikowski, Harvard
University
Russell Malmberg, University of Georgia
Jose Martinez-Zapater,
Biology Molecular y Virologia Vegetal, CIT-INIA
Natasha Raikhel, Michigan
State University
Pierre Rouze, Flanders Institute of Biotechnology
Chris
Town, Case Western Reserve University
Desh Pal S Verma, The Ohio State
University
In addition, the workshop was attended by the following observers:
Peter Bretting, USDA/ARS National Program Staff
Greg Dilworth, Department
of Energy
Machi Dilworth, National Science Foundation
Margarita Garcia,
Stanford University
Paul Gilna, National Science Foundation
Xiaoying Lin,
The Institute for Genomic Research
Bob MacDonald, US Department of
Agriculture
DeLill Nasser, National Science Foundation
II. GOALS
The general goals of the workshop were to examine the present and future
database needs of the Arabidopsis community and to outline in general terms the
main issues which should be addressed in any future proposals concerning the
development of new or expanded Arabidopsis databases. The discussions were
intentionally focused on biological and community issues and there was no
attempt to define or specify issues which are related to specific computer
hardware or specific database programs. In particular, no assumptions were made
concerning continued government funding of any current Arabidopsis database
activities.
A previous workshop with these goals was held on June 5th and 6th, 1993. A
copy of the published summary that workshop was provided to all participants and
served as a reference to earlier views and objectives of the Arabidopsis
community. [1993 Dallas Workshop Report] In addition, participants were
provided with a draft summary of a BBSRC-USDA bilateral plant bioinformatics and
coordination meeting held at Llangollen Wales, March 22-24, 1998. A copy of a
memorandum, dated February 26, 1998, from the North American Arabidopsis
Steering Committee to the curators of AtDB, concerning the current Arabidopsis
community database needs was also provided. [NAASC Memorandum] Finally,
in preparation for the meeting, written comments solicited from the community on
the Arabidopsis electronic newsgroup were provided to the participants before
the meeting. A copy of the solicitation and written comments are appended as
Appendix I.
III. RATIONALE FOR AN ARABIDOPSIS DATABASE
The genomes of higher plants, such as Arabidopsis, contain approximately
25,000 genes. During the next several years, the sequence of the Arabidopsis
genome will be completed and extensive sequence information will become
available for many other species, including many plants. Most or all of the
Arabidopsis genes will be used to develop gene chips or microarrays that permit
simultaneous measurements of the expression (mRNA levels) of all of the genes.
These will be used to generate information about the expression of all the genes
in the organism in response to a wide variety of treatments and genetic
backgrounds. Each experiment could have as many as 25,000 data points for each
time point or treatment of each genotype! Comprehensive libraries of insertional
mutations will permit the isolation, by reverse genetics, of null mutations in
any Arabidopsis gene. Extensive collections of enhancer-trap or promoter-trap
lines are being developed that permit sensitive analyses of the spatial patterns
of gene expression down to the single-cell level. Thousands of new classes of
mutants will be isolated by selecting for suppressors or enhancers of existing
mutations. The corresponding genes will be cloned by very high resolution
mapping of the mutations so that a limited number of candidate genes which are
evident in the delimited region of genomic sequence can be directly tested for
complementation. This will depend on the development of very high resolution
maps. It seems likely that high resolution proteomics methods will become
important for identifying the substrates of the thousands of kinase genes that
form many of the regulatory networks in Arabidopsis and other plants.
Additionally, extensive genomic-based work in other plant species will produce a
flood of sequence information. The value of much of that information will be
greatly enhanced by comparison with the aggregate information available in
Arabidopsis. Thus, we are entering an era of explosive growth of knowledge about
Arabidopsis in particular, and plants in general. Most of the data generated by
the projects described above will never appear in printed journals and will only
be available to the community through electronic databases.
Because Arabidopsis is one of the most intensively studied organisms, and is a direct model for 250,000 closely related species, we believe that it is appropriate to undertake a major investment in developing new information retrieval tools (IRTs) for Arabidopsis in particular and plants in general. By this we mean that because we will know everything about Arabidopsis, it is a suitable object on which to focus the building of a comprehensive database or set of linked databases. However, because the value of Arabidopsis derives from its utility in understanding other plants, it would be desirable to build a structure that permits facile high resolution linking of specific information about Arabidopsis to all other plants.
Looking into the future more generally, it is apparent that scientific
publishing is undergoing a much needed revolution. All of the major journals
will be electronic within a few years and once that transition is complete,
scientists will develop new tools for interacting with data. The complexity of
biological knowledge in many fields is such that new mechanisms for integrating
data are required. The development of computer programs that calculate genetic
maps "on the fly" from currently available data is an early example of what will
become a more general mechanism for integrating data. Integrated graphical
representations of patterns of gene expression in individual cells of three
dimensional models of organisms at various developmental stages is another
example that is under development. With such a model it will be possible to find
relationships between objects (eg., genes) and processes that would be difficult
or impossible with current information retrieval technologies.
Because of the changes taking place in publishing, there may be an opportunity to develop databases that will eventually be self supporting in the same way that journals are self supporting. As the distinction between the format blurs, the concept of paying for a database subscription will become commonplace. However, there are many complex issues associated with imposing charges for database use and the question is largely academic at present.
There are many challenges in developing a new generation database. Perhaps
the foremost is the difficulty in collecting information from the thousands of
scientists who produce primary information for conventional publication in
journals.
IV. CURRENT PUBLICLY SUPPORTED DATABASE ACTIVITIES
The principal publicly supported Arabidopsis database activities are the AtDB
database at Stanford University and the stock center databases maintained by the
Arabidopsis resource centers at Ohio State University and the University of
Nottingham. In addition, the University of Minnesota supports an EST database
for all plants, and each of the Arabidopsis genome sequencing groups provides
database access to genomic sequences, including BAC end sequences.
The AtDB goal is to provide the plant-biology research community with convenient and correlated access to the publicly available results of Arabidopsis research. This includes published and otherwise freely available information about the genome, the genes it contains, the gene products, their positions on genetic and physical maps, as well as DNA sequences. The users of the database are very diverse, ranging from Arabidopsis molecular biologists to biologists focusing on any other organism. The members of the AtDB project are currently shared with the Saccharomyces Genome Database, and the database administrator is shared with the Expression Microarray database and Genetic Footprinting database projects, all located at the Department of Genetics at Stanford University. In an effort to minimize wasteful duplication of effort, the AtDB project uses much of the same software and staffing structure as the Saccharomyces Genome Database (SGD). The combined SGD and AtDB groups thus benefit from an economy of scale by sharing computing and human resources.
At a meeting of the Arabidopsis genome community in 1992 at the Cold Spring
Harbor Banbury Center, a consensus was reached that AtDB should take
responsibility for providing centralized access to Arabidopsis databases, a
recommendation that has been repeatedly endorsed by the North American
Arabidopsis Steering Committee. Since that time AtDB has been supported by a
grant from the National Science Foundation. However, the annual level of support
for AtDB has been only a small fraction of the support provided for database
activities for similarly advanced models such as Drosophila, yeast and mouse.
V. SUMMARY OF CONCLUSIONS AND RECOMMENDATIONS
The highest priorities for database content are:
VI. WHAT SHOULD BE IN THE DATABASES?
The long-term goal is to provide interconnected access to all information
about Arabidopsis. However, certain classes of information should have a higher
priority for immediate inclusion and also require a high degree of curation in
order to be most useful to the community.
