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

doi:10.1073/pnas.0603228103

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

^aDepartment of Plant Pathology, University of Minnesota, St. Paul, MN 55108;
^bU.S. Department of Agriculture–Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, IA 50010;
^cDepartment of Plant Systems Biology (VIB), Ghent University, B-9052 Ghent, Belgium;
^dKazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan;
^eInstitute for Genomic Research, Rockville, MD 20850;
^fLaboratoire des Interactions Plantes–Microorganismes, Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, 31326 Castanet-Tolosan, France;
^gUnité de Biométrie et Intelligence Artificielle, B.P. 52627, Institut National de la Recherche Agronomique, 31326 Castanet-Tolosan, France;
^hMunich Information Center for Protein Sequences Institute for Bioinformatics, Gesellschaft für Strahlung und Umweltforschung, Research Center for Environment and Health, 85764 Neuherberg, Germany;
ⁱWellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
^jMax Planck Institute for Plant Breeding Research, 50829 Köln, Germany;
^kCentre Nationale de Séquençage, 91057 Evry, France;
^lJohn Innes Centre, Norwich NR4 7UH, United Kingdom;
^mDepartment of Plant Pathology, University of California, One Shields Avenue, Davis, CA 95616;
ⁿCenter for Computational Genomics and Bioinformatics, Minneapolis, MN 55455; and
^oDepartment of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019

Edited by Steven D. Tanksley, Cornell University, Ithaca, NY, and approved August 4, 2006 (received for review April 20, 2006)

Abstract

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).

Footnotes

^pTo whom correspondence should be addressed. E-mail: neviny{at}umn.edu
Author contributions: S.B.C., L.S., and S.R. contributed equally to this work; N.D.Y. designed research; S.S., J.G., T.S., M.S., C.N., S.J.H., H.S., K.F.X.M., J.R., F.Q., G.E.O., F.D., D.R.C., B.A.R., C.D.T., and S.T. contributed new reagents/analytic tools; S.B.C., L.S., S.R., F.C., X.W., J.M., J.V., E.M., and Y.V.d.P. analyzed data; and S.B.C., Y.V.d.P., and N.D.Y. wrote the paper.
The authors declare no conflict of interest.
This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (GenBank accession nos. available at www.medicago.org/genome and www.kazusa.or.jp/lotus).
Abbreviations:

Mt,

Medicago truncatula;

Lj,

Lotus japonicus;

WGD,

whole-genome duplication;

TC,

tentative consensus;

TAC,

transformation-competent artificial chromosome;

Ks,

substitutions per synonymous site.
Freely available online through the PNAS open access option.