Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes

Steven B. Cannon, Lieven Sterck, Stephane Rombauts, Shusei Sato, Foo Cheung, Jérôme Gouzy, Xiaohong Wang, Joann Mudge, Jayprakash Vasdewani, Thomas Scheix, Manuel Spannagl, Erin Monaghan, Christine Nicholson, Sean J. Humphray, Heiko Schoof, Klaus F.X. Mayer, Jane Rogers, Francis Quétier, Giles E. Oldroyd, Frédéric DebelléDouglas R. Cook, Ernest F. Retzel, Bruce A. Roe, Christopher D. Town, Satoshi Tabata, Yves Van De Peer, Nevin D. Young

Research output: Contribution to journalArticlepeer-review

251 Scopus citations


Genome sequencing of the model legumes, Medicago truncatula and Lotus japonicus, provides an opportunity for large-scale sequence-based comparison of two genomes in the same plant family. Here we report synteny comparisons between these species, including details about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome regions lacking clear correspondence. The Lotus and Medicago genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and frequently extending the length of whole chromosome arms. The proportion of genes syntenic and collinear within each synteny block is relatively homogeneous. Medicago-Lotus comparisons also indicate similar and largely homogeneous gene densities, although gene-containing regions in Mt occupy 20-30% more space than Lj counterparts, primarily because of larger numbers of Mt retrotransposons. Because the interpretation of genome comparisons is complicated by large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analyses to identify and date a probable whole-genome duplication event. There is no direct evidence for any recent large-scale genome duplication in either Medicago or Lotus but instead a duplication predating speciation. Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar).

Original languageEnglish
Pages (from-to)14959-14964
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number40
StatePublished - 3 Oct 2006
Externally publishedYes


  • Genome duplication
  • Polyploidy
  • Synteny


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