 |
|
|
Award Abstract #0115684
The Floral Genome Project
| NSF Org: |
IOS
Division of Integrative Organismal Systems
|
|
|
| Initial Amendment Date: |
September 27, 2001 |
|
| Latest Amendment Date: |
August 1, 2005 |
|
| Award Number: |
0115684 |
|
| Award Instrument: |
Continuing grant |
|
| Program Manager: |
Diane Jofuku Okamuro
IOS Division of Integrative Organismal Systems
BIO Directorate for Biological Sciences
|
|
| Start Date: |
October 1, 2001 |
|
| Expires: |
September 30, 2007 (Estimated) |
|
| Awarded Amount to Date: |
$7471263 |
|
| Investigator(s): |
Claude dePamphilis cwd3@psu.edu (Principal Investigator)
|
|
| Sponsor: |
Pennsylvania State Univ University Park
110 Technology Center Building
UNIVERSITY PARK, PA 16802 814/865-1372
|
|
| NSF Program(s): |
PLANT GENOME RESEARCH PROJECT
|
|
| Field Application(s): |
|
|
| Program Reference Code(s): |
BIOT, 9109
|
|
| Program Element Code(s): |
1329
|
ABSTRACT
Variations in floral architecture are of major evolutionary and economic importance, impacting various plant processes such as pollination and gene flow, as well as fruit production and seed dispersal. However, despite the central role of flowers in plant reproduction and agriculture, questions about the origin and diversification of the flower remain fundamental problems in plant biology. Recent studies in plant developmental genetics and genomics have identified dozens of genes with specific roles in flower development in Arabidopsis and other model organisms. Still, many (if not most) genes with critical roles remain undiscovered, largely because of functional redundancy. Because most economically important species are not closely related to model plant species, novel approaches are needed to build upon existing genome projects and transfer knowledge to nonmodel organisms.
THE FLORAL GENOME PROJECT will investigate the origin, conservation, and diversification of the genetic architecture of the flower, and develop conceptual and real tools for evolutionary functional genomics in plants. A set of plant 'exemplars' was selected, based on recent phylogenetic studies, to include the basal angiosperm groups where most flower diversity is found, plus key eudicot lineages where many crop species occur. THE FLORAL GENOME PROJECT will generate large EST datasets , capturing thousands of sequences of genes expressed during early flower development in each species. New sampling approaches will be used to improve the chance of obtaining rare transcripts and of obtaining comparable gene sets from each species. Finished sequencing for up to 300 unique genes per species will allow study of the evolution of key genes and gene families expressed in flowers, and test leading hypotheses about the origin of the flower THE FLORAL GENOME PROJECT will examine the site and timing of gene expression for the unique genes detected in each species using a combination of microarray analysis and new methods of high throughput in situ hybridization. Expression patterns will be evaluated for hundreds of genes in each species, and summarized in 3-D virtual reconstructions of developing flowers. This project would generate the first comparative data set of expression patterns for a large number of genes across diverse angiosperms.
These experiments will generate an enormous dataset of gene sequences and their expression in different species, and will require new informatic tools for the comparative analysis of gene history, gene function, and molecular evolution. Informatics efforts will include the generation of software for improved phylogenetic analysis of gene families and an automated data pipeline to enable researchers to move efficiently from traces to trees in an exploratory fashion. A phylogenetic database, integrated with web-based tools for flexible inquiry, will be created as a public resource to relate sequence information from expressed gene studies in a phylogenetic framework. This database will provide annotated links to genomic and functional information in Arabidopsis, rice, and maize, and to expressed gene studies in tomato, maize, and many other important crop species. THE FLORAL GENOME PROJECT will provide a key resource for generating hypotheses about common gene functions in plants and the potential sources of variation among diverse species.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
|
(Showing: 1 - 10 of 49)
(Showing: 1 - 49 of 49)
|
Show All |
Albert, V.A., D.G. Oppenheimer, and C. Lindqvist.. "Pleiotropy, redundancy and the evolution of flowers," Trends in Plant Science, v.7, 2002, p. 297.
