Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes.

Evgeni Bolotin,Ruth Hershberg

doi:10.1038/srep35168

Abstract

Gene loss is a major contributor to the evolution of bacterial gene content. Gene loss may occur as a result of shifts in environment leading to changes in the intensity and/or directionality of selection applied for the maintenance of specific genes. Gene loss may also occur in a more neutral manner, when gene functions are lost that were not subject to strong selection to be maintained, irrespective of changes to environment. Here, we used a pangenome-based approach to investigate patterns of gene loss across 15 bacterial species. We demonstrate that gene loss tends to occur mostly within a pool of genes that are less constrained within species, even in those strains from which they are not lost, and less conserved across bacterial species. Our results indicate that shifts in selection, resulting from shifts in environment are not required to explain the majority of gene loss events occurring within a diverse collection of bacterial species. Caution should therefore be taken when attributing differences in gene content to differences in environment.

Highlights

IntroductionA second, more neutral, possibility is that most of the genes lost are ones that, to begin with, were less crucial within their species and across species, independent of environment
Supporting our claim that unique and rare pangenes are the ones that are horizontally transferred into a species, we have previously shown that clonal pathogen species that undergo little or no horizontal gene transfer (HGT) have almost no unique or rare pangenes[29]
We focused on 15 bacterial species for which at least 10 genomes were sequenced (Table S1)

Summary

Introduction

A second, more neutral, possibility is that most of the genes lost are ones that, to begin with, were less crucial within their species and across species, independent of environment Under such a model most genes lost are lost irrespectively of any shift in natural selection. The typical pangenome plot is asymmetrically U-shaped, with a much higher frequency of pangenes found either in a few or the majority of the investigated strains and a relatively low frequency of pangenes found in an intermediate number of strains[27,28,29] This U-shaped distribution of pangene frequencies suggests that pangenes found in all or a majority of strains of a species are likely vertically inherited within that species[29]. Supporting our claim that unique and rare pangenes are the ones that are horizontally transferred into a species, we have previously shown that clonal pathogen species that undergo little or no HGT have almost no unique or rare pangenes[29]

Methods

Results

Conclusion