Legumes play a central role in food security and nearly every cropping system worldwide. Among cultivated plants, legumes such as beans, peas and lentils are unique in their ability to fix atmospheric nitrogen which is converted into a soluble organic form that can be taken up by plants through symbiosis with a soil bacterium. Approximately 33% of all nutritional nitrogen comes from legumes which are the most important source of protein in most developing countries. Genomic resources have been or are being developed for many legume crops, but the fragmented nature of these data resources limits the ability of researchers to leverage information generated in one species to infer function or identify candidate genes in another species. The overarching goal of this project is to address this deficiency by developing software and methods for a "Legume Federation" (LF) of diverse, independently funded and geographically separated genomic data portals (GDPs). The LF will facilitate utilization of genomic, genetic and phenotypic information across a wide range of legume species that will allow researchers and breeders to take full advantage of the data that are currently available at the GDPs. The project will provide research training opportunities for students from diverse backgrounds at different educational levels. In the context of outreach, the project will pro-actively engage the community of legume data providers through presentations and workshops at national and international meetings as well as through a central web portal that will provide information describing project goals, methods of implementation and progress reports to the community.
The pace of data collection across crop and model plants has increased dramatically. Most crop species have both a data management problem and great opportunities to access genetic "big data". The objectives of this project are to develop a federation model for legume databases, to facilitate data exchange across a wide range of legume species to enable cross-species translational genomics, and to adapt an existing set of open-source tools for biological information management that will provide a framework for project-oriented data management enabling both long-term integration and widespread use. The specific goals are to:
1). Adopt and port the data currently managed in each of the custom frameworks into a set of well-integrated, open source model organism database tools;
2). Define data formats, metadata standards, data exchange and Web service protocols to facilitate communications between species-centric databases at various levels;
3). Utilize orthology, synteny, and mappings of other significant features to integrate genetic, genomic, and phenotypic data across legume species, to enable identification of common molecular bases for important traits and enable traversal across database projects;
4). Improve the capacity of organism database projects to collect and manage complex phenotype data using ontologies, controlled vocabularies and well-defined protocols and schemas; and,
5). Facilitate productive data exchange by implementing a common, open, virtualized Data Repository for data exchange across sites and for stable, long-term archiving of data sets, standardized metadata, and robust methods for archiving, searching, and accessing data sets from federated GDPs.
A. Pasha, S. Subramaniam, A. Cleary, X. Chen, T. Berardini, A. Farmer, C. Town and N. Provart.
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics
The Plant Cell (PMID:32699173), 2020
Legume FederationG. Bauchet, K. Bett, C. Cameron, J. Campbell, E. Cannon, S. Cannon, J. Carlson, A. Chan, A. Cleary, T. Close, D. Cook, A. Cooksey, C. Coyne, S. Dash, R. Dickstein, A. Farmer, D. Fernández-Baca, S. Hokin, E. Jones, Y. Kang, M. Monteros, M. Muñoz-Amatriaín, K. Mysore, C. Pislariu, C. Richards, A. Shi, C. Town, M. Udvardi, E. Wettberg, N. Young and P. Zhao.
The future of legume genetic data resources: Challenges, opportunities, and priorities
Legume Science (e16 LEG3-2019-052.R1), n/a(n/a), e16, 2019
Legume Information System Legume Federation PeanutBase Medicago HapMap ProjectS. Lo, M. Munoz-Amatriain, S. Hokin, N. Cisse, P. Roberts, A. Farmer, S. Xu and T. Close.
A genome-wide association and meta-analysis reveal regions associated with seed size in cowpea [Vigna unguiculata (L.) Walp]
Theor. Appl. Genet. (PMID: 31367839), 2019
Legume Information System Legume FederationD. Bertioli, J. Jenkins, J. Clevenger, O. Dudchenko, D. Gao, G. Seijo, S. Leal-Bertioli, L. Ren, A. Farmer, M. Pandey, S. Samoluk, B. Abernathy, G. Agarwal, C. Ballén-Taborda, C. Cameron, J. Campbell, C. Chavarro, A. Chitikineni, Y. Chu, S. Dash, M. Baidouri, B. Guo, W. Huang, K. Kim, W. Korani, S. Lanciano, C. Lui, M. Mirouze, M. Moretzsohn, M. Pham, J. Shin, K. Shirasawa, S. Sinharoy, A. Sreedasyam, N. Weeks, X. Zhang, Z. Zheng, Z. Sun, L. Froenicke, E. Aiden, R. Michelmore, R. Varshney, C. Holbrook, E. Cannon, B. Scheffler, J. Grimwood, P. Ozias-Akins, S. Cannon, S. Jackson and J. Schmutz.
