Phylogenomic analysis reveals splicing as a mechanism of parallel evolution of non-canonical SVAs in hominine primates 06 Biological Sciences 0604 Genetics

Abstract

SVA (SINE-R-VNTR-Alu) elements are non-autonomous non-LTR (Long Terminal Repeat) retrotransposons. They are found in all hominoid primates but did not amplify to appreciable numbers in gibbons. Recently, phylogenetic networks of hominid (orangutan, gorilla, chimpanzee, human) SVA elements based on comparison of overall sequence identity have been reported. Here I present a detailed phylogeny of SVA-D elements in gorilla, chimpanzee and humans based on sorting of co-segregating substitutions. Complementary comparative genomics analysis revealed that the majority (1763 out of 1826-97%) of SVA-D elements in gorilla represent species-specific insertions - indicating very low activity of the subfamily before the gorilla/chimpanzee-human split. The origin of the human-specific subfamily SVA-F could be traced back to a source element in the hominine common ancestor. The major expanding lineage-specific subfamilies were found to differ between chimpanzee and humans. Precursors of the dominant chimpanzee SVA-D subfamily are present in humans; however, they did not expand to appreciable levels. The analysis also uncovered that one of the chimpanzee-specific subfamilies was formed by splicing of the STK40 first exon to the SVA Alu-like region. Many of the 94 subfamily members contain additional 5′ transductions - among them exons of 8 different other genes. Striking similarities to the MAST2-containing human SVA-F1 suggest parallel evolution of non-canonical SVAs in chimpanzees and humans.