Inter- and intra-specific distribution of Stowaway transposable elements in AA-genome species of wild rice

The presence or absence of miniature inverted-repeat transposable elements (MITEs) that belong to Stowaway family was analyzed at three loci, two of which are newly identified, in five wild rice species having the AA genome. The pattern of the presence or absence of MITEs was found to be highly associated with speciation in this plant group. In Oryza rufipogon, the pattern was also associated with differentiation into annual or perennial ecotypes. These results suggest either that gene flow has been highly restricted between different species, as well as between different ecotypes of O. rufipogon after they were differentiated, or that loci with or without MITEs have been selected in nature together with the linked genes that are responsible for adaptation to environments. In addition, a very low polymorphism with regard to the presence or absence of MITEs within each species or each ecotype suggests that the frequency of transposition of MITEs is very low, assuming that the loci that contain MITEs are free from selection pressure.