Evolutionary patterns of the chimerical retrogenes in Oryza

Chimerical retroposition delineate a process by which RNA reverse transcribed integration into genome accompanied with recruiting flanking sequence, which is asserted to play essential roles and drive genome evolution. Although chimerical retrogenes hold high origination rate in plant genome, the evolutionary pattern of retrogenes and their parental genes are not well understood in rice genome. In this study, using maximum likelihood method, we evaluated the substitution ratio along lineages of 24 retrogenes and parental gene pairs to retrospect the evolutionary patterns. The results indicate that some specific lineages in 7 pairs underwent positive selection. Besides the rapid evolution in the initial stage of new chimerical retrogene evolution, an unexpected pattern was revealed: soon or some uncertain period after the origination of new chimerical retrogenes, their parental genes evolved rapidly under positive selection, rather than the rapid evolution of the new chimerical retrogenes themselves. This result lend support to the hypothesis that the new copy assistant the function evolution among parental gene and retrogene. Transcriptionally, we also found that one retrogene (RCG3) have a high expression at the period of calli infection which supported by chip data while its parental gene doesnt have. Finally, by calibration to Ka/Ks analysis results in other species including Apis mellifera, we concluded that chimerical retrogenes are higher proportionally positive selected than the regular genes in the rice genome.