A. Map-Based Information
At present, many laboratories are engaged in cloning genes by map-based
cloning methods. The use of map-based cloning is expected to continue
indefinitely and to become the most widely used method of cloning genes in the
future. The ease with which this can be accomplished is directly proportional to
the availability of information about genetic and physical maps, polymorphisms,
and large clones. Thus, the greatest current need is a unified genetic and
physical map that incorporates all available information about polymorphic
markers (eg. CAPS, SSLPs, RFLPs), mutations, BAC and YAC clones, mapped clones
and insertions or other modifications of the genome.
Because of the pending completion of the genomic sequence, the state of the
genetic map is expected to change dramatically during the next several years as
sequence-based markers become anchored on the genomic sequence. The availability
of the sequence information will enhance the value of the integrated map because
it will stimulate map-based cloning efforts which will remain dependent on a
high density of polymorphic markers. The integration of the genetic and physical
maps should be undertaken by a group with appropriate expertise in both genetic
and physical maps and database management and curation.
Ready, access to primary mapping data should be given highest priority in
database development. Map information should be collected and presented in a
manner that allows the user to determine what is known, plus what remains
questionable or unresolved with respect to map locations of genetic and
molecular markers in combination with a complete physical map anchored to the
complete nucleotide sequence. In constructing the database, it should be
remembered that recombination data generally provide only rough estimates of map
location, and that mapping data may differ widely in quality and reliability.
Therefore, some database users may prefer direct access to primary mapping data
in order to compare their results with those obtained in other laboratories. A
database that provides options for visualizing several different maps
constructed with different mapping functions or subsets of markers and primary
mapping data would be particularly valuable to the Arabidopsis community.
Any proposal for database development should also discuss in some detail how
the integrity of these maps would be verified and maintained. Some mutations and
cloned genes are likely to be known by several different names. It will
therefore be important to establish a database that will accommodate multiple
changes in nomenclature. Other plant databases are moving toward the use of
standard gene names as described in the Mendel database. The Arabidopsis
databases should also adopt this policy to ensure compatibility with other
databases.
Provisions should also be made to add new types of information to genetic and
physical maps as they become available (break points of chromosomal aberrations;
regions of extensive heterochromatin; regions with a high/low degree of sequence
homology to related plants; etc.).
B. Sequence information
The value of the genomic sequence will depend on the quality of the
annotation. The goal for the quality of annotation should be similar or
identical to that of other higher organisms. It should be possible to arrive at
an integrated map of a gene by various routes. A user should be able to begin a
query with a sequence, a gene name, a keyword or a genetic map location. A user
should be able to highlight a region of the genome on a graphical display and
move to increasingly higher levels of resolution with the click of a mouse. For
example, one might start with a whole chromosome, then move to a ~10 cM region
which shows the contigs of BACs and YACs, the mapped mutations, the sites of
insertional mutations or launching pads for transposons. Next the user should be
able to visualize a ~1 cm region showing all of the above features plus the
locations of open reading frames (theoretical and verified), ESTs, polymorphic
markers, potentially polymorphic markers (ie,. SSLPs). Finally, at the next
level of resolution the user should be able to visualize the DNA sequence, the
various putative open reading frames indicated by gene finding programs,
experimentally verified genes, ESTs, BAC and YAC end sequences, polymorphisms,
mutations and other known aberrations. The open reading frames should be linked
to information about gene expression, experimentally verified information about
gene function, mutant phenotypes associated with classical mutations or over or
under expression, theoretical information about gene function based on inference
from other organisms, subcellular localization of the gene product, known or
predicted modifications of the gene product. If there are other genes of similar
structure in the genome, the presence of these genes should be indicated.
Similarity to genes from other plants should be indicated with a link to the
appropriate databases. The control regions of the genes should be annotated with
known or predicted motifs and with information about the identity of other genes
with similar motifs.
The sequence information should not simply be a link to raw sequence in
GenBank because the level of annotation and tools to manipulate that sequence do
not directly support the kinds of queries made by most biologists. Thus, the
sequence should be directly available from a specialized database which provides
useful tools for manipulating the sequence. It should be possible to retrieve
from the database sequence information based on map position, type of sequence,
or other specific requirements. All information should be linked to publications
describing the data when possible.
Because the sequencing groups are not expected to have the resources to
provide continued annotation, there will be a need for a group to take
responsibility for continued upgrading of the annotation of the genomic sequence
as information about the sequence becomes available from direct experimentation
and from computational analyses based on experimental results obtained with
other organisms.
C. Expression information
The use of microarrays and gene chips are expected to provide a massive
amount of new information. Most or all of the Arabidopsis genes will be used to
develop gene chips or microarrays that permit simultaneous measurements of the
expression (mRNA levels) of all of the genes. These will be used to generate
information about the expression of all the genes in the organism in response to
a wide variety of treatments and genetic backgrounds. Each time point or
treatment could have as many as 25,000 data points. Because the experiments are
technically straightforward, it seems likely that a common type of experiment
will be to prepare mRNA from a mutant and a wild type and to compare the
consequences of the mutation on the expression of all the genes in the organism.
In addition to simply archiving the raw data it should be possible to query the
data in various ways. For instance, as data from different treatment
accumulates, it will become possible to search for genes that are coregulated
with a gene. This kind of query may provide insights into the identity of
otherwise anonymous genes or reveal the existence of networks. It should also be
possible to identify all the factors that cause altered expression of a gene, to
identify all genes that specifically respond to certain treatments, to identify
mutations that cause similar effects on gene expression. For these kinds of
queries it will be necessary to have software that can identify data sets that
are most similar from among hundreds or thousands of different data sets
produced by different treatments.
There is also a large need for a repository for information about spatial
aspects of gene expression. There are now many transgenic lines which exhibit
specific spatial patterns of reporter gene expression, and cloned genes which
confer such patterns. In the short term a database with a controlled vocabulary
for the various cell and tissue types and linked images of the patterns of gene
expression would meet immediate needs. In the longer term, it would be useful to
have graphical tools that would integrate the patterns of gene expression into
an organismic model.
D. Phenotypic Information
Because of the diversity of processes that are being analyzed by a mutational
approach in Arabidopsis, there is a need for facile access to information about
gene function as it relates to the organism. One aspect of the problem involves
determining the genetic basis for a phenotype. In this case it should be
possible to enter a description of a phenotype and obtain a ranked list of
probable genetic alteration that could give rise to the phenotype. Conversely,
it would be very helpful to be able to enter a gene name and obtain a
description of the corresponding mutant. This capability will greatly enhance
the efficiency with which new mutations will be studied as the number of known
mutations begins to plateau. It is expected that we will soon have saturating
collections of transposon mutants, so having ways of describing these
phenotypes, and making them accessible, will be important. No capability of this
kind currently exists.
One strategy may be to use organizational schemes as entry points (phenotypic
indexes, so to speak). One such index is the genetic map position. Knowledge of
this provides an entry point to other mutants and papers. Another possible
organizing scheme could be based on the EcoCyc database format of metabolic
pathways, so that biochemical phenotypes could be correlated, or the knowledge
of existing pathways could be queried. The user would click on a pathway and
learn what was known about this. Another way of indexing and accessing the data
for development might be to have a standardized Arabidopsis growth animation -
at appropriate times during the growth animation, a user could click on a
graphic representation of an organ or other feature, and then this would lead to
additional information. Clicking on a rosette leaf might lead to various types
of leaf cells or indexed leaf morphologies.