Albert, V.A., Soltis, D.E., Carlson, J.E., Farmerie, W.G., Wall, P.K., Ilut, D.C., Solow, T.M., Mueller, L.A., Landherr, L.L., et al.. "Floral gene resources from basal angiosperms for comparative genomics research.," BMC Plant Biology, v.5, 2005, p. 5.
Altman, N., Leebens-Mack, J. H, Zahn, L., Chanderbali, A., Tian, D., Werner, L., Ma, H., and dePamphilis, C.W.. "Behind the scenes: planning a multispecies microarray experiment," Chance, v.19, 2006, p. 28.
Buzgo, M., D. E. Soltis, P. S. Soltis, H. Ma. "Towards a comprehensive integration of morphological and genetic studies of
floral development," Trends in Plant Science, v.9, 2004, p. 164.
Buzgo, M., Soltis, P. S., and Soltis, D. E.. "Floral developmental morphology of Amborella trichopoda (Amborellaceae)," International Journal of Plant Sciences, v.165, 2004, p. 925.
Buzgo, M., Soltis, P.S., Kim, S., and Soltis, D.E.. "The making of a flower.," The Biologist, v.52, 2005, p. 149.
Carlson, J.E., Leebens-Mack, J.H., Wall, K., Zahn, L.M., Mueller, L.A., Landherr, L.L., Hu, Y., Ilut, D.C., Arrington, J.M., Choirean, S., Becker, A., Field, D., Tanksley, S.D., Ma, H. and dePamphilis, C.W.. "EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6000 genes from a basal eudicot," Plant Molecular Biology, v.62, 2006, p. 351.
Cui, L., Leebens-Mack, J.H., Wang, L-S., J. Tang, Rymarquis, L., Stern, D., and dePamphilis, C.W.. "Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach," BMC Evol. Biol., v.6, 2006, p. 13.
Cui, L., Veeraraghavan, N., Richter, A., Wall, K., Jansen, R. K., Leebens-Mack, J.H., Makalowska, I., and dePamphilis, C.W.. "ChloroplastDB: the chloroplast genome database," Nucleic Acids Research, v.34, 2006, p. D692.
Cui, L., Wall K., Leebens-Mack, J.H., Lindsay, B.G., D.E., Soltis, Doyle, J.J., Soltis, P.S., Carlson, J. E. Arumuganathan , K., Barakat, A., Albert, V.A., Ma, H., and dePamphilis, C.W.. "Widespread genome duplications throughout the history of flowering plants," Genome Research (cover), v.16, 2006, p. 738.
Duarte, J. M., Cui, L., Wall, K., Zhang, Q., Zhang, X., Leebens-Mack, J.H., Ma, H., Altman, N., and dePamphilis, C.W.. "Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis," Molecular Biology and Evolution, v.23, 2006, p. 469.
Elomaa, P., Uimari, A., Mehto, M., Albert, V. A., Laitinen, R. A. E., and Teeri, T. H.. "Activation of anthocyanin biosynthesis in Gerbera hybrida (Asteraceae)
suggests conserved protein-protein and protein-promoter interactions
between the anciently diverged monocots and eudicots," Plant Physiology, v.133, 2003, p. 1.
Frohlich, M.W.. "An evolutionary scenario for the origin of flowers.," Nature Reviews Genetics, v.4, 2003, p. 559.
Gilbert M.T., J. Binladen, W. Miller, C. Wiuf, E. Willerslev, H. Poinar, J.E. Carlson, J.H. Leebens-Mack, and S.C. Schuster. "Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis," Nucleic Acids Research, v.Epub, 2006, p. Sept.18.
Hu, W., and Ma, H.. "Characterization of a novel putative zinc-finger gene MIF1: involvement in multiple hormonal regulation of Arabidopsis development," Plant Journal, v.45, 2006, p. 399.
Hu, W., Wang, Y., Bowers, C., and Ma, H.. "Isolation, sequence analysis, and expression studies of florally expressed
genes in Arabidopsis," Plant Molecular Biology, v.53, 2003, p. 545.
Kim, S., J. Koh , M-J.Yoo, H. Kong, Y. Hu, H. Ma, P.S. Soltis and D.E. Soltis.. "Expression of floral MADS-box genes in basal angiosperms: Implications for the evolution of floral regulators.," The Plant Journal, v.43, 2005, p. 724.
