Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates

Pan, Deng; Zhang, Liqing

Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates

dc.contributor.author	Pan, Deng	en
dc.contributor.author	Zhang, Liqing	en
dc.contributor.department	Computer Science	en
dc.date.accessioned	2012-08-24T12:11:45Z	en
dc.date.available	2012-08-24T12:11:45Z	en
dc.date.issued	2007-08-02	en
dc.date.updated	2012-08-24T12:11:45Z	en
dc.description.abstract	Background The rate of gene duplication is an important parameter in the study of evolution, but the influence of gene conversion and technical problems have confounded previous attempts to provide a satisfying estimate. We propose a new strategy to estimate the rate that involves separate quantification of the rates of two different mechanisms of gene duplication and subsequent combination of the two rates, based on their respective contributions to the overall gene duplication rate. Results Previous estimates of gene duplication rates are based on small gene families. Therefore, to assess the applicability of this to families of all sizes, we looked at both two-copy gene families and the entire genome. We studied unequal crossover and retrotransposition, and found that these mechanisms of gene duplication are largely independent and account for a substantial amount of duplicated genes. Unequal crossover contributed more to duplications in the entire genome than retrotransposition did, but this contribution was significantly less in two-copy gene families, and duplicated genes arising from this mechanism are more likely to be retained. Combining rates of duplication using the two mechanisms, we estimated the overall rates to be from approximately 0.515 to 1.49 x 10-3 per gene per million years in human, and from approximately 1.23 to 4.23 x 10-3 in mouse. The rates estimated from two-copy gene families are always lower than those from the entire genome, and so it is not appropriate to use small families to estimate the rate for the entire genome. Conclusion We present a novel strategy for estimating gene duplication rates. Our results show that different mechanisms contribute differently to the evolution of small and large gene families.	en
dc.description.sponsorship	This work was supported by a VPI&SU ASPIRES (A Support Program for Innovative Research Strategies) grant.	en
dc.description.version	Published version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	Genome Biology. 2007 Aug 02;8(8):R158	en
dc.identifier.doi	https://doi.org/10.1186/gb-2007-8-8-r158	en
dc.identifier.uri	http://hdl.handle.net/10919/18924	en
dc.identifier.volume	8	en
dc.language.iso	en	en
dc.publisher	BioMed Central	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Deng Pan et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.title	Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates	en
dc.title.serial	Genome Biology	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en