E. Stock-Based Information
The databases maintained by the two Arabidopsis resource centers at Ohio
State University and the University of Nottingham provide excellent access to
information on the availability of biological and chemical materials related to
Arabidopsis research. These databases have implemented many of the
recommendations of the 1993 workshop report and should continue to assume
responsibility for descriptive information concerning seed stocks, clones,
vectors, libraries, cDNAs, oligonucleotides, and any other materials that may
require distribution to the Arabidopsis community. Emphasis should be placed on
careful documentation of biological materials, controlled vocabularies, and
maximal utilization of sophisticated graphics to display plant phenotypes,
molecular hybridization patterns, and other data where appropriate.
With respect to seed stocks, it should be possible to search the database by general phenotype, not just by gene symbol, in order to obtain a broad listing of ecotypes and mutant lines with similar features. Information on phenotypes, screening methods, growth conditions, and differences between alleles should be included for all mutants available through the stock centers. It should also be possible to obtain information on additional mutants or alleles that have been isolated in specific laboratories but are not available from the stock centers.
Individuals should be able to search for specialized libraries, vectors,
transgenic lines, and molecular reagents (antibodies, purified proteins, unusual
compounds, and biochemical standards) required for Arabidopsis research.
The stock center databases should be directly linked to a central Arabidopsis
database so that queries about the properties of a gene or mutant can lead
directly to a query about the availability of the resources used to study these
or related aspects of the biology.
F. Community-Based Information
During the past several years there has been a proliferation of electronic resources that provide easy access to information on a wide range of community issues. For instance, it is now relatively easy to retrieve contact information for colleagues or previous postings on the Arabidopsis newsgroup, the abstracts for meetings are available on line and there is an electronic Arabidopsis journal, Weeds World, which provides a forum for discussion of methods and problems and publication of short papers. Many laboratories have mounted web pages that provide detailed information about specialized methods, specialized databases or collections of genetic materials. The curators of AtDB have provided convenient access to these diverse resources by providing a web page that facilitates connection to these resources.
While it is desirable to continue having one group take responsibility for
maintaining a centralized launcher or "data warehouse" for Arabidopsis-related
web sites, this should be a relatively inexpensive activity and should not
require significant public financial support. The distinction between this
activity and a database does not seem to be fully appreciated by the community.
The result is that, because of the proliferation of sites which are all
superficially similar, the users do not know how to efficiently find
information. Therefore, it may be desirable to maintain a clear distinction
between a centralized internet launcher and any future attempts to develop a
unified Arabidopsis database.
G. Biology-Based Information
The focus of research with Arabidopsis is likely to change in the future from
the immediate emphasis on mapping, sequencing, and gene identification, to the
long-term questions of general biology and gene function during plant growth and
development. Thus, there is a long-term need to develop Arabidopsis database(s)
that provide facile access to information that may be of critical importance
during this second phase. In proposing a vision of the future requirements one
correspondent wrote the following (Appendix I):
"I envision a data base organized by levels of organization that can be
addressed at different levels. This database should contain both structural and
functional data organized at different levels. In this way starting, for
example, with the keyword root, one can access information about root structure,
root cell components, root development, nutrients uptake, etc. and end up in the
interactive pathways and proteins responsible for these processes and the
corresponding genes. It should also be possible to address the database by
processes - for example elongation or flowering or pollination. Of course this
is likely far away from real possibilities. Going down to the specifics, the
information in the database could be implemented with information on pathways
and networks, protein interaction maps, protein structures, subcellular
organelles, cell structure, etc. This will be a way to reach to a database as
described above."
Examples of topics that might be included in this category, include:
information on plant pathogens that infect Arabidopsis and details on the
molecular interactions that take place between host and pathogen; information on
the chemical composition of specific plant parts (sugars, lipids, proteins,
polysaccharides, specialized compounds, etc.); physiological data on the normal
life cycle and the response of mutant and wild-type plants to various
environmental and experimental treatments; protein profiles of different plant
parts revealed through 2-D gel electrophoresis; information on the natural
distribution and ecology of Arabidopsis and closely related species; detailed
comparisons of the different ecotypes with respect to morphology, physiology,
and molecular biology; information on the taxonomy of Arabidopsis with
particular attention to related plants used in agriculture; light and electron
micrographs of different types of cells in wild-type plants; records of
expression patterns of specific genes during growth and development; and
computer-enhanced reconstructions of serial sections through various plant
structures.
At present it appears that the development of these resources will be best
accomplished by the individual initiative of members of the community with
specific knowledge and interests in specialized information of the kinds
described above. The eventual integration of specialized databases of this type
into a unified Arabidopsis database will be facilitated by encouraging the open
exchange of schema between database developers. Therefore, public support for
Arabidopsis databases should be contingent on unrestricted access to all schema
and source code used in Arabidopsis databases.
VII. STANDARDS FOR QUALITY OF DATA
All data that is acquired by the databases should be available to users. However, where data is suspect or in conflict with other data, it may be desirable or necessary to provide various views of data. Thus, it may be desirable to provide a user with a curated version of a certain kind of data and an uncurated version. A specific example might be in the interpretation of open reading frames. Since the various gene finder programs do not always make the same prediction, it should be possible to provide the curators best guess as one view and the various alternatives as another view. A simple tab associated with each view would provide a convenient tool for meeting this need. It is also desirable to provide access to the primary mapping data used to position mutations and genes on the genetic map.
Publication of data should not be a prerequisite for inclusion in the
databases. Indeed, the vast majority of data is unlikely to ever be available
via traditional publishing methods.
VIII. HOW WILL THE DATABASE BE USED? WHAT LINKS SHOULD BE MADE
BETWEEN CATEGORIES OF INFORMATION?
In addition to the specific ability to perform searches as described in the previous sections, the categories of information must be linked with user friendly interfaces. To facilitate maximal utility of Arabidopsis databases, there is a need to develop a standard interface for access to Arabidopsis genomic sequence information. All information must have the name of the individuals that provided the data. Attention should be paid to tight coordination between the genetic map and related genes, clones, and sequences, so that selection of any of these will lead transparently to accession of the others. Also, it is highly desirable for the database to have simple links for comparative sequence and mutant analysis with other plants and beyond that, with all organisms. The interface should allow viewing in a variety of ways.
As examples of the types of links desired, we list below a series of
questions that the system should be able to answer.
(1) If a user enters two cloned markers, the system should return a list of
all markers of a specified type that map between them.
(2) If a user points to a location on a genetic map, the genes, clones, and
sequences should appear. Likewise, a user should be able to derive map position
if a DNA sequence is used as the starting point.
(3) For any gene, the expression pattern of the RNA encoded, by the clone
should be readily accessed. Since information may be available about how the
expression of the gene changes with different treatments, or in different
mutants, it will be necessary to allow the user to define a set of comparator
genes that can serve as standards. If available, links to spatially resolved
information should be available as images.
(4) If a user finds a mutant that is altered in a particular way, the system
should retrieve all mutants altered in a similar manner. A cross-species
accession to similar mutants in other plants might be useful.
(5) It should be possible for a user to rapidly determine the map positions
for all genes in a given biochemical or developmental pathway.
(6) If a user has new mapping information, the system should have the ability
to download archived data in that region for manipulation.
IX. COMMUNITY ISSUES THAT MUST BE CONSIDERED IN THE DESIGN AND OPERATION
OF THE DATABASE
A. Advisory Committee
All Arabidopsis database proposals should include a provision for an
oversight committee that will represent the community of Arabidopsis researchers
and will advise database investigators on priorities and data to be included.
