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 is best described as paralogous ribosomal RNA gene unification that serves to preserve the essential house-keeping functions of the converted genes. Transposed elements (TE), especially Alu short interspersed elements (SINE) that have more than a million copies in primate genomes, are a significant source of homologous units and a verified target of gene conversion. The consequences of such a recombination-based process are diverse, including multiplications of functional TE internal binding domains and, for evolutionists, confusing divergent annotations of orthologous transposable elements in related species. We systematically extracted and compared 68,097 Alu insertions in various primates looking for potential events of TE gene conversion and discovered 98 clear cases of Alu–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 homologous sequence, and we detected 69 cases of partial gene conversion that resulted in virtual hybrids of two elements. Phylogenetic screening of gene-converted Alus revealed three clear hotspots of the process in the ancestors of Catarrhini, Hominoidea, and gibbons. In general, our systematic screening of orthologous primate loci for gene-converted TEs provides a new strategy and view of a post-integrative process that changes the identities of such elements.
Highlights
Genomes of most eukaryotic organisms contain a large number of repetitive sequences, a notable portion of which is composed of transposable elements (TE)
We previously showed that parallel insertions and precise deletions of Alus are rare in primates, confirming their usefulness as virtually homoplasy-free markers in phylogenetic studies [23]
To determine the extent of possible homoplasy caused by gene conversion and the frequency of gene conversion in TEs of different ages, we performed a systematic screening for gene conversion among Alu elements belonging to clearly different primate Alu subfamilies and types (AluY/AluS and AluY/AluYc)
Summary
Genomes of most eukaryotic organisms contain a large number of repetitive sequences, a notable portion of which is composed of transposable elements (TE). Accumulating changes in master copies leads to new subfamilies and types of TEs that commonly differ by several diagnostic sites and spread in limiting activity waves through the genome [4]. Due to their repetitive nature, high similarity, and large quantities in the genome, TEs present a significant substrate for non-allelic gene conversion. A whole-genome gene conversion analysis among Alus in humans [8] focused on non-diagnostic mutations in Alu sequences revealed significant. To determine the extent of possible homoplasy caused by gene conversion and the frequency of gene conversion in TEs of different ages, we performed a systematic screening for gene conversion among Alu elements belonging to clearly different primate Alu subfamilies and types (AluY/AluS and AluY/AluYc)
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