Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicagogenus (L.)

Joan Ho-Huu,Joëlle Ronfort,Audrey Weber,Isabelle Hochu,Nathalie Chantret,Thomas Bataillon,Stéphane De Mita

doi:10.1186/1471-2148-12-195

Abstract

BackgroundGene duplications are a molecular mechanism potentially mediating generation of functional novelty. However, the probabilities of maintenance and functional divergence of duplicated genes are shaped by selective pressures acting on gene copies immediately after the duplication event. The ratio of non-synonymous to synonymous substitution rates in protein-coding sequences provides a means to investigate selective pressures based on genic sequences. Three molecular signatures can reveal early stages of functional divergence between gene copies: change in the level of purifying selection between paralogous genes, occurrence of positive selection, and transient relaxed purifying selection following gene duplication. We studied three pairs of genes that are known to be involved in an interaction with symbiotic bacteria and were recently duplicated in the history of the Medicago genus (Fabaceae). We sequenced two pairs of polygalacturonase genes (Pg11-Pg3 and Pg11a-Pg11c) and one pair of auxine transporter-like genes (Lax2-Lax4) in 17 species belonging to the Medicago genus, and sought for molecular signatures of differentiation between copies.ResultsSelective histories revealed by these three signatures of molecular differentiation were found to be markedly different between each pair of paralogs. We found sites under positive selection in the Pg11 paralogs while Pg3 has mainly evolved under purifying selection. The most recent paralogs examined Pg11a and Pg11c, are both undergoing positive selection and might be acquiring new functions. Lax2 and Lax4 paralogs are both under strong purifying selection, but still underwent a temporary relaxation of purifying selection immediately after duplication.ConclusionsThis study illustrates the variety of selective pressures undergone by duplicated genes and the effect of age of the duplication. We found that relaxation of selective constraints immediately after duplication might promote adaptive divergence.

Highlights

Gene duplications are a molecular mechanism potentially mediating generation of functional novelty
In this paper we examined patterns of molecular evolution of three paralogous gene pairs, in order to detect signatures of post-duplication functional divergence
We focused on three sets of paralogs from the Medicago truncatula genome, Lax2/Lax4, Pg3/Pg11 and Pg11a/ Pg11c

Summary

Introduction

Gene duplications are a molecular mechanism potentially mediating generation of functional novelty. The relaxation of purifying selection (due to the initial redundancy) may allow some amount of divergence and occasionally can let one copy acquire a new function and be subsequently maintained by natural selection (neofunctionalization) This scenario is essential for the creative role of duplication envisioned by Ohno [1]. These two scenarios are not mutually exclusive and may act jointly [13] Besides these models, the maintenance of functionally redundant copies (without functional divergence) could be adaptive under specific circumstances, either through dosage effect or as a means of genetic robustness against deleterious mutations [14,15,16] and explain the fixation of duplications in species [11]

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Conclusion