Comparative Genomics in Legumes

Abstract

The legume family will soon include three sequenced genomes. The majority of the euchromatic portions of the model legumes Medicago truncatula and Lotus japonicus have been sequenced in clone-by-clone projects, and the sequencing of the soybean genome is underway in a whole-genome shotgun project. Genome-wide sequence-based comparisons between three genomes with common ancestry at less than ∼50 million years will enable us to infer many features of the ancestral genome, to trace evolutionary differences such as rates of particular gene- or transposon-family expansions or losses, to better understand processes of genome remodeling that follow polyploidy, and to transfer knowledge to other crop and forage legumes. Comparisons among these genomes show a lack of large-scale genome duplications within the Lotus or Medicago genomes following separation of those lineages approximately 40 mya, evidence of an older shared polyploidy event, and clear evidence of a more recent duplication in soybean following the separation from the Medicago and Lotus common ancestor at approximately 50 mya. In contrast to the extensive rearrangements observed in the Arabidopsis genome, the Lotus and Medicago genomes have retained substantial gene collinearity, at the scale of whole chromosomes or chromosome arms – good news for translational genomics across a broad spectrum of forage and crop legumes.