Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

Abstract

Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic gene-sharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification. Our results indicate that, on average, at least 81 ؎ 15% of the genes in each genome studied were involved in lateral gene transfer at some point in their history, even though they can be vertically inherited after acquisition, uncovering a substantial cumulative effect of lateral gene transfer on longer evolutionary time scales.community structure ͉ molecular phylogeny ͉ microbial genomes

Horizontal gene transfer in evolution: facts and challenges

“…In addition, the results of a network analysis of shared genes (Dagan et al 2008) agree with the idea that horizontal gene transfer leaves no gene family untouched.…”

“…Several studies suggest that gene transfer could effectively be more frequent for short and intermediate evolutionary distances but uncommon between organisms that are separated by large evolutionary time frames (Ochman et al 2000;Brugger et al 2002;Nakamura et Dagan et al 2008). A recent study (Wagner & De la Chaux 2008) has analysed the evolution of 2091 insertion sequences in 438 completely sequenced prokaryotic genomes and found only 30 cases of presumed transfer events among distantly related clades.…”

Predicting microbial traits with phylogenies

“…Working at such a broad taxonomic resolution can decrease the magnitude of the phylogenetic signal as microbial traits tend to be conserved at shallower clade depths (Martiny et al, 2013; see Supplementary Information S5 for examples with simulated and empirical data). The weaker phylogenetic signals detected in prokaryotes compared with eukaryotes can also arise from the horizontal transfer of genes, which is a remarkable natural source of variation (Dagan et al, 2008). This might weaken the signal by partly shuffling the traits in the phylogeny but does not blur it as the fixation of horizontally transferred genes is not substantial between phylogenetically distant microbes (Choi and Kim, 2007).…”

Global biogeography of Prochlorococcus genome diversity in the surface ocean

“…Traditionally, horizontal gene transfer events are identified by finding topologically incongruent gene trees; however, knowing the organismal origin is necessary, but adequate coverage with metagenomic reads can be difficult to obtain especially in highly complex communities (Guo et al, 2015). Network analyses provide an alternative method to gene phylogenies (Dagan et al, 2008) but still require enough genomic context to identify the taxonomic origin to adequately capture the evolutionary dynamics. Other analyses have been undertaken to identify metagenomic community recombination rates by utilizing metagenomic assemblies (Konstantinidis and DeLong, 2008;Johnson and Slatkin, 2009 Figure 4 Distribution of sequences making up metagenomic assemblies with and without lower-temperature genes.…”