Abstract
Oryza rufipogon, Asian wild rice, is believed to be the progenitor of the cultivated rice O. sativa, whose cultivars can be classified into several diverse groups including japonica and indica. In this study, to decipher the evolutionary processes of wild and cultivated rice, we used ~2000 full-length cDNAs of O. rufipogon W1943 as well as genomic sequences of japonica and indica cultivars. Our genome-wide analysis resulted in one major and two minor gene tree topologies, showing expected gene tree discordance. The major gene tree topology implied that O. rufipogon W1943 is closely related to japonica, which is consistent with previous studies. These gene tree topologies also suggested incomplete lineage sorting and hybridization between japonica and indica cultivars after their divergence. In addition, we identified genes that were possibly lost in the japonica cultivar. We found that fifteen O. rufipogon-specific genes were related to submergence and/or wounding conditions. We highlighted the importance of gene tree discordance analysis on unraveling complicated evolutionary histories of closely related species and suggested possible gene loss events during rice domestication.