The oversight committee should also include individuals with technical expertise
in database design and management. It may also be desirable to have
representation from individuals involved in development and operation of other
plant databases. In order to maximize accountability, it would be desirable to
have the oversight committee formally approved by the North American Arabidopsis
Steering Committee (NASC).
B. Curation, Entry, Correction, and Long-Term storage of Data
One of the major problems associated with developing a database is collecting data. Because database deposits do not currently generate a citation for inclusion in an individuals vita, there is no incentive to make the effort to deposit data. One mechanisms for encouraging deposits may be to implement a citation system for database deposits which would resemble those currently used for journal publications (ie., Author, title, date, accession number).
The task of data acquisition would be greatly facilitated if the journals would require authors to make deposits of data directly into appropriate databases at the time of publication in much the same way that all journals now require GenBank accession numbers. There was unanimous agreement that this would be a desirable development and there are indications that at least some of the plant journals are willing to implement such a change. Future proposals should include a plan for creating user-friendly interfaces that can be used by the authors of journal articles to enter data directly into an internet accessible form. Such forms could also be used by members of the community to enter unpublished data into the database. There was broad enthusiasm for a requirement that anyone receiving public research support be obliged by the funding agencies to describe how the data and research materials from previous supported research have been made available to the stock centers and databases.
Previous attempts to acquire data by soliciting input from the community have
been generally unsuccessful and curation of data by the community is not
considered feasible. Thus, the Arabidopsis databases must be curated by
professional curators. Professional curators of Arabidopsis databases should
make every effort to leverage the database activities undertaken elsewhere and
to adapt existing software when appropriate for use in the Arabidopsis research
community. Thus, the major activity of Arabidopsis databases should be the
collection, entry, and correction of data rather than writing software for
storing, retrieval, and presentation of data. It is clear from past experience
that full time professional curators are required for the development and
operation of an adequate database. In order to recruit and retain highly skilled
personnel to develop and operate the Arabidopsis databases, it is essential that
there be a reasonable expectation of stable long- term funding.
C. Relation to Other Databases and Programs
All Arabidopsis databases should use industry-standard hardware and software,
so that they are both compatible with and can communicate transparently with
other data bases. However, as stated elsewhere in this report, the primary goal
should be to collect and store data using currently accepted database models
rather than to develop new database software. The most important principle,
therefore, in the design of next generation databases is that the data be
entered in a form that makes it possible to interface easily with other
databases and which makes the data portable to future generation database
software. Any software that is written specifically for an Arabidopsis database
(display of genetic maps, for example) should be layered and use industry
standard interfaces so that the software, as well as the underlying data, is
also compatible with and portable to future generation databases. In adition,
consideration should be given to production of generic database structures that
can be used for a variety of different organisms.
Databases are currently being developed for most plants of economic
significance. Because all higher plants are very closely related and are thought
to contain a similar basic gene set, the information in these databases can be
readily interrelated by biological criteria. However, because of the various
concerns of the groups developing other plant databases, and because of the
different kinds and amount of information available, it is not feasible at this
time to consider a common database structure that would accommodate Arabidopsis
and other plants. Therefore, in order to facilitate future interconnectivity
between the Arabidopsis databases and other plant databases, a concerted effort
must be made to adopt common standards whenever possible. The use of the Mendel
gene nomenclature conventions is a case in point. The developers of Arabidopsis
databases should be informed about major activities with other plants and
wherever possible should endeavor to share software.
D. Access of Databases
Data accumulated by a publicly funded database should be community property.
There should be no restrictions on the availability of the data in the databases
and they must be accessible internationally by the internet.
E. One or Several Databases?
It is desirable to facilitate full expression of the collective genius of the
world Arabidopsis community. Because talent in bioinformatics and enthusiasm for
Arabidopsis is distributed around the world, and because of the ease with which
databases can communicate via the internet, a distributed database should be the
goal. However, based on past experience, the users experience difficulty if
information is fragmented or presented in a variety of different interfaces.
Thus, the current situation in which users must navigate six separate databases
to view genome sequence information is unacceptable. Bringing all genome
sequence annotation into a common format should have a top priority. Thus, if
there are several databases, each should have a clear and defined subset of the
database task, and appropriate links to the others. It is imperative that they
be integrated and that the staff operating the different databases be committed
to cooperating with each other. Unrestricted access to all schema and source
codes should be a requirement for public support. The goal should be to have a
single user interface for a specific class of information. Proposals requesting
support for database development must address this issue.
F. Education
The ADB investigators should be provided funding for the provision of
community education and training. This would include the development of on-line
help, training manuals, workshops, and short courses. The ADB developers should
maintain complete documentation and source code. This information should be in
the public domain. Because educators and students in higher education (including
high-school students) may make use of ADB, sufficient documentation for
non-sophisticated users should be made available.
G. Financial Support for Arabidopsis Databases
Although there is a general willingness of most members of the community to
pay directly for database services in much the same way that journal
subscriptions are currently purchased, it was concluded that the disadvantages
of imposing charges outweigh the likely benefits for the foreseeable future.
Thus, at present, it would be inappropriate to impose charges for the use of
publicly supported databases. As with other organism-specific databases, the
burden of funding must be borne by government agencies. In order to retain
highly qualified database curators and developers, there must be reasonable
assurance of continuing support.
H. Ownership of Databases
Because of the convergence of electronic publishing and database activities,
potential liability issues, and because of the intrinsic value of established
databases, consideration needs to be given to the legal ownership of databases.
At present, databases developed with US federal grants are the property of the
institutions that administer the grants. Because of the importance of ensuring
unrestricted public access to Arabidopsis databases, proposals for funding of
future database activities should provide assurances that institutional policies
are consistent with the continuing need for free unrestricted access.
X. WHAT DESIGN-FEATURE ISSUES NEED TO BE CONSIDERED?
The design considerations for Arabidopsis databases are essentially unchanged
from the 1993 workshop report. One of the most pressing needs reported was for
improved graphical visualization tools for various forms of data.
A. Design Considerations that Should be Discussed in any Proposal:
B. Research Goals
Developers should consider and propose to carry out some short-term research
relevant to improving the quality of the Arabidopsis thaliana database. Some
possibilities for short-term research would be:
C. Possible Long-Term Research Goals
NATIONAL SCIENCE FOUNDATION
DEADLINE: MARCH 22, 1999
MATRIX OF PROGRAM REQUIREMENTS
The Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF), through the Biological Database Activities Program in the Division of Biological Infrastructure, has identified as a priority support for the design, development, and implementation of biological information resources for the Multinational Coordinated Arabidopsis thaliana Genome Research project. Therefore, the Biological Database Activities Program announces a special competition for an on-line resource to extend, maintain and distribute a user focused, on-line resource for biological information on Arabidopsis thaliana, termed here the Arabidopsis thaliana Information Resource (AtIR). The successful awardee of this competition will be required to incorporate and build on the existing Arabidopsis thaliana Database (AtDB), which continues to be an unique resource in its role as a primary repository of Arabidopsis information.
Proposal preparation instructions: Standard Grant Proposal Guide (GPG) plus supplementary guidance
Deviations from standard GPG proposal preparation instructions: PIs must complete the BIO Proposal Classification Form (PCF)
Cost sharing/matching requirements: None
Indirect cost (F&A) limitations: None
Other budgetary limitations: Funds may not be requested or used for construction or renovation of facilities.
