Abstract
We characterized ectopic gene conversions in the genome of ten hemiascomycete yeast species. Of the ten species, three diverged prior to the whole genome duplication (WGD) event present in the yeast lineage and seven diverged after it. We analyzed gene conversions from three separate datasets: paralogs from the three pre-WGD species, paralogs from the seven post-WGD species, and common ohnologs from the seven post-WGD species. Gene conversions have similar lengths and frequency and occur between sequences having similar degrees of divergence, in paralogs from pre- and post-WGD species. However, the sequences of ohnologs are both more divergent and less frequently converted than those of paralogs. This likely reflects the fact that ohnologs are more often found on different chromosomes and are evolving under stronger selective pressures than paralogs. Our results also show that ectopic gene conversions tend to occur more frequently between closely linked genes. They also suggest that the mechanisms responsible for the loss of introns in S. cerevisiae are probably also involved in the gene 3′-end gene conversion bias observed between the paralogs of this species.
Highlights
The repair of double strand DNA breaks is a critical biological process which maintains genome stability
The primary process whereby double-strand DNA breaks are repaired is via homologous recombination; this process requires the use of a repair template gene which provides a copy of the missing information caused by the double-strand DNA breaks
The S. cerevisiae, S. paradoxus, S. mikatae, S. bayanus, S. kudriavzevii, and S. castellii genome sequences were retrieved from the Saccharomyces Genome Database (SGD; ftp://genome-ftp.stanford.edu/pub/yeast/ sequence/)
Summary
The repair of double strand DNA breaks is a critical biological process which maintains genome stability. An end product of the homologous recombination pathway is the replacement of the broken part of the damaged gene by a homologous portion of the repair template gene. In Escherichia coli, a 2%–4% decrease in sequence similarity between a damaged gene and its repair template can cause a 10- to 40-fold decrease in recombination frequency [2, 3]. Linked genes are converted more frequently than dispersed genes in Drosophila and humans [5, 6]. In S. cerevisiae, genes conversions between dispersed paralogs are more frequent at their 3 -ends [4]. This 3 -bias is likely the result of gene conversion with incomplete cDNA molecules [9]. Ohnologs Biological regulation Regulation of biological process Regulation of cellular process External encapsulating structure organization and biogenesis Cell wall organization and biogenesis Protein amino acid phosphorylation Cellular polysaccharide biosynthetic process Polysaccharide biosynthetic process Carbohydrate biosynthetic process Cellular carbohydrate metabolic process Carbohydrate metabolic process
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