Abstract
Gene conversion is the unidirectional transfer of genetic information between orthologous (allelic) or paralogous (nonallelic) genomic segments. Though a number of studies have examined nucleotide replacements, little is known about length difference mutations produced by gene conversion. Here, we investigate insertions and deletions produced by nonallelic gene conversion in 338 Drosophila and 10,149 primate paralogs. Using a direct phylogenetic approach, we identify 179 insertions and 614 deletions in Drosophila paralogs, and 132 insertions and 455 deletions in primate paralogs. Thus, nonallelic gene conversion is strongly deletion-biased in both lineages, with almost 3.5 times as many conversion-induced deletions as insertions. In primates, the deletion bias is considerably stronger for long indels and, in both lineages, the per-site rate of gene conversion is orders of magnitudes higher than that of ordinary mutation. Due to this high rate, deletion-biased nonallelic gene conversion plays a key role in genome size evolution, leading to the cooperative shrinkage and eventual disappearance of selectively neutral paralogs.
Highlights
IntroductionIn diploids, such segments can be classified as orthologs or paralogs
Ordinary mutation is generally AT-biased for nucleotide replacements [2,3,4] and deletion-biased for length difference mutations [5]
A number of studies have examined nucleotide replacements produced by allelic and nonallelic gene conversion, some of which have uncovered a GC bias [6,7,8,9]
Summary
In diploids, such segments can be classified as orthologs or paralogs. Paralogs, or nonallelic segments, are found at different genomic loci and can have any copy number, in which each copy is derived from an ancestral sequence via gene duplication [1]. Ordinary mutation is generally AT-biased for nucleotide replacements [2,3,4] and deletion-biased for length difference mutations [5]. A number of studies have examined nucleotide replacements produced by allelic and nonallelic gene conversion, some of which have uncovered a GC bias [6,7,8,9]. We explore length difference mutations produced by nonallelic gene conversion
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