The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio).

Jiong-Tang Li,Xiao-Min Li,Guang-Yuan Hou,Jian-Ming Zeng,Xiao-Wen Sun,Chun-Yan Li,Gui-Bao Xiao,Xiang-Fei Kong,Heng-De Li

doi:10.1038/srep08199

Abstract

Whole genome duplication (WGD) results in extensive genetic redundancy. In plants and yeast, WGD is followed by rapid gene deletions and intense expression differentiation with slow functional divergence. However, the early evolution of the gene differentiation processes is poorly understood in vertebrates because almost all studied WGDs are extremely ancient, and the genomes have returned to a diploid status. Common carp had a very recent fourth round of WGD dated to 8 million years ago. It therefore constitutes an ideal model to study early-stage functional divergence and expression differentiation in vertebrates. We identified 1,757 pairs of recently duplicated genes (RDGs) originating from this specific WGD and found that most ancestral genes were retained in duplicate. Most RDGs were conserved and under selective pressure. Gene expression analysis across six tissues revealed that 92.5% of RDG pairs were co-expressed in at least one tissue and that the expression of nearly half pairs ceased to be strongly correlated, indicating slow spatial divergence but rapid expression dissociation. Functional comparison revealed that 25% of pairs had functional divergence, of which neo- and sub-functionalization were the main outcomes. Our analysis revealed slow gene loss but rapid and intense expression and function differentiation after WGD.

Highlights

The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio)
To analyse gene evolution after Whole genome duplication (WGD) in detail, we compared the common carp and zebrafish genomes and obtained 736 pairs of high-confidence double-conserved syntenic (DCS) regions
This would mean that only 7.8% of the common carp-specific genome duplication (CcaGD) duplicated gene pairs have undergone gene loss and returned to a single-copy state, whereas 92.2% have retained both paralogues

Summary

Introduction

The fate of recent duplicated genes following a fourth-round whole genome duplication in a tetraploid fish, common carp (Cyprinus carpio). WGD is followed by rapid gene deletions and intense expression differentiation with slow functional divergence. Roulin et al found that among recently duplicated genes, only a small proportion (4%) have been either neo- or non-functionalized, but approximately 50% were differentially expressed[9]. These results indicate slow functional divergence but intense expression differentiation. They subsequently deleted approximately 88% of the duplicated genes following WGD11 Based on these observations, it is hypothesized that WGDs are followed by massive and rapid gene deletions and intense expression differentiation with slow functional divergence. To date, the early evolution of these processes has been poorly investigated in vertebrates because almost all genomes of well-characterised WGDs have returned to a diploid status[12,13]

Methods

Results

Conclusion