The genome sequence of segmental allotetraploid peanut Arachis hypogaea
Nature Genetics (PMID: 31043755), 51(5), 877--884, 2019
Legume Information System Legume Federation PeanutBaseS. Lonardi, M. Muñoz-Amatriaín, Q. Liang, S. Shu, S. Wanamaker, S. Lo, J. Tanskanen, A. Schulman, T. Zhu, M. Luo, H. Alhakami, R. Ounit, A. Hasan, J. Verdier, P. Roberts, J. Santos, A. Ndeve, J. Doležel, J. Vrána, S. Hokin, A. Farmer, S. Cannon and T. Close.
The genome of cowpea (Vigna unguiculata [L.] Walp.)
The Plant Journal (PMID: 31017340), 98(5), 767--782, 2019
Legume Information System Legume FederationA. Cleary and A. Farmer.
Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny
Bioinformatics (PMID: 29194466), 34(9), 1562--1564, 2017
Legume Information System Legume FederationP. Zhou, K. Silverstein, T. Ramaraj, J. Guhlin, R. Denny, J. Liu, A. Farmer, K. Steele, R. Stupar, J. Miller, P. Tiffin, J. Mudge and N. Young.
Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes
BMC Genomics (PMID: 28347275), 18(1), 2017
Legume Federation Medicago HapMap ProjectM. Munoz-Amatriain, H. Mirebrahim, P. Xu, S. Wanamaker, M. Luo, H. Alhakami, M. Alpert, I. Atokple, B. Batieno, O. Boukar, S. Bozdag, N. Cisse, I. Drabo, J. Ehlers, A. Farmer, C. Fatokun, Y. Gu, Y. Guo, B. Huynh, S. Jackson, F. Kusi, C. Lawley, M. Lucas, Y. Ma, M. Timko, J. Wu, F. You, N. Barkley, P. Roberts, S. Lonardi and T. Close.
Genome resources for climate-resilient cowpea, an essential crop for food security
Plant J. (PMID: 27775877), 89(5), 1042--1054, 2017
Legume Information System Legume FederationR. Penmetsa, N. Carrasquilla-Garcia, E. Bergmann, L. Vance, B. Castro, M. Kassa, B. Sarma, S. Datta, A. Farmer, J. Baek, C. Coyne, R. Varshney, E. Wettberg and D. Cook.
Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor
New Phytologist (PMID: 27193699), 211(4), 1440--1451, 2016
Legume Information System Legume FederationD. Bertioli, S. Cannon, L. Froenicke, G. Huang, A. Farmer, E. Cannon, X. Liu, D. Gao, J. Clevenger, S. Dash, L. Ren, M. Moretzsohn, K. Shirasawa, W. Huang, B. Vidigal, B. Abernathy, Y. Chu, C. Niederhuth, P. Umale, A. Araújo, A. Kozik, K. Kim, M. Burow, R. Varshney, X. Wang, X. Zhang, N. Barkley, P. Guimarães, S. Isobe, B. Guo, B. Liao, H. Stalker, R. Schmitz, B. Scheffler, S. Leal-Bertioli, X. Xun, S. Jackson, R. Michelmore and P. Ozias-Akins.
The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut
Nature Genetics (PMID: 26901068), 48(4), 438--446, 2016
Legume Information System Legume Federation PeanutBase
The National Center for Genome Resources is a not-for-profit research institute that innovates, collaborates, and educates in the field of genomic data science. As leaders in DNA sequence analysis, we partner with government, industry, and academia to drive biological discovery in all kingdoms of life. We deliver value through expertise in experimental design, software, computation, data integration and training a skilled workforce.More
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Effective November 4, 2019
The National Center for Genome Resources ("NCGR") website (the "Website") is owned and managed by The National Center for Genome Resources, a New Mexico nonprofit corporation ("Owner," or "we" or "us").
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IN NO EVENT MAY USER BRING ANY CLAIM OR CAUSE OF ACTION AGAINST OWNER MORE THAN ONE (1) YEAR AFTER SUCH CLAIM OR CAUSE OF ACTION ARISES.