Kim, S., Koh, J., Ma, H., Hu, Y., Endress, P., Hauser, B., Buzgo, M., Soltis, P.S., and Soltis, D.E.. "Sequence and expression studies of A-, B-, and E-class MADS-box genes in Eupomatia
(Eupomatiaceae): Support for the bracteate origin of the calyptra.," International Journal of Plant Sciences, v.166, 2005, p. 185.
Kim, S., M-J. Yoo, V. A. Albert, J. S. Farris, P. S. Soltis, and D. E. Soltis. "Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary
and functional implications of a 260 million year old duplication.," American Journal of Botany, v.91, 2004, p. 2102.
Kim, S., Soltis, P.S., Wall, K., and Soltis, D. E.. "Phylogeny and domain evolution in the APETALA2-like gene family.," Molecular Biology and Evolution, v.23, 2006, p. 107.
Kirik, V., Lee, M.M., Wester, K., Herrmann, U., Zheng, Z., Oppenheimer, D., Schiefelbein, J. and Hülskamp, M.. "Functional diversification of MYB23 and GL1 genes in trichome morphogenesis and
initiation.," Development, v.132, 2005, p. 1477.
Kong, H.-Z., Leebens-Mack, J., Ni, W., dePamphilis, C. W., and Ma, H.. "Highly heterogeneous rates of evolution in the SKP1 gene family in animals
and plants: functional and evolutionary implications," Molecular Biology and Evolution, v.21, 2004, p. 117.
Kuhl, J.C., Havey, M.J., Martin, W.J., Cheung, F., Yuan, Q., Landherr, L., Hu, Y., Leebens-Mack, J., Town, C.D., and Sink, K.C.. "Comparative genomic analyses in Asparagus," Genome, v.48, 2005, p. 1052.
Leebens-Mack, J.H. and 27 others. "Taking the first steps towards a standard for reporting on phylogenies: minimal information about a phylogenetic analysis (MIAPA)," Omics, v.10, 2006, p. 231.
Leebens-Mack, J.H., Raubeson, L. A., Cui, L., Kuehl, J. V., Fourcade, M. H., Chumley, T. W., Boore, J. L., Jansen, R. K., and dePamphilis, C. W.. "Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.," Molecular Biology and Evolution, v.22, 2005, p. 1948.
Leebens-Mack, J.H., Soltis, D.E., and Soltis, P.S.. "Plant reproductive genomics at the Plant and Animal Genome Conference," Comparative and Functional Genomics, v.6, 2005, p. 159.
Lindqvist, C., A.-C. Scheen, M.-J. Yoo, M. Bendiksby, P. Grey, D. G. Oppenheimer, J. H. Leebens-Mack, D. E. Soltis, P. S. Soltis, and V. A Albert. "An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers," BMC Plant Biology, v.6, 2006, p. 16.
Ma, H.. "Molecular genetic analysis of microsporogenesis and microgametogenesis.," Annu. Rev. Plant Biol., v.56, 2005, p. 393.
Moore, M. J., A. Dhingra, P. S. Soltis, R. Shaw, W. G. Farmerie, K. M. Folta, and D. E. Soltis. "Rapid and accurate pyrosequencing of angiosperm plastid genomes," BMC Plant Biology, v.6, 2006, p. 17.
Park, S.O., Zheng, Z., Oppenheimer, D.G., and Hauser, B.A.. "The PRETTY FEW SEEDS 2 gene encodes an Arabidopsis homeodomain protein that
regulates ovule development.," Development, v.132, 2005, p. 841.
Qiu, Y., O. Dombrovska, J. Lee, L. Li, B. A. Whitlock, F. Bernasconi-Quadroni, J. S. Rest, T. Borsch, K. W. Hilu, S. Renner, D. E. Soltis, P. S. Soltis, M. J. Zanis, J. Cannone, R. Gutell, M. Powell, V. Savolainen, L. W. Chatrou, and M. W. Chase. "Phylogenetic analysis of basal angiosperms based on nine plastid, mitochondrial, and nuclear genes," International Journal of Plant Sciences, v.166, 2005, p. 815.
Ronse de Craene, L., Soltis, D. E., and Soltis P.S.. "Evolution of floral structures in basal angiosperms," International Journal of Plant Sciences, v.164, 2003, p. S329.
