Cytoplasmic male sterility(CMS)is widespread in flowering plants and is associated with extra mitochondrial open reading frames,but how CMS genes evolve remains unclear.The Wild Abortive type CMS(CMS-WA)system has been widely used for hybrid rice breeding.We have cloned the chimeric CMS gene,WA352,for CMS-WA.In this study we further traced the origin and evolution of WA352.We detected 9 intermediate recombinant structures and WA352-like variants in wild rice.WA352 and its variants have been generated in wild rice species by multiple steps of rearrangements among mitochondrial genomic sequences,coupled with substoichiometirc shifting.Analysis of the structural compositions and sequence variations enabled us to depict the evolutionary route among these intermediate recombinant structures and WA352-like variants.A mitochondrial genomic sequence that is conserved among several monocot and dicot plant species is involved in all of these recombinant structures,and plays a central biological function on affecting anther tapetum development by interacting with the nucleus-encoded mitochondrial protein COX11,which involves in ROS biogenesis and PCD signaling.We found that an intermediate structure,WA314,encodes a protein that interacts with COX11,and this gene can cause CMS when transferring into cultivated rice without Rf gene(s).Our results reveal for the first time the evolutionary mechanism of CMS gene origination,and the identified new CMS genes may be potentially useful for hybrid rice breeding.