Common and distinguishing characteristics of genes and genomes and their evolution in the genome sequenced legumes

Abstract

By March 2013, genome sequences have been published for five legume species- Cicer arietinum (pulse crop chickpea), Cajanus cajan (pulse crop pigeonpea), Glycine max (pulse-cum-oil seed crop soybean), Lotus japonicus and Medicago truncatula (both model plants). The genome sequenced legumes belong to the subfamily papilionoideae of the angiosperm family leguminoseae, C. arietinum, L. japonicus and M. truncatula to the galegoid clade and C. cajan and G. max to millettioid clade. These diploid species have 2n number varying from 12 in L. japonicus, 16 in M. truncatula and C. arietinum, 22 in C. cajan and 40 in G. max. Comparisons among their genome sequences have revealed several important properties about structure and evolution of their genomes. Thirty five to 60% of genome is in the form of repititive elements, mainly transposons. Genome carries less than 50,000 protein-coding genes, 56 to 87% in two or more copies. All the five species arose from a common pre-papilionoid parent produced by inter-species hybridization accompanied by whole genome duplication (WGD or allotetraploidy) about 58 million years ago (Mya). Separation of clades and speciation occurred via sequence changes, over a period of > 40 million years. Individual genes underwent substitution and frameshift mutations. Chromosomal level rearrangements involved deletions, inversions, translocations, fission and fusions. There was spread of individual genes or blocks of genes followed by their tandem duplication. Deletion of orthologues was also involved in lineage specific changes. Ancestors of Glycine underwent an allotetraploid event after separation of C. cajan in the millettioid clade about 13 Mya. Developments relating to the applications of legume genome sequence knowledge are also discussed.