Evolution of Centromeres in Common Bean and Cowpea

In higher eukaryotes, centromeres typically contain large arrays of satellite repeats that evolve rapidly and homogenize within a genome resulting in species-specific centromeric repeats. It is unclear why centromeric repeats evolving rapidly while function is conserved. In addition, our knowledge of the structure and evolution of centromeric satellites within a genome is limited. Here, we report the analysis of centromeric repeats of two legume species, Phaseolus vulgaris (common bean) and Vigna unguiculata (cowpea).

            In common bean, two satellite repeats are present at centromeres; CentPv1 on eight centromeres and CentPv2 on three centromeres. Using a genomics and cytogenetic approach, we found several chromosome-specific variants of CentPv1 and CentPv2 that originated after the divergence of common bean from other Phaseolus species. Centromeric satellite repeats and other repeats were used to develop a fluorescence in situ hybridization (FISH)-based karyotype map for common bean. This karyotype map allowed us to further analyze centromere evolution within common bean and other related Phaseolus species. Comparison of karyotype maps within closely related species indicated that chromosomal distribution of the centromeric satellite repeats are stable, while the copy number of the repeats was subject to change. In other more diverged Phaseolus species, ~2-4 million years, copy numbers of CentPv1 and CentPv2 were largely reduced and chromosomal distributions were changed. These data indicate centromeric satellite repeats evolve rapidly by changing their copy numbers and chromosomal distributions over a short evolutionary time frame in Phaseolus species.

            In cowpea, which diverged from common bean ~5 million years ago, we found that the centromeric repeats are not conserved between these two species. DAPI-stained pachytene chromosomes exhibit very large centromeric regions and seven out of 11 centromeres possess a 455-bp tandem repeat, identified using computational approaches. No other highly abundant repeats were found at centromeres. This analysis show centromeric regions have evolved rapidly in both sequences and structure after the divergence of common bean and cowpea and contributes to our understanding of centromere structure and evolution in higher eukaryotes.