Gene Conversion amongst Alu SINE Elements

Doronina L, Reising, O, Schmitz J

Abstract

The process of non-allelic gene conversion acts on homologous sequences during recombination,replacing parts of one with the other to make them uniform. Such concerted evolution isbest described as paralogous ribosomal RNA gene unification that serves to preserve the essentialhouse-keeping functions of the converted genes. Transposed elements (TE), especially Alu shortinterspersed elements (SINE) that have more than a million copies in primate genomes, are a significantsource of homologous units and a verified target of gene conversion. The consequences ofsuch a recombination-based process are diverse, including multiplications of functional TE internalbinding domains and, for evolutionists, confusing divergent annotations of orthologous transposableelements in related species. We systematically extracted and compared 68,097 Alu insertions invarious primates looking for potential events of TE gene conversion and discovered 98 clear cases ofAlu–Alu gene conversion, including 64 cases for which the direction of conversion was identified(e.g., AluS conversion to AluY). Gene conversion also does not necessarily affect the entire homologoussequence, and we detected 69 cases of partial gene conversion that resulted in virtual hybridsof two elements. Phylogenetic screening of gene-converted Alus revealed three clear hotspots ofthe process in the ancestors of Catarrhini, Hominoidea, and gibbons. In general, our systematicscreening of orthologous primate loci for gene-converted TEs provides a new strategy and view of apost-integrative process that changes the identities of such elements.