a strong deletion bias in nonallelic gene conversion强大的非等位的基因转换删除的偏见.pdfVIP

A Strong Deletion Bias in Nonallelic Gene Conversion 1 2,3 Raquel Assis *, Alexey S. Kondrashov 1 Department of Integrative Biology, Center for Theoretical Evolutionary Genomics, University of California Berkeley, Berkeley, California, United States of America, 2 Department of Ecology and Evolutionary Biology, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America, 3 Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America 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. Citation: Assis R, Kondrashov AS (2012) A Strong Deletion Bias in Nonallelic Gene Conv