Use of FastLane in Proposal Preparation & Submission: Entire Proposal Required
FastLane point of contact for this program: E-mail biofl@nsf.gov.
Full Proposal Deadline: March 22, 1999
Description of supplementary criteria: In addition, reviewers will focus on the following issues:
Where appropriate, reviewers will also consider:
Special grant conditions anticipated: None
The Directorate for Biological Sciences (BIO) of the National Science Foundation (NSF), through the Biological Database Activities Program in the Division of Biological Infrastructure, has identified as a priority support for the design, development, and implementation of biological information resources for the Multinational Coordinated Arabidopsis thaliana Genome Research project.
The Multinational Coordinated Arabidopsis thaliana Genome Research project was established in 1990 to develop Arabidopsis thaliana as an experimental model system for flowering plants. During the next several years, the sequence of the Arabidopsis genome will be completed and extensive sequence and mapping information will become available for this and many other plant species. New technologies such as microarrays and gene chips now present the capacity to study the functional expression of thousands of genes at a time, while new capabilities in creating libraries of insertional mutations will allow detailed studies and ultimately manipulation of specific gene function. Drawing on the original goals of embarking on model organism genomes, the value of the Arabidopsis project lies in the utility of the information gathered in seeking to understand the biology of flowering plants.
Therefore, the Biological Database Activities Program announces a special competition for an on-line resource to extend, maintain and distribute a user focused, on-line resource for biological information on Arabidopsis thaliana, termed here the Arabidopsis thaliana Information Resource (AtIR). The successful awardee of this competition will be required to incorporate and build on the existing Arabidopsis thaliana Database (AtDB), which continues to be an unique resource in its role as a primary repository of Arabidopsis information
The Arabidopsis thaliana Information Resource (AtIR) is expected to serve as a repository for data and information generated from multiple genomic studies on Arabidopsis. Operational priorities for this project will be predominantly needs-driven as defined by the Arabidopsis (and related) research communities, and as gathered through mechanisms established by the awardee. While it is understood that some software development will be required to meet these needs, the major mission of AtIR should be viewed as the collection, entry, and updating of data and information.
The project will be expected to focus on specific needs that have been defined by the Arabidopsis research community during the course of meetings held in Dallas, Texas in 1993 and updated in a meeting in Madison, Wisconsin, in 1998.
The greatest current need is a unified genetic and physical map that incorporates all available information about polymorphic markers (e.g., CAPS, SSLPs, RFLPs), mutations, BAC and YAC clon>
Because of the diversity of processes that are being analyzed by a mutational approach in Arabidopsis, there is a need for the entire scientific community to have facile access to information about gene function as it relates to the organism. This capability will greatly enhance the efficiency with which new mutations will be studied as the number of known mutations begins to plateau. AtIR will be expected to incorporate this capability.
AtIR should contain cross-references to all other relevant databases (e.g., GenBank nucleotide sequence database; Arabidopsis thaliana stock center databases; cell and/or probe repository catalogue number(s); and genetic map databases for other species showing significant synteny with Arabidopsis thaliana).
Storage and dissemination of expression data. Most or all of the Arabidopsis genes will be used to develop gene chips or microarrays that permit simultaneous measurements of the expression (mRNA levels) of all of the genes. The use of microarrays and gene chips are expected to provide a massive amount of new information. The ability to query this information may provide insights into the identity of otherwise anonymous genes, reveal the existence of networks or identify factors that cause altered expression of a gene. While it is not necessarily expected that the AtIR will serve as a primary repository for such data, it is expected that user access to such resources will be enabled through the use of appropriate links to other such databases.
Links to stock-based information. The databases maintained by the two Arabidopsis resource centers at Ohio State University and the University of Nottingham provide excellent access to information on the availability of biological and chemical materials related to Arabidopsis research. These databases will continue to assume responsibility for descriptive information concerning seed stocks, clones, vectors, libraries, cDNAs, oligonucleotides, and any other materials that may require distribution to the Arabidopsis community. The AtIR should be directly linked to the stock center databases so that queries about the properties of a gene or mutant can lead in turn to information about the availability of, and ordering procedures for, associated reagents.
The task of data acquisition would be greatly facilitated if members of the Arabidopsis research community could deposit data directly. The AtIR should include a plan for creating user-friendly interfaces that can be used by scientists to deposit data directly to the AtIR via the internet, and address approaches to be taken to encourage direct submission of data from the research community.
Curation and maintenance refers to the need to add, validate and update the biological attributes of repository data. Approaches to this task have ranged from an "in-house" staff of curators or annotators to dependency on community-based methods of data correction, maintenance and updating, to, conceivably, a highly automated suite of computational tools. Curation of data in an Arabidopsis data resource has been and will continue to be an important community need and will be an important facet of the AtIR operation. Proposors will be expected to outline approaches to this task and address the utility of automated or community-based approaches to data curation.
The Arabidopsis database should use industry-standard hardware and software, so that it is both compatible, and can communicate transparently with, other databases. An important principle in designing the resource will be that the storage architecture is structured in a form that makes it possible to interface easily with other databases. Some consideration should be given to production of generic database structures that can potentially be adopted for use in a variety of different organisms and particularly in related mapping and/or sequencing activities in the Plant Genome Research community.
Proposals submitted in response to this announcement must discuss the structure of the proposed database with these goals and scope in mind, and provide detailed plans for long-term management and distribution of the database. The data should be structured and maintained in a way that permits the development and use of complex queries by knowledgeable users or by third party software developers. The AtIR will be expected to collaborate with other efforts relevant to plant databases, both nationally and internationally. Plans detailing how such collaborations might work should be provided. However, formal arrangements for the collaborations need not be made prior to an award. The proposals must also provide plans for the incorporation into the AtIR of information currently found in the Arabidopsis thaliana Database (AtDB) and for the timely assumption of responsibility for data entry, repository maintenance and database distribution, all of which are now provided by AtDB.
The Arabidopsis thaliana Information Resource Project competition, will accept applications from eligible institutions as described in the NSF "Grant Proposal Guide" (GPG), NSF 99-2, Chapter I, Section D, in categories 1 and 2 only. The GPG is available on the NSF web site at the URL ( https://www.nsf.gov/cgi-bin/getpub?nsf992). Paper copies of the GPG may be purchased from the NSF Publication Clearinghouse, P.O. Box 218 Jessup, Maryland 20794-0218, telephone (301) 947-2722, or by e-mail from pubs@nsf.gov.
Consortia of eligible individuals or organizations may also apply, but a single individual or organization must accept overall management responsibility. International collaboration is encouraged; however, financial support for any non-U.S. participant organization must be provided from within the participant's country or other non-U.S. sources.
The Principal Investigator (PI) and other senior staff responsible for the project must have the necessary skills to successfully carry out the tasks covered in this announcement, or the proposal must present convincing plans to hire such staff. The PI should have demonstrated the leadership necessary to meet the challenges of managing a large community database in a rapidly changing technological and scientific environment. The PI and other members of the senior staff should, in the aggregate, have experience with aspects of plant biology research relevant to the database, have current knowledge about computerized databases and their management, and have a demonstrated ability to interact with the members of the various scientific disciplines and other groups important for the successful operation of the database. Experience with the successful management of a database effort of comparable scope and complexity will be considered an important asset.
The NSF expects to make one five year award in Fiscal Year 1999 depending on the quality of submissions and the availability of funds. The total award size is expected to range up to $1 million per year. The exact amount will depend on the advice of reviewers and on the availability of funds. It is anticipated that the award will be administered as a grant or cooperative agreement.
