Distribution and diversity of PIF-like transposable elements in the Bambusoideae subfamily

PIF-like transposable elements were classified as members of the PIF/Harbinger superfamily that has been characterized in many eukaryotes. Complete and partial sequences of PIF-like transposable elements have been isolated from hundreds of plant species, but only two have been identified in bamboo species. We isolated 139 sequences from 44 bamboo species, and phylogenetic analysis showed that PIF-like transposable elements are widespread, diverse and abundant in the Bambusoideae subfamily. A molecular phylogeny of the Bambusoideae subfamily was also established using the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA, and was incongruent with the tree derived from PIF-like transposase genes. These results indicate that PIF-like transposable elements may have been involved in horizontal transfer events between phylogenetically distant bamboo species, or that an ancestral polymorphism has been followed by divergent evolution and stochastic loss of PIF-like transposable elements in different bamboo species. Neutralist tests show that PIF-like transposase gene coding sequences were negatively selected during evolution and introns of PIF-like transposase genes evolve neutrally with minus negative selection.