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A Strong Deletion Bias in Nonallelic Gene Conversion
- Source :
- PLoS Genetics, Vol 8, Iss 2, p e1002508 (2012), PLoS Genetics
- Publication Year :
- 2012
- Publisher :
- Public Library of Science (PLoS), 2012.
-
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.<br />Author Summary Gene conversion is a process whereby a DNA sequence is copied from one segment of the genome (donor) to another (recipient), resulting in the replacement, insertion, or deletion of a DNA sequence in the recipient. This exchange is facilitated by the high sequence similarity of the two segments, which is due to their evolutionary relationship. Here, we study insertions and deletions produced by gene conversion between paralogs, segments related by DNA duplication events. By comparing paralog sequences in multiple species of fruit flies and primates, we find that deletions occur more than three times as frequently as insertions. We also discover that the rate of gene conversion between paralogs is quite high. The deletion bias and high rate of this process causes paralogs to shrink cooperatively and eventually be eliminated from the genome. Because of the abundance of paralogs in animal genomes, this phenomenon can lead to a significant reduction in genome size. Therefore, our finding enhances our understanding of the forces that lead to changes in genome size during evolution.
- Subjects :
- Primates
Cancer Research
Genome evolution
animal structures
lcsh:QH426-470
Gene Conversion
Biology
medicine.disease_cause
Genome
INDEL Mutation
Species Specificity
Genetics
medicine
Animals
Gene conversion
Insertion
Allele
Indel
Molecular Biology
Alleles
Genetics (clinical)
Ecology, Evolution, Behavior and Systematics
Sequence Deletion
Evolutionary Biology
Mutation
Sequence Inversion
fungi
Genomics
Biological Evolution
lcsh:Genetics
Drosophila
Research Article
Subjects
Details
- ISSN :
- 15537404
- Volume :
- 8
- Database :
- OpenAIRE
- Journal :
- PLoS Genetics
- Accession number :
- edsair.doi.dedup.....85edb4d26a74b78574edefaf73643ee0