The Wide Distribution and Change of Target Specificity of R2 Non-LTR Retrotransposons in Animals

Transposons, or transposable elements, are the major components of genomes in most eukaryotes. Some groups of transposons have developed target specificity that limits the integration sites to a specific nonessential sequence or a genomic region to avoid gene disruption caused by insertion into an essential gene. R2 is one of the most intensively investigated groups of sequence-specific non-LTR retrotransposons and is inserted at a specific site inside of 28S ribosomal RNA (rRNA) genes. R2 is known to be distributed among at least six animal phyla even though its occurrence is reported to be patchy. Here, in order to obtain a more detailed picture of the distribution of R2, we surveyed R2 using both in silico screening and degenerate PCR, particularly focusing on actinopterygian fish. We found two families of the R2C lineage from vertebrates, although it has previously only been found in platyhelminthes. We also revealed the apparent movement of insertion sites of a lineage of actinopterygian R2, which was likely concurrent with the acquisition of a 28S rRNA-derived sequence in their 3′ UTR. Outside of actinopterygian fish, we revealed the maintenance of a single R2 lineage in birds; the co-existence of four lineages of R2 in the leafcutter bee Megachile rotundata; the first examples of R2 in Ctenophora, Mollusca, and Hemichordata; and two families of R2 showing no target specificity. These findings indicate that R2 is relatively stable and universal, while differences in the distribution and maintenance of R2 lineages probably reflect characteristics of some combination of both R2 lineages and host organisms.