Diane Jofuku Okamuro IOS Division Of Integrative Organismal Sys
BIO Direct For Biological Sciences
June 1, 2012
May 31, 2017 (Estimated)
Awarded Amount to Date:
Doreen Ware firstname.lastname@example.org (Principal Investigator)
Pankaj Jaiswal (Co-Principal Investigator)
Cold Spring Harbor Laboratory
1 BUNGTOWN ROAD
COLD SPRING HARBOR, NY
PLANT GENOME RESEARCH RESOURCE
Program Reference Code(s):
1329, 9109, 9178, 9179, 9232, BIOT
Program Element Code(s):
PI: Doreen Ware (Cold Spring Harbor Laboratory)
Co-PI: Pankaj Jaiswal (Oregon State University)
Senior Personnel: Paul Kersey and Helen Parkinson (European Molecular Biology Laboratory-European Bioinformatics Institute), Lincoln Stein (Ontario Institute for Cancer Research) and Crispin Taylor (American Society of Plant Biologists)
Key Collaborators: Peter D'Eustachio (New York University School of Medicine), Joshua Stein (Cold Spring Harbor Laboratory) and Palitha Dharmawardhana (Oregon State University)
Research in plant biology is reaching a tipping point at which the facility to examine entire systems, increasing integration of information, and ever more sophisticated analyses of experimental data are poised to enable sweeping advances in knowledge and insight. Meanwhile, progress in understanding plant genomes and novel information technologies are transforming the pace, scale, and strategies used to conduct plant science research, allowing, for example, much richer appreciation for the connections among genes, environments, and plant form and function. These advances in plant science promise to revolutionize crop breeding and help to keep pace with future population growth, environmental pressures, and energy needs. In the past decade, the Gramene (www.gramene.org) database has served the research community as a portal to information about gene structure and function for multiple plant species. Tools offered through the Gramene portal allow researchers to develop novel hypotheses on the bases of the most recent information and analyses, using a standardized framework. Yet, there are many remaining opportunities to more fully leverage functional information available from diverse plant species. In this project, Gramene will substantially expand the number of plant genomes incorporated into the portal, add new capabilities for studying gene expression, pathways, and networks, and fundamentally improve the database architecture and user interfaces to facilitate sophisticated systems-level analyses. At least twenty reference genomes, annotated by the scientists who are studying them and including crop plant, model organism, and other species, will be incorporated into the expanded Gramene portal. Rice, maize, and Arabidopsis will be emphasized through the addition of publicly available data from expression, epigenomic, and genome-wide association studies (GWAS). A single internationally-coordinated resource for these data types will be maintained through collaboration with the Ensembl Plants project (plants.ensembl.org). To better capture information about the function of plant genes, Gramene will adopt two powerful tools: the Reactome (www.reactome.org) platform, which can be used to represent curated pathways and for performing pathways-based analyses; and the ATLAS (www.ebi.ac.uk/gxa/) platform, which can be used to display and analyze expression profiles. These interfaces, along with Ensembl, BioMart, and a GWAS viewer, will form an integrated analysis system that is built on structured metadata and implemented through a high-capacity data warehouse and an advanced search engine.
To engage and nurture early career scientists, the project will provide research training opportunities for postdoctoral associates and students at all levels. Training on the use of Gramene tools will be accomplished through presentations and workshops held at internationally attended conferences; broader audiences will be reached through a series of webinars. Another major objective is to achieve broad interoperability among community resources. Standards development will be accomplished via outreach to collaborative data partners and scientists identified through several NSF-supported Research Coordination Networks (RCNs). Establishing common protocols, vocabularies, and semantics will have the powerful effect of bringing scientists together in research and educational fields, both domestically and abroad. A further objective is to engage biologists who are best qualified in their field to contribute to genome annotations on the basis of experimental evidence. Gramene will hold annual jamborees to train scientists in the use of standard curation tools that produce consistent definitions of data types and metadata. Finally, the ubiquitous publication of peer-reviewed journals online enables new opportunities to better link genome databases with the scientific literature. Gramene will collaborate with the American Society of Plant Biologists (ASPB), publisher of two high-impact journals, to prototype ways to couple collection of structured experimental data to the manuscript acceptance and publication process. As a whole, this project will contribute to long-term progress in merging information sciences with natural sciences that will ultimately lead to positive impacts on technology and society.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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Tomato Genome Consortium. "The tomato genome sequence provides insights into fleshy fruit evolution," Nature, v.485, 2012, p. 635-41.
Spooner W, Youens-Clark K, Staines D, Ware D. "GrameneMart: the BioMart data portal for the Gramene project," Database (Oxford), v.2012, 2012, p. bar056.
International Arabidopsis Informatics Consortium. "Taking the Next Step: Building an Arabidopsis Information Portal," Plant Cell, v.24, 2012, p. 2248?2256.
Liu Z, Kumari S, Zhang L, Zheng Y, Ware D. "Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays," PLoS One, v.7, 2012, p. e39786.
Olson, Klein RR, Dugas DV, Lu Z, Regulski M, Klein PE, Ware D. "Expanding and Vetting Sorghum bicolor Gene Annotations through Transcriptome and Methylome Sequencing," Plant Genome, v.7, 2013, p. 1.
