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 MtrunA17r5.0-ANR assembly update published in 2018. The nuclear genome has eight chromosomes.

Assembly

This assembly, MtrunA17r5.0-ANR, of Medicago truncatula was sequenced using the high-depth (more than 100×) long-read (PacBio) sequencing technique as well as using the optical maps. A highly contiguous reference genome of 430 Mb (termed Mt5.0) was generated in only 64 sequence contigs (including 3.59 Mb in 32 unanchored contigs). This assembly spans chromosome arms from telomeres to centromeres, with half of the eight M.truncatula pseudo-chromosomes containing a single sequence gap at the centromere position. This genome assembly was produced by the INRA/CNRS.

Annotation

Gene models were predicted by the plant genome annotation pipeline egn-ep release 1.4. Four protein databases were aligned with blastx to detect the translated regions: TAIR10, Swiss-Prot (October 2016), a plant subset of Uniprot proteins (October 2016) and the proteome of Brachypodium distachyon release 192. Non-coding RNA genes were detected based on the transcriptomic data performed by EuGene and also predicted by tRNAScan-SE, RNAMMER and infernal 1.1.2. Finally, 44,623 protein-coding genes, 974 tRNAs, 62 rRNAs and 5,657 lncRNAs were annotated in the release 1.6 with 24,645 full-length transposable elements. A putative function was assigned to 31,362 proteins and 13,261 proteins were tagged as ‘hypothetical proteins’.

References

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. Whole-genome landscape of Medicago truncatula symbiotic genes.
   Pecrix, Y., Staton, S.E., Sallet, E. et al. Nature Plants 4, 1017–1025 (2018). https://doi.org/10.1038/s41477-018-0286-7

Picture credit: By Ninjatacoshell, CC BY-SA 3.0, via Wikimedia Commons(Image source)