Multicentric origin and diversification of --like structures reveal mitochondrial gene flows in and .

Cytoplasmic male sterility (CMS) is a widely used genetic tool in modern hybrid rice breeding. Most genes conferring rice gametophytic CMS are homologous to and co-transcribe with . However, the origin, differentiation and flow of these mitochondrial genes in wild and cultivated rice species remain unclear. In this study, we performed de novo assembly of the mitochondrial genomes of 221 common wild rice ( Griff.) and 369 Asian cultivated rice ( L.) accessions, and identified 16 haplotypes of -like structures and 11 alleles. These homologous structures were classified into 4 distinct groups (AO-I, AO-II, AO-III and AO-IV), all of which were observed in but only AO-I was detected in , causing a decrease in the frequency of -like structures from 19.9% to 8.1%. Phylogenetic and biogeographic analyses revealed that the different groups of these gametophytic CMS-related genes in evolved in a multicentric pattern. The geographical origin of the -like structures was further traced back, and a candidate region in north-east of Gangetic Plain on the Indian Peninsula (South Asia) was identified as the origin centre of AO-I. The alleles were detected in all three cytoplasmic types (Or-CT0, Or-CT1 and Or-CT2) of , but only two alleles ( and ) were observed in Or-CT0 type of , while no allele was found in other types of . Our results also revealed that the alleles in cultivated rice originated from the wild rice population in South and South-East Asia. In addition, strong positive selection pressure was detected on the sequence variations of alleles, and a special evolutionary strategy was noted in these gametophytic CMS-related genes, suggesting that their divergence could be beneficial to their survival in evolution.