The sequenced genomes of medicago truncatula

Nevin D. Young, Peng Zhou

Research output: Chapter in Book/Report/Conference proceedingChapter


Because Medicago truncatula is such an important model legume, its genome has been sequenced multiple times. The original M. truncatula reference was constructed in accession A17 by an international consortium that began work in 2002 and finished in 2011. This version, Mt3.5, was primarily bacterial artificial chromosome (BAC)‐based and physically anchored with optical mapping. An improved version, Mt4.0, released in 2014, involved very deep Illumina sequencing, use of the ALLPATHS‐LG assembly algorithm, and integration with Mt3.5. Version Mt4.0 is 390 Mbp in length with ∼51 000 total (∼32 000 high confidence) gene models. In 2016, a reference quality sequence for a second accession important in functional genomics, R108, was completed based entirely on PacBio sequencing and BioNano (capillary optical mapping) and Dovetail (chromatin proximity) technologies. The Medicago hapmap project survey sequenced 325 accessions to discover single nucleotide polymorphisms (SNPs) genome wide and went on to release 20 high quality draft genome sequences between 2014 and 2017. This large set of Medicago genome assemblies provides resources for exploring genome variation, large gene families, and the pan‐genome. Genome sequencing has also begun in alfalfa, Medicago sativa, beginning with the diploid accession, CADL (Cultivated Alfalfa at the Diploid Level). However, alfalfa's highly heterozygous nature has significantly complicated sequence assembly, something that will be even more challenging as researchers move to sequencing tetraploid alfalfa.

Original languageEnglish (US)
Title of host publicationThe Model Legume Medicago truncatula
PublisherTaylor and Francis
Number of pages7
ISBN (Electronic)9781119409144
ISBN (Print)9781119409151
StatePublished - Dec 13 2019

Bibliographical note

Publisher Copyright:
© 2020 John Wiley & Sons, Inc. Published 2020 by John Wiley & Sons, Inc.


  • A17
  • CADL
  • De novo sequencing
  • Medicago
  • Mt4.0
  • R108
  • Reference genome


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