Note, while the term "award" and "awardee" used herein imply a single entity, NSF is not necessarily constrained by this model and is open to proposals of innovative models involving more than one entity by which the primary functions of AtIR might be administered (e.g., a "virtual resource"). Again, a single individual or organization must accept overall management responsibility.
Proposals to Arabidopsis thaliana Information Resource (AtIR) Project competition require electronic submission via the NSF FastLane system in accordance with the guidelines provided in the "Instructions for Proposal Preparation" found in the GPG, Chapter II. The GPG is available on the NSF Web Site at the URL https://www.nsf.gov/cgi-bin/getpub?nsf992. Paper copies of the GPG may be purchased from the NSF Publication Clearinghouse, P.O. Box 218 Jessup, Maryland 20794-0218, telephone (301) 947-2722, or by e-mail from pubs@nsf.gov.
Include in proposals to AtIR the components listed in GPG, Chapter II, Section D. State information in each component as clearly and concisely as possible for merit review. Take special care in adhering to the requirements for page limitations, font size, and margins (see GPG, Chapter II, Section C). Proposals not strictly adhering to the requirements of the GPG and these guidelines are returned without review. Instructions and guidelines for the FastLane submission of proposals are detailed in Instructions for Preparing and Submitting a Standard Proposal via FastLane located at http://www.fastlane.nsf.gov/a1/newstan.htm. Also, see the "FastLane Submission" section below.
Guidelines are provided for specific sections of the proposal as follows:
In the NSF FastLane system follow instructions on proposal preparation. When completing the Cover Sheet click on the "Add Org Unit" button. Highlight "DIRECT FOR BIOLOGICAL SCIENCES" and click "OK." Highlight "Database Activities" and click "OK." Clicking "OK" designates this program as the NSF organizational unit of consideration. In the box labeled "Program Announcement/Solicitation No." enter "NSF 99-50" with no additional characters.
Begin the title of the proposal with "AtIR: . . . ."
The first-listed Principal Investigator (PI) is designated as the primary PI and is responsible for coordinating the entire proposed project.
Provide a brief (200 words or less) description of the project.
Particular attention must be paid to the following major aspects in preparing a description of the proposed project. Although some relevant technical issues are mentioned below, these details are intended only as guidelines. This section must not exceed 25 pages inclusive of tables, diagrams or other visual material. Clearly label sections and major subdivisions of the project description.
Describe your vision for the long-term future of such a database as the AtIR and the role this operation should play in the overall plant genome research forum. Address issues such as long-term economic sustainability of the database, potential economic models that invoke alternative sources of support, and possible transition plans to such models.
The proposal should provide a description of (1) the logical or conceptual model for the data, and (2) a general outline of the physical implementation schema for the repository. The general features and overall design of both must be justified in the context of efficient data management and researcher support functions. Extensibility of the design to the maintenance of data and information from other databases of plant research information may be discussed here.
Proposals should describe the manner in which the data to be placed in the resource will be acquired. Specifically, if it is intended that data be acquired from investigators as the original source of the data, procedures for the handling of such submissions should be described, including any standard or proprietary data exchange formats or tools to be used.
Because it is anticipated that the volume and rate of data generation will continue to increase in the future, an important technical issue to be considered is the development and use of approaches which are capable of scaling to anticipated increases in the volume of data.
Proposals should describe precisely the expected content of the database. The description should include some definition of what constitutes a minimum dataset, as well as a description of what might constitute a fully annotated dataset.
Minimum criteria for insuring the completeness and consistency of entries at the time they are placed in the database should be described, as should procedures for assuring that the criteria have been met. It is expected that the utility of the criteria and procedures will be periodically reviewed and approved using the formal external advisory mechanism.
Proposals should address the technical issues involved in the maintenance of a highly automated information repository, with convenient public access and off-site backup or other provision for protection from software or hardware failure. Provisions for maintenance of internal and external links should be discussed. The focus of the proposal should be the operation of a basic repository.
Proposals should also describe the distribution methods envisioned, for example network access to the complete collection using the WWW or other means, and periodic production of tapes, CD-ROM or other media containing current entries.
If mirror sites are to be used, describe how the central and mirror sites will interact, estimate the time and effort required to operate a typical mirror and provide the criteria to be used in selecting mirror sites.
Any planned charges for copies on tape or other media, or for permission to provide such copies, should be discussed briefly in the proposal. All such charges will be subject to approval by the NSF. Periodic assessment of the utility of the distribution methods will be expected as part of the management and oversight of the AtIR.
NSF expects that Principal Investigators agree to complete and open sharing of data and material in an expeditious manner. By submitting a proposal, it is understood that the submitting institution and all participants agree to these guidelines (see the NSF GPG, NSF 99-2, Chapter VII, Section H).
Describe how users will be able to develop and use direct queries of the database. The interaction with the repository and the means to insure stability and security should be specified.
Provide a timetable for the assumption of responsibility for new data entry and distribution of the database, including any efforts necessary for incorporation of entries now found in the AtDB into the new database. It is anticipated that the time required for complete assumption of the responsibility will not exceed one year from the date of the award.
Describe provisions for insuring the quality of the database and its operation, including procedures for obtaining and responding to user feedback on issues related to quality.
A sound management plan will be a crucial aspect of the proposal. The responsibilities of the various senior personnel must be clearly described, as must the time and effort to be committed by each. A mechanism for replacing key personnel who leave the project must also be described. In the event senior personnel will participate in multiple activities related to the database (e.g., outreach, data acquisition, etc.), estimate the anticipated effort with respect to each activity.
The awardee will be expected to establish a formal mechanism for insuring ongoing external input from relevant groups and interested individuals regarding AtIR policies and practices. An appropriate mechanism could, for example, consist of a standing external advisory board with relevant technical and managerial expertise. The function of such an advisory board could be to advise senior management of the AtIR and the awardee institution(s) on policies such as those regarding operational priorities, format, content and validation of entries and reports, those related to other aspects of use or distribution of the database, etc. Periodic review and approval of the utility and appropriateness of any such criteria will be expected.
Implementation of the mechanism should insure that the views of relevant research communities are represented as part of this advice. In general, the mechanism should provide an opportunity for input from the international Arabidopsis research community. The appropriateness and adequacy of the mechanism, as implemented, will be subject to approval by the NSF.
Describe provisions for timely and widespread communication of activities of the AtIR, in particular procedures for alerting user/developer communities to impending changes in software/formats/policies, etc. Describe any activities planned to train new or experienced users in use of the resource. Activities supported by this award may provide an ideal environment to train young scientists in cutting-edge research technologies and to expose them to new paradigms in plant biology informatics. In addition, these activities should promote increased participation by members of under-represented groups. Proposers should describe plans to increase diversity whenever feasible.
If the PI or any Co-PI has received federal support for the establishment or operation of a publicly available database within the last five years, provide a brief description of the relevant features of the database together with the name of the agency providing support, the award number and title, and the amount and duration of the award. This section should include a general description of the type of database, number of users, means of distribution, etc. If the database is available electronically, provide the relevant URL. If awards for more than one project have been received, describe the project most relevant to the current proposal. This section is limited to a maximum of 5 pages, including any references and is included as part of the Project Description 25 page limit.
