Medicago truncatula (MtrunA17r5.0_ANR)

Medicago truncatula Assembly and Gene Annotation

About Medicago truncatula

Medicago truncatula (Barrel Medic) is a small annual legume native to the Mediterranean region. As other legumes, it forms symbioses with nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi. This species has been chosen as a model organism for legume biology because it has a small diploid genome, is self-fertile, has a rapid generation time and prolific seed production, and is amenable to genetic transformation. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox. The complete reference sequence displayed here is the 4.0 assembly update published in 2014. The nuclear genome has eight chromosomes.


Medicago truncatula cultivar A17 was sequenced and assembled by the Medicago truncatula Sequencing Consortium in 2011 (Mt3.5, then updated in 2014 (Mt4.0). The Mt4.0 comprises approximately 360 Mb of sequences in psudeomolecules spanning 390 Mb of which ~330 Mb aligns accurately with the Optical Map, with only ~20 Mb of unplaced sequence.


JCVI published the current gene set in 2014. Altogether, Pseudomolecules and unassigned BACs contain a total of 50,444 protein-coding gene loci (~31,500 high confidence genes and ~19,000 low confidence genes). The pseudomolecules were annotated by combining Mt3.5 gene models, with predictions from Augustus and FGENESH as well as expression data and protein matches primarily using Evidence Modeler (EVM). Whenever possible, gene identifiers have been preserved between Mt3.5 and Mt4.0.

Additional analysis was carried out in house: non coding RNA genes have been annotated using tRNAScan-SE, Rfam, and RNAmmer.

Repeated sequences were called with the Repeat Detector, which is part of the Ensembl Genomes repeat feature pipelines. Repeats length: 134713950 - Repeats content: 32.6%


269,501 EST sequences have been aligned to the genome with STAR.


  1. The Medicago genome provides insight into the evolution of rhizobial symbioses.
    Young N,Debell F,Oldroyd GED,Geurts R, Cannon ED,Udvardi MK,Benedito VA,Mayer KFX,Gouzy J,Schoof H et al. 2011. Nature. 480:520-524.
  2. 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 et al. 2014. BMC Genomics. 15:312.
  3. Image from WikiCommons.



AssemblyMtrunA17r5.0_ANR, INSDC Assembly GCA_003473485.2,
Database version112.3
Golden Path Length429,196,467
Genebuild byINRA/CNRS
Genebuild methodImport
Data sourceINRA/CNRS

Gene counts

Coding genes44,450
Non coding genes6,097
Small non coding genes2,219
Long non coding genes3,878
Gene transcripts50,739