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Legume Information System

LIS contains agronomically useful information in legume species, including genome sequences, genetic maps, genes, gene families, and mapped traits. The "legumeinfo" site makes use of several open-source projects (Intermine, Tripal, Chado, GBrowse, JBrowse, and many others), facilitating more efficient collaboration with other research groups using and developing these tools.

Publications

  • K. Chiteri, A. Rairdin, K. Sandhu, S. Redsun, A. Farmer, J. O'Rourke, S. Cannon and A. Singh.
    Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean
    BMC Genomics, 25(1), 270, 2024, PMID 38475739, PMCID PMC10935824
    Legume Information System 
  • J. Botkin, A. Farmer, N. Young and S. Curtin.
    Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance
    BMC Genomics, 25(1), 204, 2024, PMID 38395768
    Legume Information System 
  • A. Cleary and A. Farmer.
    Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes
    Nucleic Acids Res, 51(W1), W225-W231, 2023, PMID 37207325, PMCID PMC10320139
    Legume Information System 
  • A. Fayyaz, G. Robinson, P. Chang, D. Bekele, S. Yimer, N. Carrasquilla-Garcia, K. Negash, A. Surendrarao, E. Wettberg, S. Kemal, K. Tesfaye, A. Fikre, A. Farmer and D. Cook.
    Hiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in Fusarium oxysporum f.sp. ciceris
    Proc Natl Acad Sci U S A, 120(27), e2220570120, 2023, PMID 37364097, PMCID PMC10318998
    Legume Information System 
  • Q. Liang, M. n, S. Shu, S. Lo, X. Wu, J. Carlson, P. Davidson, D. Goodstein, J. Phillips, N. Janis, E. Lee, C. Liang, P. Morrell, A. Farmer, P. Xu, T. Close and S. Lonardi.
    A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.)
    Plant Genome, e20319, 2023, PMID 36946261
    Legume Information System  Legume Federation 
  • S. Cervantes-Pérez, S. Thibivilliers, C. Laffont, A. Farmer, F. Frugier and M. Libault.
    Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume
    Mol Plant, 15(12), 1868--1888, 2022, PMID 36321199
    Legume Information System 
  • S. Redsun, S. Hokin, C. Cameron, A. Cleary, J. Berendzen, S. Dash, A. Brown, A. Wilkey, J. Campbell, W. Huang, S. Kalberer, N. Weeks, S. Cannon and A. Farmer.
    Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources
    Methods Mol Biol, 2443, 81--100, 2022, PMID 35037201
    Legume Information System 
  • D. Bertioli, J. Clevenger, I. Godoy, H. Stalker, S. Wood, J. Santos, C. Ballén-Taborda, B. Abernathy, V. Azevedo, J. Campbell, C. Chavarro, Y. Chu, A. Farmer, D. Fonceka, D. Gao, J. Grimwood, N. Halpin, W. Korani, M. Michelotto, P. Ozias-Akins, J. Vaughn, R. Youngblood, M. Moretzsohn, G. Wright, S. Jackson, S. Cannon, B. Scheffler and S. Leal-Bertioli.
    Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange
    Proc Natl Acad Sci U S A, 118(38), 2021, PMID 34518223
    Legume Information System  Legume Federation  PeanutBase 
  • J. Quilbé, L. Lamy, L. Brottier, P. Leleux, J. Fardoux, R. Rivallan, T. Benichou, R. Guyonnet, M. Becana, I. Villar, O. Garsmeur, B. Hufnagel, A. Delteil, D. Gully, C. Chaintreuil, M. Pervent, F. Cartieaux, M. Bourge, N. Valentin, G. Martin, L. Fontaine, G. Droc, A. Dereeper, A. Farmer, C. Libourel, N. Nouwen, F. Gressent, P. Mournet, A. D'Hont, E. Giraud, C. Klopp and J. Arrighi.
    Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium-legume symbiosis
    Nat Commun, 12(1), 829, 2021, PMID 33547303
    Legume Information System  Legume Federation 
  • G. 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, n/a(n/a), e16, 2019, DOI 10.1002/leg3.16
    Legume Information System  Legume Federation  PeanutBase  Medicago HapMap Project 
  • S. 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., 2019
    Legume Information System  Legume Federation 
  • D. 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, 51(5), 877--884, 2019, DOI 10.1038/s41588-019-0405-z
    Legume Information System  Legume Federation  PeanutBase 
  • S. 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, 98(5), 767--782, 2019, DOI 10.1111/tpj.14349
    Legume Information System  Legume Federation 
  • A. Cleary and A. Farmer.
    Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny
    Bioinformatics, 34(9), 1562--1564, 2017, DOI 10.1093/bioinformatics/btx757
    Legume Information System  Legume Federation 
  • J. Singh, S. Kalberer, V. Belamkar, T. Assefa, M. Nelson, A. Farmer, W. Blackmon and S. Cannon.
    A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes
    Theoretical and Applied Genetics, 131(2), 333--351, 2017, DOI 10.1007/s00122-017-3004-3
    Legume Information System 
  • M. 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., 89(5), 1042--1054, 2017
    Legume Information System  Legume Federation 
  • R. 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, 211(4), 1440--1451, 2016, DOI 10.1111/nph.14010
    Legume Information System  Legume Federation 
  • D. 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, 48(4), 438--446, 2016, DOI 10.1038/ng.3517
    Legume Information System  Legume Federation  PeanutBase 
  • M. Gonzales, E. Archuleta, A. Farmer, K. Gajendran, D. Grant, R. Shoemaker, W. Beavis and M. Waugh.
    The Legume Information System (LIS): an integrated information resource for comparative legume biology
    Nucleic Acids Res., 33(Database issue), D660--665, 2005
    Legume Information System 

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