For each of the key personnel, including senior staff and any other staff whose participation is critical to the success of the project, provide a curriculum vitae or short biographical sketch. Briefly describe relevant experience and list up to 10 publications (to include the individual's 5 most important and up to 5 other relevant publications). Include an alphabetical list of current and past collaborators of all key personnel whose biosketches are included, and of any other staff or collaborators mentioned by name in the proposal. Additionally, include names of all graduate students and postdoctoral fellows who have trained with these individuals, as well as anyone with whom these individuals have co-authored a paper within the last 4 years. The information may not exceed 2 pages for each individual. Applicants may include letters of support in the FastLane submission by scanning the documents and adding them at the end of the Project Description file, clearly labeled.
Copies of letters indicating agreement to participate should be provided by all senior personnel who do not endorse the cover page as PI or Co-PI. Such letters should include a brief description of the individual's expected role in the project and an estimate of the time and effort to be required. Scan the letters and add them at the end of the Project Description file, clearly labeled as Appendix A. This information is not counted as part of the 25 page limit of the Project Description.
Provide a budget and budget justification for each year of support requested as well as a separate, cumulative budget for all years. If funds for subcontracts are requested, then a separate budget and budget justification must be prepared by each subcontractor to show the distribution of subcontract funds across categories. Funds for facility construction or renovation may not be requested.
A brief justification for funds in each budget category should be provided. For major equipment or software materials, a particular model or source and the current or expected price should be specified whenever possible. A brief explanation of the need for each item whose cost exceeds $10,000 should be provided. This section should also include details of institutional cost sharing, if any, and of other sources of support for the project, such as government, industry, or private foundations. Although cost sharing is not required, any such commitment specified in the proposal will be referenced and included as a condition of an award resulting from this solicitation.
Appropriate documentation of any such commitments should be provided in an appendix (Appendix B). Scan the documents and add them at the end of the Project Description file, clearly labeled as Appendix B. This information is not counted as part of the 25 page limit of the Project Description.
Provide a complete list of current and pending support for all PIs and Co-PIs
Include a brief description of available facilities, including space and computational equipment available for the project. Where requested equipment or materials duplicate existing items, explain the need for duplication. This section is limited to 2 pages.
Complete the BIO PCF, available on the NSF FastLane system. The PCF is an on-line coding system that allows the Principal Investigator to characterize his/her project when submitting proposals to the Directorate for Biological Sciences. Once a PI begins preparation of his/her proposal in the NSF FastLane system and selects a division, cluster, or program within the Directorate for Biological Sciences as the first or only organizational unit to review the proposal, the PCF will be generated and available through the Form Selector screen. Additional information about the BIO PCF is available in FastLane at http://www.fastlane.nsf.gov/a1/BioInstr.htm.
Plans requiring collaborative effort by an individual not employed at the submitting institution(s) should be supported by a signed letter from the individual. Besides indicating a willingness to collaborate, the letter should provide a brief outline of the goals of the collaboration and estimate the time and effort the individual expects to devote to the collaboration. Biographical sketches should not be provided for such individuals, unless requested by NSF. A collaborator whose primary purpose is advisory (e.g., service on a committee that will provide policy advice) does not need to provide/submit such a letter.
Scan the letters and other relevant Special Information and Supplementary Documentation, as specifically described in the GPG, Chapter II, Section D.12, and add them at the end of the Project Description file after Appendices A and B, clearly labeled as "Special Information and Supplementary Documentation." Only documentation as described in the GPG, Chapter II, Section D.12 and detailed above is allowed. This information is not counted as part of the 25 page limit of the Project Description.
Only the appendices described in the "Budget Justification", and "Biographical Sketches", are allowed. Other letters of endorsement may not be included.
Proposals must be sent by 5:00 p.m., submitter's local time, March 22, 1999 via the NSF FastLane system.
Mail the following materials directly to the Biological Database Activities Program:
Do not mail copies of the full proposal. NSF will make the appropriate number of copies of the proposal.
The grantee is responsible for ensuring that the materials are received by March 26, 1999. Send materials to:
Arabidopsis thaliana Information Resource Project-NSF 99-50
Division of Biological Infrastructure
National Science Foundation
4201 Wilson Boulevard
Room 615
Arlington, VA 22230
Unless requested by NSF, additional information may not be sent following proposal submission.
In order to use NSF FastLane to prepare and submit a proposal, you must have the following software: Netscape Navigator 3.0 or above, or Microsoft Internet Explorer 4.01 or above; Adobe Acrobat Reader 3.0 or above for viewing PDF files; and Adobe Acrobat 3.X or Aladdin Ghostscript 5.10 or above for converting files to PDF.
To use FastLane to prepare the proposal your institution needs to be a registered FastLane institution. A list of registered institutions and the FastLane registration form are located on the FastLane Home Page. To register an organization, authorized organizational representatives must complete the registration form. Once an organization is registered, PIN for individual staff are available from the organization's sponsored projects office.
To access FastLane, go to the NSF Web site at https://www.nsf.gov/, then select "FastLane," or go directly to the FastLane home page at http://www.fastlane.nsf.gov/. Please see "Instructions for Preparing and Submitting a Proposal to the NSF Directorate for Biological Sciences" located at http://www.fastlane.nsf.gov/a1/BioInstr.htm. Additionally, read the "PI Tipsheet for Proposal Preparation" and the "Frequently Asked Questions about FastLane Proposal Preparation," accessible at https://www.fastlane.nsf.gov/a1/A1Prep.htm.
IMPORTANT NOTE: For technical assistance with FastLane, please send an e-mail message to biofl@nsf.gov. If you have inquiries regarding other aspects of proposal preparation or submission, please contact the cognizant program officer, preferably at least three weeks before the competition deadline.
Reviews of proposals submitted to NSF are solicited from peers with expertise in the substantive area of the proposed research or education project. These reviewers are selected by Program Officers charged with the oversight of the review process. NSF invites the proposer to suggest, at the time of submission, the names of appropriate or inappropriate reviewers. Special care is taken to ensure that reviewers have no immediate and obvious conflicts with the proposer. Special efforts are made to recruit reviewers from non-academic institutions, minority serving institutions, adjacent disciplines to that principally addressed in the proposal, first time NSF reviewers, etc.
Proposals will be reviewed against the following general merit review criteria established by the National Science Board. Following each criterion are potential considerations that the reviewer may employ in the evaluation. These are suggestions and not all will apply to any given proposal. Each reviewer will be asked to address only those that are relevant to the proposal and for which he/she is qualified to make judgments.
How important is the proposed activity to advancing knowledge and understanding within its own field and across different fields? How well qualified is the proposer (individual or team) to conduct the project? To what extent does the proposed activity suggest and explore creative and original concepts? How well conceived and organized is the proposed activity? Is there sufficient access to resources?
How well does the activity advance discovery and understanding while promoting teaching, training, and learning? How well does the proposed activity broaden the participation of underrepresented groups (e.g., gender, ethnicity, geographic, etc.)? To what extent will it enhance the infrastructure for research and education, such as facilities, instrumentation, networks, and partnerships? Will the results be disseminated broadly to enhance scientific and technological understanding? What may be the benefits of the proposed activity to society?
In addition, reviewers will focus on the following issues:
Where appropriate, reviewers will also consider:
One of the principal strategies in support of NSF's goals is to foster integration of research and education through the programs, projects and activities it supports at academic and research institutions. These institutions provide abundant opportunities where individuals may concurrently assume responsibilities as researchers, educators, and students and where all can engage in joint efforts that infuse education with the excitement of discovery and enrich research through the diversity of learner perspectives. PIs should address this issue in their proposal to provide reviewers with the information necessary to respond fully to both NSF merit review criteria. NSF staff will give this careful consideration in making funding decisions.
