Gene Gain and Gene Loss in Streptococcus: Is It Driven by Habitat?

Abstract

Bacterial genomes can evolve either by gene gain, gene loss, mutating existing genes, and/or by duplication of existing genes. Recent studies have clearly demonstrated that the acquisition of new genes by lateral gene transfer (LGT) is a predominant force in bacterial evolution. To better understand the significance of LGT, we employed a comparative genomics approach to model species-specific and intraspecies gene insertions/deletions (ins/del among 12 sequenced streptococcal genomes using a maximum likelihood method. This study indicates that the rate of gene ins/del is higher on the external branches and varies dramatically for each species. We have analyzed here some of the experimentally characterized species-specific genes that have been acquired by LGT and conclude that at least a portion of these genes have a role in adaptation.

Inferring genomic flux in bacteria

“…This is consistent with a previous study which found that maximum Cold Spring Harbor Laboratory Press on May 11, 2018 -Published by genome.cshlp.org Downloaded from likelihood estimates for the rate of genomic flux was higher on the external branches than on the internal branches of a phylogeny of Streptococcus (Marri et al 2006). Another possibility is that prophage integration occurred at a constant rate, but is balanced by prophage excision or deletion.…”

“…Therefore, our model does not assume that evolution proceeds according to a constant molecular clock (Linz et al 2007). The importance of modeling the changes in the rate of gene flux has been recognized before Golding 2004, 2008;Marri et al 2006), but our method is the first to be able to infer from the data where such changes may have happened instead of relying on the user's prior knowledge.…”

Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data

“…It is becoming clear that a typical species taxon recognised by systematics is highly heterogeneous in its genome content and physiology, as well as its ecology (Touchon et al, 2009;Walk et al, 2009;Kettler et al, 2007;Lefebure and Stanhope, 2007;Marri et al, 2006;Paul et al, 2010;Vernikos et al, 2007). A more fine-grained taxonomy, which recognises the closely related, ecologically distinct populations that are now subsumed by bacterial systematics within a single species taxon, would benefit microbiologists from many subfields.…”

Demarcation of bacterial ecotypes from DNA sequence data: A comparative analysis of four algorithms

“…In the last two decades, bacterial taxonomy has adopted various universal molecular criteria for identifying species as clusters, first based on an indirect measure of shared genome content (i.e., DNA-DNA hybridization) [5,6], and more recently based on measures of sequence identity of shared genes, including 16S rRNA sequence similarity [7], multilocus sequence analysis [8], and most recently, genome-wide average nucleotide identity [9]. Due to these efforts, it is becoming clear that a typical species taxon recognized by systematics is highly heterogeneous in its genome content and physiology, as well as its ecology [10][11][12][13][14][15][16]. A more fine-grained taxonomy, which recognizes the closely related, ecologically distinct populations that are now subsumed by bacterial systematics within a single species taxon, would benefit microbiologists from many fields including epidemiology and biotechnology.…”