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

Deng Pan,Liqing Zhang

doi:10.1186/gb-2007-8-8-r158

Abstract

By studying two mechanisms of gene duplication, unequal crossover and retrotranspostion, and looking at both small gene families and the entire genome, a new estimate for the rate of gene duplication is made which is more accurate for both small and large gene families.

Highlights

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
In order to examine whether gene duplication rates estimated from small gene families can be used to represent duplication rates in the entire genome, we estimated rates using two sets of data: all duplicated genes in the entire genome and only the duplicated genes in the twocopy gene families
In this study we considered the relative extent to which the various mechanisms contribute to recent gene duplications in human and mouse, and we estimated the gene duplication rate occurring via different duplication mechanisms

Summary

Introduction

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. R158.2 Genome Biology 2007, Volume 8, Issue 8, Article R158 Pan and Zhang http://genomebiology.com/2007/8/8/R158 ones To solve this problem, two methods were proposed in previous studies. The first method is to use Ks (the synonymous distance) [3] or other neutral markers [4] as the time proxy to define newly born duplicates This method was first used by Lynch and Conery [3] to estimate gene duplication rates in the genomes of yeast, Drosophila, and Caenorhabtidis elegans. The marker is neutral and the molecular clock model holds, the first method still has problems One of these is that it cannot distinguish true newly born duplicates from old duplicates that appear to be young because of gene conversion. Because gene conversion occurs frequently in the genome [8,9], this first method can yield inflated estimates of rate

Methods

Results

Conclusion