Sampedro, J., Y. Lee, R. E. Carey, C. W. dePamphilis and D. J. Cosgrove. "Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family," The Plant Journal, v.44, 2005, p. 409.
Soltis, D. E. and P. S. Soltis. "The role of phylogenetics in comparative genetics," Plant Physiology, v.132, 2004, p. 1790.
Soltis, D. E. and Soltis, P. S.. "Amborella not a basal angiosperm? Not so fast," American Journal of Botany, v.91, 2004, p. 997.
Soltis, D.E., Fishbein, M., and Kuzoff R. K.. "Reevaluating the evolution of epigyny: data from phylogenetics and floral
ontogeny," International Journal of Plant Sciences, v.164, 2003, p. S251.
Soltis, D.E., P.S. Soltis, V.A. Albert, D.G. Oppenheimer, C.W. dePamphilis, M.W. Frolich, G. Theissen.. "Missing links: the genetic architecture of flowers and floral diversification," Trends in Plant Science, v.7, 2002, p. 22.
Soltis, P. S. and D. E. Soltis. "Applying the bootstrap in phylogeny reconstruction," Statistical Science, v.18, 2003, p. 1.
Soltis, P. S. and Soltis, D. E.. "Origin and diversification of angiosperms," American Journal of Botany, v.91, 2004, p. 1614.
Tuskan, G. A. and 103 others. "The genome of black cottonwood, Populus trichcarpa (Torr. & Gray ex Brayshaw)," Science, v.313, 2006, p. 1596.
Wang, G., Kong, H., Sun, Y., Zhang, X., Zhang, W., Altman, N., dePamphilis, C. W., and Ma, H.. "Genome-wide analysis of cyclin family in Arabidopsis and comparative
phylogenetic analysis of plant cyclin-like proteins," Plant Physiology, v.135, 2004, p. 1084.
Wang, J-P.Z. Lindsay, B.G., Leebens-Mack, J, Cui, L., Wall, K, Miller, W.C. and dePamphilis, C.W.. "EST Clustering Error Evaluation and Correction," Bioinfomatics, v.20, 2004, p. 2973.
Wang, J., B. G. Lindsay, L. Cui, P. K. Wall, J. Marion, J. Zhang, and dePamphilis, C. W.. "Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries," BMC Bioinfomatics, v.6, 2005, p. 300.
Yoo M.J., Albert V.A., Soltis P.S., and Soltis D.E.. "Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants," BMC Plant Biology, v.6, 2006, p. 3.
Yoo, M., Bell, C. D., Soltis, P. S., and Soltis, D. E.. "Divergence times and historical biogeography in Nymphaeales.," Systematic Botany, v.30, 2005, p. 693.
Zahn, L. M., Kong, H., Leebens-Mack, J., Kim, S., Soltis, P.S., Landherr, L.L., Soltis, D.E., dePamphilis, C. W., and Ma, H.. "The evolution of the SEPALLATA subfamily of MADS-box genes: A pre-angiosperm origin
with multiple duplications throughout angiosperm history," Genetics, v.169, 2005, p. 2209.
Zahn, L. M., Leebens-Mack, J., dePamphilis, C. W., Ma, H., and Theissen, G.. "To B or not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of
the angiosperms.," J. Hered., v.93, 2005, p. 225.
Zahn, L.M., Leebens-Mack, J., Arrington, J.M., Hu, Y., Landherr, L., dePamphilis, C., Becker, A., Theissen, G., and Ma, H.. "Conservation and divergence in the AGAMOUS Subfamily of MADS-Box Genes: Evidence of Independent Sub- and Neofunctionalization Events.," Evolution and Development, v.8, 2006, p. 30.
Zhang, X., Feng, B., Zhang, Q., Zhang, D., Altman, N., and Ma, H.. "Genome-wide expression profiling and identification of gene activities during early flower development in Arabidopsis," Plant Mol. Biol., v.58, 2005, p. 401.
|
(Showing: 1 - 10 of 49) (Showing: 1 - 49 of 49) |
Show All |
Please report errors in award information by writing to: awardsearch@nsf.gov.
|
|
|
