Overview

Medicago truncatula, a close relative of alfalfa, is a preeminent model for the study of the processes of nitrogen fixation, symbiosis, and legume genomics.

(1) BAC-based sequencing and genome assembly (Mt3.5)

The sequencing project was initiated with a generous grant from the Samuel Roberts Noble Foundation to the University of Oklahoma. In 2003 (and renewed in 2006), the National Science Foundation and the European Union's Sixth Framework Programme provided funding to complete sequencing of the euchromatic genespace. Sequencing was conducted in the US by the NSF-funded projects, in France by Genoscope with funding from the EU and INRA, and in the United Kingdom with funding from the EU and BBSRC. Reference: Young et al. 2011, BioProject: PRJNA10791.

(2) Illumina sequencing and genome assembly (Mt4.0)

An improved and refined version of the M. truncatula genome (Mt4.0) based on de novo whole genome shotgun assembly of a majority of Illumina and 454 reads. The scaffolds were anchored onto the pseudomolecules through alignments to the OpGen optical map and a genotyping-by-sequencing (GBS) map. The project was funded by the NSF (#0821966). Reference: Tang et al. 2014, BioProject: PRJNA10791.

(3) Long read sequencing and genome assembly

There are currently three more complete assemblies based on PacBio and Oxford Nanopore sequencing.

(a) MtrunA17r5.0-ANR
A PacBio assembly (>100x) improved by previous OpGen and new BioNano technology optical maps, generated at the Université de Toulouse, INRA, France. This is the most complete and should be considered the community-accepted version. Reference: Pecrix et al. 2018, BioProject: PRJNA431767.
(b) JCVI-NCGR Mt5.0-PMv1.5a
A PacBio/Dovetail assembly improved by OpGen optical map and GBS map alignments, generated by a collaboration between JCVI and NCGR. Unpublished, BioProject: PRJNA565224.
(c) JCVI Mt5.0-ONT
An Oxford Nanopore assembly at 28x depth, generated by JCVI. Unpublished, BioProject: PRJNA565224.

Mt4.0 Chromosome Map
MedicMine

Run flexible queries, export results and analyse lists of data using MedicMine, which integrates many types of data for Medicago truncatula.

JBrowse
Interactively explore the Medicago truncatula genome and annotation in a graphical browser.
Please visit our Downloads page for various genome assembly and annotation files:
  • Assembly FASTA
  • Optical Map XML files
  • Protein and CDS FASTA files
  • Gene and TE GFF3 files
  • Promoter FASTA files
  • Mt3.5 to Mt4.0 conversion table