Current Methods for Recombination Detection in Bacteria

Abstract

The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of software. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic approaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.

Using Genomes and Evolutionary Analyses to Screen for Host-Specificity and Positive Selection in the Plant Pathogen Xylella fastidiosa

“… X. fastidiosa is naturally transformant and undergoes homologous recombination ( 9 , 89 ), but recombined genomic regions can obscure vertical phylogenetic relationships. To account for potential recombination among the X. fastidiosa genomes, we applied Gubbins v. 3.2.1 ( 36 , 90 ), again using the subset of genes that were found in all 64 samples. From this input, Gubbins identified regions that were likely to have undergone recombination and removed them from the alignment.…”

Using genomes and evolutionary analyses to screen for host-specificity and positive selection in the plant pathogen Xylella fastidiosa

“…X. fastidiosa is naturally transformant and undergoes homologous recombination (9, 60), but recombined genomic regions can obscure vertical phylogenetic relationships. To account for potential recombination among X. fastidiosa genomes, we applied Gubbins v. 3.2.1 (61, 62), using again the subset of genes that were found in all 64 samples. From this input, Gubbins identified regions that were likely to have undergone recombination and removed them from the alignment.…”

hgtseq: a standard pipeline to study horizontal gene transfer

“…The measure of rates and patterns of HGT loci in metazoan relies on the methods used to identify HGT candidates in genomes and transcriptomes [22]. Parametric methods, including gmos [23], GeneMates [24], ShadowCaster [25] and nearHGT [26], are aimed at finding genetic loci distinguished from their new host genome either by GC content, oligonucleotide spectrum, DNA structure modelling or based on their genomic context.…”

“…The indication however that other sequencing studies, carried out in control individuals, display a similar presence of microbial-derived sequences in unmapped reads suggests that HGT events might be more widespread than initially thought. The measure of rates and patterns of HGT loci in metazoan relies on the methods used to identify HGT candidates in genomes and transcriptomes [22]. Parametric methods, including gmos [23], GeneMates [24], ShadowCaster [25] and nearHGT [26], are aimed at finding genetic loci distinguished from their new host genome either by GC content, oligonucleotide spectrum, DNA structure modelling or based on their genomic context.…”