Recombine and survive: evolutionary history of the V highly conserved domain in the mammalian genome after the V-SINE superfamily extinction

Short interspersed elements (SINEs) are non-autonomous retrotransposons. Because of high turnover rate, they exhibit widely divergent nucleotide sequences but highly conserved domains (HCDs) may occur. Three different HCDs originated before the Radiata-Bilateria split and two underwent repeatedly to exaptation. The "V" HCD has been retrieved in 16 nonamniotes'SINE families and within a miniature inverted-repeat transposon, MER6, in the human genome. Through in silico searches in sequenced genomes and transcriptomes, we found MER6 in all primates and its variant, MER6A, in bats and in the star-nosed mole. Moreover, we found evidence of MER6 in a salamander and retrieved its parental Tc1/ mariner element in the painted turtle. Data indicate that MER6 originated by recombination between a V- SINE and the parental Tc1/mariner element. Nucleotide substitution rate, computed on 10 primates orthologous insertions, places MER6 main activity burst as contemporary to Placentalia diversification. Moreover, age analyses suggest that MER6 was no longer active in mammals, except in the tarsier where a recent replication burst originated a new MER6A subfamily. Finally, unlike frog and fishes V-SINEs, genomic distribution of MER6 does not appear biased toward genic regions in human, chimp and mole genomes. Present data show how the V domain managed to survive and replicate after V-SINEs extinction. Although the impact of HCDs is still unclear, their wide conservation suggests some role; the study of V- elements with different replicative biology may help to disentangle transposon- related aspects from putative HCD functions