A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains.

Xiangchen Li,Gehong Wei,Wenjun Tong,Shiheng Tao,Siddiq Ur Rahman,Lina Wang

doi:10.3389/fmicb.2018.00973

Xiangchen Li, Gehong Wei + Show 4 more

Open Access

https://doi.org/10.3389/fmicb.2018.00973

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Abstract

Recent horizontal gene transfer (HGT) is crucial for enabling microbes to rapidly adapt to their novel environments without relying upon rare beneficial mutations that arise spontaneously. For several years now, computational approaches have been developed to detect HGT, but they typically lack the sensitivity and ability to detect recent HGT events. Here we introduce a novel strategy, named RecentHGT. The number of genes undergoing recent HGT between two bacterial genomes was estimated by a new algorithm derived from the expectation-maximization algorithm and is based on the theoretical sequence-similarity distribution of orthologous genes. We tested the proposed strategy by applying it to a set of 10 Rhizobium genomes, and detected several large-scale recent HGT events. We also found that our strategy was more sensitive than other available HGT detection methods. These HGT events were mainly mediated by symbiotic plasmids. Our new strategy can provide clear evidence of recent HGT events and thus it brings us closer to the goal of detecting these potentially adaptive evolution processes in rhizobia as well as pathogens.

Highlights

Horizontal gene transfer (HGT), known as lateral gene transfer, is a major process contributing to the evolution of microbes (Soucy et al, 2015)
We tested the approach on 10 Rhizobium genomes
To compare our method with state-of-the-art horizontal gene transfer (HGT) prediction methods, we picked two core genes, fixC and repB, presenting in all selected strains and detected as being putative recently transferred among the strains nodulating P. vulgaris

Summary

Introduction

Horizontal gene transfer (HGT), known as lateral gene transfer, is a major process contributing to the evolution of microbes (Soucy et al, 2015). This process can be mediated by the integration of viruses (bacteriophages), transposable elements, or integrative plasmids, often via non-homologous recombination (Soucy et al, 2015). Compared with ancient HGT events, recent ones are of paramount importance for the uptake of ready-made genes or operons from the “mobile gene pool,” facilitating rapid adaptation to novel environments without the reliance upon rare beneficial mutations arising spontaneously in the population (Treangen and Rocha, 2011). The effectiveness of the HGT is acutely demonstrated by the rapid global spread of antibiotic resistance throughout many bacterial populations (Donnenberg, 2000; Pallen and Wren, 2007; von Wintersdorff et al, 2016)

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