REPRESENTATIONS BY USERS; INDEMNIFICATION
USER IS SOLELY RESPONSIBLE FOR THE CONTENTS OF HIS/HER SUBMISSIONS TO THE WEBSITE. USER REPRESENTS THAT HE/SHE HAS ALL RIGHTS NECESSARY TO POST THE INFORMATION, CONTENT OR MATERIALS SUBMITTED TO THE WEBSITE WITHOUT VIOLATING THE COPYRIGHTS OR ANY OTHER INTELLECTUAL PROPERTY RIGHTS OF THIRD PARTIES, AND THAT NO SUBMISSION BY THE USER WILL VIOLATE APPLICABLE LAWS OR THE RIGHTS OF THIRD PERSONS. USER HEREBY INDEMNIFIES AND AGREES TO HOLD HARMLESS OWNER AND ITS OFFICERS, DIRECTORS, SHAREHOLDERS, EMPLOYEES, AGENTS AND REPRESENTATIVES FROM ANY AND ALL CLAIMS ASSERTED AGAINST THEM AND ANY LIABILITY, LOSS, DAMAGE, COSTS OR EXPENSES (INCLUDING REASONABLE ATTORNEYS' FEES) INCURRED OR SUFFERED BY THEM IN CONNECTION WITH OR ARISING OUT OF USER'S ACTS OR OMISSIONS OR THE MATERIALS OR INFORMATION USER SUBMITS TO THE WEBSITE.
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RESTRICTION, SUSPENSION AND TERMINATION
PROCEDURES FOR REQUESTING THE REMOVAL OF INFRINGING MATERIAL
Owner respect the intellectual property of others. If a person or organization (a "Copyright Owner") believes that his, her or its work has been copied on the Website in a way that constitutes copyright infringement, provide Owner the written information specified below. Please note that this procedure is exclusively for the Copyright Owner to notify Owner that copyrighted material of the Copyright Owner has been infringed. If a Copyright Owner believes that its own copyrighted work has been copied in a way that constitutes copyright infringement and is accessible via the Website, the Copyright Owner may notify Owner's copyright agent in accordance with the following procedures and the Digital Millennium Copyright Act of 1998 (DMCA).
For a complaint to be valid under the DMCA, the Copyright Owner must provide the following information when providing notice of the claimed copyright infringement: (1) a physical or electronic signature of a person authorized to act on behalf of the Copyright Owner; (2) identification of the copyrighted work or other intellectual property that the Copyright Owner owns and claims to have been infringed; (3) identification of the material that the Copyright Owner claims is infringing as well as information reasonably sufficient to permit Owner to locate the material on the Website; (4) the address, telephone number, and e-mail address of the Copyright Owner or its designee; (5) a statement by the Copyright Owner that the Copyright Owner as the complaining party has a good faith belief that use of the material in the manner complained of is not authorized by the Copyright Owner, its agent, or the law; and (6) a statement, made under penalty of perjury, that the information in the notification is accurate, and that the complaining party is authorized to act on behalf of the Copyright Owner of an exclusive right that is allegedly infringed. The foregoing information must be submitted as a written notification to the following Designated Agent:
- Site: www.ncgr.org
- Designated agent for infringement claims: Callum Bell, President
- Address:National Center for Genome Resources2935 Rodeo Park Drive EastSanta Fe, New Mexico 87505
- Telephone of designated agent: 505-982-7840
- E-mail of designated agent: email@example.com
WE CAUTION YOU THAT UNDER FEDERAL LAW, IF YOU KNOWINGLY MISREPRESENT THAT ONLINE MATERIAL IS INFRINGING, YOU MAY BE SUBJECT TO CIVIL PENALTIES. THESE INCLUDE MONETARY DAMAGES, COURT COSTS, AND ATTORNEYS' FEES INCURRED BY US, BY ANY COPYRIGHT OWNER, OR BY ANY COPYRIGHT OWNER'S LICENSEE THAT IS INJURED AS A RESULT OF OUR RELYING UPON YOUR MISREPRESENTATION. YOU MAY ALSO BE SUBJECT TO CRIMINAL PROSECUTION FOR PERJURY.
This information should not be construed as legal advice. For further details on the information required for valid DMCA notifications, see 17 U.S.C. 512(c)(3).
NOTE: This information is provided exclusively for notifying the service providers referenced above that the Copyright Owner's own copyrighted material(s) might have been infringed. All other inquiries, including technical requests, reports of e-mail abuse and third party reports of piracy, will not receive a response through this process.
HOW TO CONTACT OWNER