Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae

Abstract

The tribe Phaseoleae includes several legume crops with assembled genomes. Comparative genomic studies have evidenced the preservation of large genomic blocks among legumes, although chromosome dynamics during Phaseoleae evolution has not been investigated. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We identified GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata and searched for GBs in different genomes of the Phaseolinae ( P. lunatus ) and Glycininae ( Amphicarpaea edgeworthii ) subtribes and Spatholobus suberectus (sister to Phaseolinae and Glycininae), using Medicago truncatula as the outgroup. We also used oligo-FISH probes of two P. vulgaris chromosomes to paint the orthologous chromosomes of two non-sequenced Phaseolinae species. We inferred the APK as having n  = 11 and 19 GBs (A to S), hypothesizing five chromosome fusions that reduced the ancestral legume karyotype to n  = 11. We identified the rearrangements among the APK and the subtribes and species, with extensive centromere repositioning in Phaseolus . We also reconstructed the chromosome number reduction in S. suberectus . The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.