MBE Advance Access published online on January 11, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msj093
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1 Division of Population Genetics, National Institute of Genetics, Mishima 411-8540, Japan
* To whom correspondence should be addressed. Gene conversion is considered to play important roles in the formation of genomic makeup such as homogenization of multigene families and diversification of alleles. We devised two statistical tests on ‘quartet’s for detecting gene conversion events. Each quartet consists of two pairs of orthologous sequences supposed to have been generated by a duplication event and a subsequent speciation of two closely related species. As example data, EnsEMBL mouse and rat cDNA sequences were used to obtain a genome-wide picture of gene conversion events. We extensively sampled 2,641 quartets that appear to have resulted from duplications after the divergence of primates and rodents and before mouse-rat speciation. Combination of our new tests with Sawyer's and Takahata's tests enhanced the detection sensitivity while keeping false positives as few as possible. About 18% (488 quartets) were shown to be highly positive for gene conversion using this combined test. Out of them, 340 (13% of the total) showed signs of gene conversion in mouse sequence pairs. Those gene conversion-positive gene pairs are mostly linked in the same chromosomes, with the proportion of positive pairs in the linked and unlinked categories being 15% and 1%, respectively. Statistical analyses showed that (i) the susceptibility to gene conversion correlates negatively with the physical distance, especially the frequency of 29% was observed for gene pairs whose distances are smaller than 55 Kb; (ii) the occurrence of gene conversions does not depend on the transcriptional direction; (iii) small gene families consisting of between 3 and 6 contiguous genes are highly prone to gene conversion; (iv) frequency of gene conversions greatly varies depending on functional categories, and cadherins favor gene conversion while vomeronasal receptors type 1 and immunoglobulin V-type proteins disfavor it. These findings will be useful to deepen the understanding of the roles of gene conversion.
Accepted January 5, 2006
Research Article
Genomewide Search of Gene Conversions in Duplicated Genes of Mouse and Rat
Kiyoshi Ezawa 1,
Satoshi OOta 2,
and
Naruya Saitou 1 *
2 Division of Population Genetics, National Institute of Genetics, Mishima 411-8540, Japan; Present address: Department of Biological Systems, RIKEN Bioresource Center, Tsukuba 305-0074, Japan
Naruya Saitou, E-mail: nsaitou{at}genes.nig.ac.jp
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