Zwickl DJ, Stein JC, Wing RA, Ware D, and Sanderson MJ. "Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3," Systems Biology, 2014.
Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, Jaiswal P. "WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks," Rice, 2013.
Eveland AL, Goldshmidt A, Pautler M, Morohashi K, Liseron-Monfils C, Lewis MW, Kumari S, Hiraga S, Yang F, Unger-Wallace E, Olson A, Hake S, Vollbrecht E, Grotewold E, Ware D and Jackson D. "Regulatory modules controlling maize inflorescence architecture," Genome Research, 2014.
Campbell M, Law M, Holt C, Stein J, Moghe G, Hufnagel D, Lei J, Achawanantakun R, Jiao D, Lawrence C, Ware D, Shiu SH, Childs K, Sun Y, Jiang N, Yandell M. "MAKER-P: a tool-kit for the rapid creation, management, and quality control of plant genome annotations," Plant Physiology, 2014.
Regulski M, Lu Z, Kendall J, Donoghue MT, Reinders J, Llaca V, Deschamps S, Smith A, Levy D, McCombie WR, Tingey S, Rafalski A, Hicks J, Ware D, Martienssen RA. "The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA," Genome Research, 2013.
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, Hughes DS, Humphrey J, Kerhornou A, Khobova J, Langridge N, McDowall MD, Maheswari U, Maslen G, Nuhn M, Ong CK, Paulini M, Pedro H, Toneva I, Tuli MA, Walts B, Williams G, Wilson D, You. "Ensembl Genomes 2013: scaling up access to genome-wide data," Nucleic Acids Research, 2014.
Luo MC, Gu YQ, You FM, Deal KR, Ma Y, Hu Y, Huo N, Wang Y, Wang J, Chen S, Jorgensen CM, Zhang Y, McGuire PE, Pasternak S, Stein JC, Ware D, Kramer M, McCombie WR, Kianian SF, Martis MM, Mayer KF, Sehgal SK, Li W, Gill BS, Bevan MW, Simková H, Dolezel J,. "A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor," Proc Natl Acad Sci, 2013.
Taylor-Teeples M, Lin L, de Lucas M, Turco G, Toal TW, Gaudinier A, Young NF, Trabucco GM, Veling MT, Lamothe R, Handakumbura PP, Xiong G, Wang C, Corwin J, Tsoukalas A, Zhang L, Ware D, Pauly M, Kliebenstein DJ, Dehesh K, Tagkopoulos I, Breton G, Pruneda. "An Arabidopsis gene regulatory network for secondary cell wall synthesis," Nature, v.571, 2015.
Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M. "Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes," Plant Physiology, v.167, 2015, p. 25.
Kumari S, Ware D. "Genome-wide Computational Prediction and Analysis of Core Promoter Elements Across Plant Monocots and Dicots," PLOS One, v.8, 2013, p. e79011.
Monaco MK, Sen T, Dharmawardhana PD, Ren L, Schaeffer M, Naithani S, Amarasinghe V, Thomason J, Harper L, Gardiner J, Cannon EKS, Lawrence CJ, Ware D, Jaiswal P. "Maize Metabolic Network Construction and Transcriptome Analysis," The Plant Genome, v.6, 2013, p. 4-12.
Andrew R. Deans , Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot, Sándor Csösz, Hong Cui, Wasila Dahdul, Sand. "Finding our way through phenotypes," PLOS Biology, v.13, 2015, p. e1002033.
Seaver SM, Gerdes S, Frelin O, Lerma-Ortiz C, Bradbury LM, Zallot R, Hasnain G, Niehaus TD, El Yacoubi B, Pasternak S, Olson R, Pusch G, Overbeek R, Stevens R, de Crécy-Lagard V, Ware D, Hanson AD, Henry CS. "High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource," Proceedings of the National Academy of Sciences, v.111, 2014, p. 9645.
Chen C, DeClerck G, Tian F, Spooner W, McCouch S, Buckler E. "PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants," PLoS One, v.7, 2012, p. e46596.
Anika Oellrich, Ramona L. Walls, Ethalinda K.S. Cannon, Steven B. Cannon, Laurel Cooper, Jack Gardiner, Georgios V. Gkoutos, Lisa Harper, Mingze He, Robert Hoehndorf, Pankaj Jaiswal, Scott Kalberer, John Lloyd, David Meinke, Naama Menda, Laura Moore, Rex. "An Ontology Approach to Comparative Phenomics in Plants," Plant Methods, v.11, 2015.
Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR and McCombie WR. "New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica," Genome Research, v.15, 2014, p. 506.
Dharmawardhana P, Ren L, Amarasinghe V, Monaco MK, Thomason J, Ravenscroft D, McCouch SR, Ware D and Jaiswal P. "Genome Scale metabolic network for rice and analysis of tryptophan and derivative biosynthesis regulation during biotic stress," Rice, v.6, 2013, p. 15.
Fox SE, Preece J, Kimbrel JA, Marchini GL, Sage A, Youens-Clark K, Cruzan MB, Jaiswal P. "Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)," Applications in Plant Sciences, v.1, 2013, p. 1200011.