The evolution of metazoan genomes and highly conserved SINE domains (51881)

Short interspersed elements (SINEs) are non-autonomous retrotransposons with modular structures: a small RNA-related head, a body and an AT-rich tail. Despite their high turnover rate and de novo emergence, the body may retain highly conserved domains (HCD) among different SINE families: in metazoan, up to seven HCD-SINEs have been recognized. Interestingly, two HCD-SINEs (CORE- and Deu-SINEs) have been repeatedly subject to exaptation in mammalian genomes, becoming part of gene regulatory networks. Analyzing molluscan transcriptomes and genomic sequences we characterized four new HCD-SINE families, whose insertion site analyses suggest recent activity. Two HCDs were previously found in chordates' SINEs: the V-domain (here found in gastropods, bivalves and chitons), and the CORE-domain (here found in bivalves and gastropods). A CORE-SINE has been further identified in the horseshoe crab and one more family isolated in snails retains the cephalopods’ Ceph domain. Tracking the ancestry of HCDs in the metazoan phylogeny revealed that some of them date back to the Radiata-Bilateria and the Protostomia- Deuterostomia splits. We suggest that the evolutionary conservation of HCD may account for the high SINE diversity (“module exchange” model) and for their long-term inheritance in metazoan genomes.