Evolutionary fate of SVA2 elements in primate genomes

SVA (SINE/VNTR/Alu) transposable element, one of non-LTR retrotransposons, emerged in the primate genome about 25 million years ago. Currently, ~2,800 SVA copies exist in the human genome. Recently, a group of transposable elements named SVA2 is discovered. SVA2 elements share the VNTR region with the SVA element but do not contain the SINE-R region of the SVA elements. In this study, we studied the SVA2 evolution and the impact of the SVA2 elements on primate genomes. We first identified 144, 139, 136, 139, and 116 SVA2 elements in the human, chimpanzee, gorilla, orangutan, and rhesus macaque genomes, respectively. To examine the evolutionary state and structure of the elements, we performed comparative genomics, comparing human SVA2 with its orthologous counterpart from non-human primates. The result suggests that SVA2 subfamily is not, at present, retrotranspositionally active in the primate genomes because none of the SVA2 elements identified in this study are species-specific. In addition, we found that four human SVA2 elements locate in human genes and two of them have miRNA target sites, indicating that they might regulate gene expression and involve in the gene-related human diseases.