Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer events

Abstract

Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between cyanobacteria and other phyla. A novel method of detecting and enumerating potential horizontal gene transfer events within a group of organisms based on analyses of “embedded quartets” allows us to identify phylogenetic signal consistent with a plurality of gene families, as well as to delineate cases of conflict to the plurality signal, which include horizontally transferred genes. To infer horizontal gene transfer events between cyanobacteria and other phyla, we added homologs from 168 available genomes. We screened phylogenetic trees reconstructed for each of these extended gene families for highly supported monophyly of cyanobacteria (or lack of it). Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets’ plurality signals. We find more conflicts within cyanobacteria than between cyanobacteria and other phyla. We also find that genes from all functional categories are subject to transfer. However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases.

Gene transfer agents: phage-like elements of genetic exchange

“…6,9,11,12 . Such patterns are probably a consequence of existing barriers to HGT, which have been reviewed in detail elsewhere 13,14 .…”

“…For illegitimate recombination, in which the incoming DNA is not homologous to the recipient DNA, the frequency is expected to be orders of magnitude lower than the frequency for homologous sequences, especially for linear fragments as opposed to circular molecules, as reviewed elsewhere 14 . In silico analyses of gene transfer patterns indicate that HGT is much more frequent between closely related organisms than between distantly related ones 9,11,71 . This is consistent with the idea that GTAs have played an important part in creating such HGT patterns, as GTA-mediated HGT requires specific interactions between the host and the GTA particle for successful attachment and injection of the DNA 72 , as well as DNA sequence similarity to facilitate incorporation of a transferred allele by homologous recombination 14 .…”

“…7). HGT occurs within and between all three domains of life, and it has been estimated that 0.05-80% of genes in bacterial and archaeal genomes have been affected by HGT, depending on the analytical method used and the genome analysed [8][9][10] . Although HGT is widespread, it is not random: patterns of preferential gene exchange among specific groups of organisms that share ancestry or habitat have been * Present address.…”

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

“…strain-A or B 0 ). Comparative genomic studies have shown that, although gene transfer among cyanobacteria is evident (Zhaxybayeva et al, 2006), these events have been infrequent to the degree that they do not obscure inferences about the phylogenetic relationships in this kingdom (Kettler et al, 2007;Swingley et al, 2008;Zhaxybayeva et al, 2009;Melendrez et al, 2011;Popa et al, 2011).…”

Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea

“…This gene diversity and genome fluidity frequently underlies the emergence of new pathogens and the natural attenuation of important environmental pollutants, and hence, has important health and economical consequences (Handelsman et al, 2007). Horizontal gene transfer (HGT) accounts for a substantial fraction, if not the majority, of the bacterial genomic fluidity and diversity (Beiko et al, 2005;Zhaxybayeva et al, 2006;Lang and Beatty, 2007). However, a robust understanding of the rates of genetic exchange for most bacterial species under natural conditions and the influence of the ecological settings on the rates remain elusive (Gevers et al, 2005;Konstantinidis et al, 2006a;Handelsman et al, 2007).…”