Broadening opportunities and enabling the participation of all citizens-women and men, underrepresented minorities, and persons with disabilities-is essential to the health and vitality of science and engineering. NSF is committed to this principle of diversity and deems it central to the programs, projects, and activities it considers and supports. PIs should address this issue in their proposal to provide reviewers with the information necessary to respond fully to both NSF merit review criteria. NSF staff will give this careful consideration in making funding decisions.
Most proposals submitted to the NSF are reviewed by mail review, panel review, or some combination of mail and panel review.
Proposals submitted to this activity will be evaluated by a special emphasis panel formed to review the applications and mail reviewers. Site visits may be conducted as needed. NSF will be able to tell applicants whether their proposals have been declined or recommended for funding within six months for 95 percent of proposals in this category.
Notification of the award is made to the submitting organization by a Grants Officer in the Division of Grants and Agreements. Organizations whose proposals are declined will be advised as promptly as possible by the cognizant NSF Program Division administering the program. Verbatim copies of reviews, not including the identity of the reviewer, will be provided automatically to the lead Principal Investigator.
Grants awarded as a result of this announcement are administered in accordance with the terms and conditions of NSF GC-1 (10/98), "Grant General Conditions" (10/98), or FDP-III (7/97), "Federal Demonstration Partnership General Terms and Conditions," or CA-1 "Cooperative Agreement General Terms and Conditions" (2/98), depending on the grantee organization. Copies of these documents are available at no cost from the NSF Publications Clearinghouse, P.O. Box 218, Jessup, Maryland 20794-0218, telephone (301) 947-2722, or via e-mail to pubs@nsf.gov. More comprehensive information is contained in the NSF Grant Policy Manual (NSF 95-26), available on the NSF OnLine Document System located at https://www.nsf.gov/, or for sale through the Superintendent of Documents, Government Printing Office, Washington, D.C. 20402.
For all multi-year grants (including both standard and continuing grants), the PI must submit an annual project report to the cognizant Program Officer at least 90 days before the end of the current budget period.
Within 90 days after expiration of a grant, the PI also is required to submit a final project report. Approximately 30 days before expiration, NSF will send a notice to remind the PI of the requirement to file the final project report. Failure to provide final technical reports delays NSF review and processing of pending proposals for the PI. PIs should examine the formats of the required reports in advance to assure availability of required data.
NSF has implemented a new electronic project reporting system, available through FastLane, which permits electronic submission and updating of project reports, including information on: project participants (individual and organizational); activities and findings; publications; and other specific products and contributions. Reports will continue to be required annually and after the expiration of the grant, but PIs will not need to re-enter information previously provided, either with the proposal or in earlier updates using the electronic system.
Effective October 1, 1998, PIs are required to use the new reporting format for annual and final project reports. PIs are strongly encouraged to submit reports electronically via FastLane. For those PIs who cannot access FastLane, paper copies of the new report formats may be obtained from the NSF Clearinghouse as specified above. NSF expects to require electronic submission of all annual and final project reports via FastLane beginning in October, 1999.
If the submitting organization has never received an NSF award, it is recommended that the organization's appropriate administrative officials become familiar with the policies and procedures in the NSF Grant Policy Manual which are applicable to most NSF awards. The "Prospective New Awardee Guide" (NSF 97-100) includes information on: Administration and Management Information; Accounting System Requirements and Auditing Information; and Payments to Organizations with Awards. This information will assist an organization in preparing documents that NSF requires to conduct administrative and financial reviews of an organization. The guide also serves as a means of highlighting the accountability requirements associated with Federal awards. This document is available electronically on NSF's Web site at https://www.nsf.gov/cgi-bin/getpub?nsf97100.
Inquiries regarding the announcement should be directed to the cognizant NSF official: Dr. Paul Gilna, Division of Biological Infrastructure, National Science Foundation, 4201 Wilson Boulevard, Room 615, Arlington, VA 22230. Telephone: (703) 306-1469; FAX: (703) 306-0356; E-mail: pgilna@nsf.gov
The National Science Foundation (NSF) funds research and education in most fields of science and engineering. Grantees are wholly responsible for conducting their project activities and preparing the results for publication. Thus, the Foundation does not assume responsibility for such findings or their interpretation.
NSF welcomes proposals from all qualified scientists, engineers, and educators. The Foundation strongly encourages women, minorities, and persons with disabilities to compete fully in its programs. In accordance with federal statutes, regulations, and NSF policies, no person on grounds of race, color, age, sex, national origin, or disability shall be excluded from participation in, be denied the benefits of, or be subjected to discrimination under any program or activity receiving financial assistance from NSF. Some programs may have special requirements that limit eligibility.
Facilitation Awards for Scientists and Engineers with Disabilities (NSF 91-54) provide funding for special assistance or equipment to enable persons with disabilities (investigators and other staff, including student research assistants) to work on NSF-supported projects.
The National Science Foundation has Telephonic Device for the Deaf (TDD) and Federal Information Relay Service (FIRS) capabilities that enable individuals with hearing impairments to communicate with the Foundation regarding NSF programs, employment, or general information. TDD may be accessed at (703) 306-0090; FIRS at 1-800-877-8339.
The information requested on proposal forms and project reports is solicited under the authority of the National Science Foundation Act of 1950, as amended. The information on proposal forms will be used in connection with the selection of qualified proposals; project reports submitted by awardees will be used for program evaluation and reporting within the Executive Branch and to Congress. The information requested may be disclosed to qualified reviewers and staff assistants as part of the review process; to applicant institutions/grantees to provide or obtain data regarding the proposal-review process, award decisions, or the administration of awards; to government contractors, experts, volunteers, and researchers and educators as necessary to complete assigned work; to other government agencies needing information as part of the review process or in order to coordinate programs; and to another Federal agency, court or party in a court or Federal administrative proceeding if the government is a party. Information about Principal Investigators may be added to the Reviewer file and used to select potential candidates to serve as peer reviewers or advisory committee members. See Systems of Records, NSF-50, "Principal Investigator/Proposal File and Associated Records," 63 Federal Register 267 (January 5, 1998), and NSF-51, "Reviewer/Proposal File and Associated Records," 63 Federal Register 268 (January 5, 1998). Submission of the information is voluntary. Failure to provide full and complete information, however, may reduce the possibility of receiving an award.
Public reporting burden for this collection of information is estimated to average 120 hours per response, including the time for reviewing instructions. Send comments regarding this burden estimate and any other aspect of this collection of information, including suggestions for reducing this burden, to: Reports Clearance Officer; Information Dissemination Branch, DAS; National Science Foundation; Arlington, VA 22230.
The program described in this announcement is in the category 47.074 (BIO) of the Catalog of Federal Domestic Assistance.
In accordance with NSF Important Notice No. 120 dated June 27, 1997, Subject: Year 2000 Computer Problem, NSF awardees are reminded of their responsibility to take appropriate actions to ensure that the NSF activity being supported is not adversely affected by the Year 2000 problem. Potentially affected items include computer systems, databases, and equipment. The National Science Foundation should be notified if an awardee concludes that the Year 2000 will have a significant impact on its ability to carry out an NSF-funded activity. Information concerning Year 2000 activities can be found on the NSF Web site at https://www.nsf.gov/oirm/y2k/start.htm.
OMB NO. 3145-0058
P.T.: 34
K.W.: 1002037
NSF 99-50 Electronic Dissemination Only