Medicago truncatula Genome Database

Medicago truncatula, a close relative of alfalfa, is a preeminent model for the study of the processes of nitrogen fixation, symbiosis, and legume genomics. The genome was initially sequenced in a collaboration between the University of Oklahoma, TIGR (now JCVI), the Sanger Institute in the UK and Genoscope in France with funding from Samuel Roberts Noble Foundation, the National Science Foundation and the European Union's Sixth Framework Programme INRA (France) , and the BBSRC (UK).in the United Kingdom with funding from the EU and BBSRC.

Sequencing Strategies

The initial published sequence Mt3.5 assembly was based upon a BAC-by-BAC approach. Later, we generated 454 mate pair sequence and extensive Illumina paired end (PE) and mate pair (MP) sequence that was used together with the previously generated BAC- and fosmid-end sequences to produce an AllPaths assembly. The ALLPATHS scaffolds were anchored onto the 8 linkage groups on the basis of alignments to both the optical map (OM) and genetic map derived from genotyping-by-sequencing (GBS) data. High quality contiguous BAC sequences were patched into the new Mt4.0 pseudomolecules to close gaps and reduce polymorphisms between the assembly versions, where possible.

Annotation Overview

The new version of the genome (Mt4.0) was re-annotated using JCVI in-house structural and functional annotation pipelines, integrating a number of tiers of evidence: ab initio gene predictors, legacy Mt3.5v5 annotation, EST/RNA-seq assemblies and proteomic data, culminating in an annotation release, Mt4.0v2. A total of 50,376 gene loci (encompassing 57,585 gene models) were annotated by this pipeline, which were then binned into high (HC) and low (LC) confidence classes (~32k HC and ~19k LC loci), based on different levels of EST/RNA-seq/protein support and synteny to related plant genomes.

The Medicago Genome DataBase and Legume Data Federation

JCVI hosts the M. truncatula genome sequence and annotation in three forms: a Tripal database, JBrowse and an instance of InterMine named MedicMine. These databases also form part of a larger consortium of legume databases known as the Legume Federation ( The Legume Federation is a joint project with USDA-ARS-Iowa State and the National Center for Genome Resources. Together, these three centers house genomic, genetic and phenotypic (QTL) data for around 10 legume crop species including soybean, common bean, peanut, chickpea, clover, lupin and others. The goal of the project is to provide cross-species links between these plants at the genomic, genetic and phenotypic levels to further legume research and breeding.


BMC genomics. 2014-04-27; 15.312.
An improved genome release (version Mt4.0) for the model legume Medicago truncatula
Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H, Mayer KF, Schwartz DC, Town CD
PMID: 24767513
Nature. 2011-11-16; 480.7378: 520-4.
The Medicago genome provides insight into the evolution of rhizobial symbioses
Young ND, Debellé F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Bergès H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, González AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jöcker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Dénarié J, Dixon RA, May GD, Schwartz DC, Rogers J, Quétier F, Town CD, Roe BA
PMID: 22089132
Plant biotechnology journal. 2011-10-01; 9.8: 922-31.
Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa
Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, Kavikishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK
PMID: 21615673
Plant molecular biology. 2008-08-01; 67.6: 567-80.
Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling
Verdier J, Kakar K, Gallardo K, Le Signor C, Aubert G, Schlereth A, Town CD, Udvardi MK, Thompson RD
PMID: 18528765
Plant methods. 2008-07-08; 4.18.
A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula
Kakar K, Wandrey M, Czechowski T, Gaertner T, Scheible WR, Stitt M, Torres-Jerez I, Xiao Y, Redman JC, Wu HC, Cheung F, Town CD, Udvardi MK
PMID: 18611268
Plant physiology. 2007-06-01; 144.2: 538-49.
Legume transcription factors: global regulators of plant development and response to the environment
Udvardi MK, Kakar K, Wandrey M, Montanari O, Murray J, Andriankaja A, Zhang JY, Benedito V, Hofer JM, Chueng F, Town CD
PMID: 17556517
The Plant journal : for cell and molecular biology. 2007-05-01; 50.3: 529-44.
Arbuscular mycorrhizal symbiosis is accompanied by local and systemic alterations in gene expression and an increase in disease resistance in the shoots
Liu J, Maldonado-Mendoza I, Lopez-Meyer M, Cheung F, Town CD, Harrison MJ
PMID: 17419842
BMC genomics. 2006-10-24; 7.272.
Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology
Cheung F, Haas BJ, Goldberg SM, May GD, Xiao Y, Town CD
PMID: 17062153
Proceedings of the National Academy of Sciences of the United States of America. 2006-10-03; 103.40: 14959-64.
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, Scheix T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KF, Rogers J, Quétier F, Oldroyd GE, Debellé F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND
PMID: 17003129
Current opinion in plant biology. 2006-04-01; 9.2: 122-7.
Annotating the genome of Medicago truncatula
Town CD
PMID: 16458040
BMC plant biology. 2005-08-15; 5.15.
Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana
Mudge J, Cannon SB, Kalo P, Oldroyd GE, Roe BA, Town CD, Young ND
PMID: 16102170
Plant physiology. 2005-05-01; 138.1: 38-46.
Databases and information integration for the Medicago truncatula genome and transcriptome
Cannon SB, Crow JA, Heuer ML, Wang X, Cannon EK, Dwan C, Lamblin AF, Vasdewani J, Mudge J, Cook A, Gish J, Cheung F, Kenton S, Kunau TM, Brown D, May GD, Kim D, Cook DR, Roe BA, Town CD, Young ND, Retzel EF
PMID: 15888676
Plant physiology. 2005-04-01; 137.4: 1174-81.
Sequencing the genespaces of Medicago truncatula and Lotus japonicus
Young ND, Cannon SB, Sato S, Kim D, Cook DR, Town CD, Roe BA, Tabata S
PMID: 15824279
The Plant cell. 2003-09-01; 15.9: 2106-23.
Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis
Liu J, Blaylock LA, Endre G, Cho J, Town CD, VandenBosch KA, Harrison MJ
PMID: 12953114
Plant physiology. 2002-10-01; 130.2: 519-37.
Genome-wide identification of nodule-specific transcripts in the model legume Medicago truncatula
Fedorova M, van de Mortel J, Matsumoto PA, Cho J, Town CD, VandenBosch KA, Gantt JS, Vance CP
PMID: 12376622


Funding provided through the National Science Foundation (NSF).


Nevin Young
University of Minnesota

Bruce Roe
Oklahoma University

Steven Cannon

Andrew Farmer
National Center for Genome Resources

Eric Lyons
University of Arizona

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