Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

Abstract

Genome sequencing has revealed that horizontal gene transfer (HGT) is a major evolutionary process in bacteria. Although it is generally assumed that closely related organisms engage in genetic exchange more frequently than distantly related ones, the frequency of HGT among distantly related organisms and the effect of ecological relatedness on the frequency has not been rigorously assessed. Here, we devised a novel bioinformatic pipeline, which minimized the effect of overrepresentation of specific taxa in the available databases and other limitations of homology-based approaches by analyzing genomes in standardized triplets, to quantify gene exchange between bacterial genomes representing different phyla. Our analysis revealed the existence of networks of genetic exchange between organisms with overlapping ecological niches, with mesophilic anaerobic organisms showing the highest frequency of exchange and engaging in HGT twice as frequently as their aerobic counterparts. Examination of individual cases suggested that interphylum HGT is more pronounced than previously thought, affecting up to B16% of the total genes and B35% of the metabolic genes in some genomes (conservative estimation). In contrast, ribosomal and other universal protein-coding genes were subjected to HGT at least 150 times less frequently than genes encoding the most promiscuous metabolic functions (for example, various dehydrogenases and ABC transport systems), suggesting that the species tree based on the former genes may be reliable. These results indicated that the metabolic diversity of microbial communities within most habitats has been largely assembled from preexisting genetic diversity through HGT and that HGT accounts for the functional redundancy among phyla.

The chimeric nature of the genomes of marine magnetotactic coccoid‐ovoid bacteria defines a novel group ofProteobacteria

“…Then, we surveyed the mosaic genome features by using the criterion that a genome is mosaic when more than 10% each of total genes are affiliated with at least two classes of Proteobacteria. We chose higher than 10% because inter‐phylum horizontal gene transfer is generally believed to affect up to 16% of the total genes with an average < 10% (Garciavallve et al ., ; Caroquintero and Konstantinidis, ). We identified 29 genomes satisfying this criterion (Table ).…”

Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage

“…HGT represents a relatively rapid process for trait acquisition, as opposed to gene creation either from preexisting genes (via duplication, fission, fusion, or exon shuffling) or through de novo gene birth from noncoding sequences (2)(3)(4)(5)(6). In prokaryotes, the occurrence, patterns, frequency, and impact of HGT on the genomic architecture (7), metabolic abilities (8,9), physiological preferences (10,11), and ecological fitness (12) has been widely investigated, and the process is now regarded as a major driver of genome evolution in bacteria and archaea (13,14). Although eukaryotes are perceived to evolve principally through modifying existing genetic information, analysis of HGT events in eukaryotic genomes has been eliciting increasing interest and scrutiny.…”

Phenotypic reconstruction of the last universal common ancestor reveals a complex cell

“…While HGT plays a role in prokaryotic evolution, often seen as obscuring the assumption of vertical descent with modification, the traits under investigation in our study are multigene entities and as such our ancestral reconstructions are less likely to be influenced by HGT [49][50][51] . Furthermore, a number of studies show that HGT occurs predominantly among near phylogenetic relatives and closely interacting species [85][86][87] and is far less common between distantly related organisms. To test the accuracy of our reconstruction methods to cases of horizontal trait transfer (HTT) we conduct two sets of simulations.…”