Detecting Horizontal Gene Transfer between Closely Related Taxa

Abstract

Horizontal gene transfer (HGT), the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived) genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive.We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM). Using CRM, the algorithm assigns a confidence score based on “unusual” sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set.When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.

Syntenizer 3000: Synteny-based analysis of orthologous gene groups

“…Synteny analysis of genomes has been employed in studies involving orthology verification [Frantzeskakis 2018], examining chromosomal reconstruction using synteny blocks in distantly related species such as humans and mice [Singa 2007], and detection of horizontal gene transfer [Adato 2015]. Until S3K, no synteny based tools capable of assigning a numerical value to the degree of synteny between two genes, and use this measurement to remove paralogs from gene groups has been made available for general research use.…”

A Phylogenomic Study Quantifies Competing Mechanisms for Pseudogenization in Prokaryotes

“…We now report on another evolutionary difference between the two gene sets -pseudogenes and non-pseudogenes -that we measured only between mycobacterial species. The tool we employ here to analyze the gene sets, the synteny index (SI, see expansion on the procedure in the supplementary text and [1,35]) relies on a different evolutionary signal that is useful when analyzing closely related taxa.…”

Detecting horizontal gene transfer: a probabilistic approach

“…Such a signal may not exists when dealing with closely related species or even strains of the same species. In two recent works [1,24], we have defined the notion of synteny index (SI) between two genomes (species) and used it as a marker of evolutionary footprints. Gene synteny [8,23] is the conservation of gene order across species along the evolutionary course.…”