Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution.

Debarun Acharya,Tapash C Ghosh

doi:10.1186/s12864-016-2392-0

Abstract

BackgroundGene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. The levels of gene duplication may vary from small-scale duplication (SSD) to whole genome duplication (WGD). Studies with yeast revealed ample differences between these duplicates: Yeast WGD pairs were functionally more similar, less divergent in subcellular localization and contained a lesser proportion of essential genes. In this study, we explored the differences in evolutionary genomic properties of human SSD and WGD genes, with the identifiable human duplicates coming from the two rounds of whole genome duplication occurred early in vertebrate evolution.ResultsWe observed that these two groups of duplicates were also dissimilar in terms of their evolutionary and genomic properties. But interestingly, this is not like the same observed in yeast. The human WGDs were found to be functionally less similar, diverge more in subcellular level and contain a higher proportion of essential genes than the SSDs, all of which are opposite from yeast. Additionally, we explored that human WGDs were more divergent in their gene expression profile, have higher multifunctionality and are more often associated with disease, and are evolutionarily more conserved than human SSDs.ConclusionsOur study suggests that human WGD duplicates are more divergent and entails the adaptation of WGDs to novel and important functions that consequently lead to their evolutionary conservation in the course of evolution.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2392-0) contains supplementary material, which is available to authorized users.

Highlights

Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time
We binned our dataset according to different Nonsynonymous nucleotide substitution per nonsynonymous sites (dN) ranges and compared the functional similarity between small-scale duplication (SSD) and whole genome duplication (WGD) duplicate pairs
We found that SSD duplicate pairs are functionally more similar than the WGD pairs in each dN range (Table 1) considering both their involvement in biological processes and molecular function (Fig. 1)

Summary

Introduction

Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. Gene duplication is a key source for generating new gene copies from pre-existing ones [1,2,3] These newly-made gene copies are initially functionally redundant and relieved from selective pressure, and may adapt themselves to new functions [2, 4,5,6]. Many of the previous studies concluded gene duplication as the primary guiding force of organism evolution for providing raw genetic materials for genome evolution [1, 2, 7]. Evidence of two rounds of whole-genome duplication was prominent in the early vertebrate evolution [28,29,30,31,32,33], which provides the raw materials for increasing genome and organism complexity and extensive species diversity [29, 31] and is an important process in vertebrate evolution [30, 31]

Methods

Results

Conclusion