Comparison of and Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions.

Centromeres are dynamic chromosomal regions, and the genetic and epigenetic environment of the centromere is often regarded as oppressive to protein-coding genes. Here, we used comparative genomic and phylogenomic approaches to study the evolution of centromeres and centromere-linked genes in the genus We report a 12.4-Mb high-quality BAC-based pericentromeric assembly for , which diverged from cultivated rice () ∼15 million years ago. The synteny analyses reveal seven medium (>50 kb) pericentric inversions in and 10 in Of these inversions, three resulted in centromere movement (, , and ). Additionally, we identified a potential centromere-repositioning event, in which the ancestral centromere on chromosome 12 in jumped ∼400 kb away, possibly mediated by a duplicated transposition event (>28 kb). More strikingly, we observed an excess of syntenic gene loss at and near the centromeric regions (P < 2.2 × 10). Most (33/47) of the missing genes moved to other genomic regions; therefore such excess could be explained by the selective loss of the copy in or near centromeric regions after gene duplication. The pattern of gene loss immediately adjacent to centromeric regions suggests centromere chromatin dynamics (e.g., spreading or microrepositioning) may drive such gene loss.