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

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.

The pseudogenes of barley

“…Gene duplication is a genomic process that creates new genes and functionalities via neo‐ and subfunctionalization. In most cases, however, it leads to pseudogenization (Kondrashov et al ., ; Ho‐Huu et al ., ; Xiao et al ., ). We identified 4100 (10.8%) functional gene duplicates with a shortened CDS, 255 of which exhibit premature termination codons but are otherwise highly similar to the original version.…”

The Opportunistic Pathogen Propionibacterium acnes: Insights into Typing, Human Disease, Clonal Diversification and CAMP Factor Evolution

“…In the case of the CAMP factor gene family, camps 1, 4 and 5 lie within a relatively limited region of the whole P. acnes genome (type IB isolate 6609; positions 1305067–1462007), while camp 2 (position 756691–757494) and 3 (position 2282724–2283539) are more widely dispersed. In regards to gene duplication, it provides an opportunity for a rapid period of genetic change due to relaxed selective constraints, and represents a significant mechanism for the emergence of genes with the same, altered or novel cellular functions via mutation, drift and selective pressures [61]. Based on our current understanding, these include ecoparalogs, which are functionally equivalent genes adapted to perform under different ecological conditions [62], subfunctionalization, where the ancestral functions are partitioned between paralogue sequences [63] and, less frequently, neofunctionalization, which generates a new function in one of the duplicates which is subsequently maintained by purifying selection [64].…”

Pseudogenes and Their Genome-Wide Prediction in Plants

“…At this stage, no selective pressure should be against any loss-of-function mutation affecting either copy. This relaxation of purifying selection results in most instances the pseudogenization of one copy, as well as some amount of divergence, such as neo-functionalization and sub-functionalization for generating new functional paralog genes, which are subsequently maintained by purifying selection [27]. Overall, the tendency to become inactive pseudogenes is a general fate of duplicated genes [22].…”