A comparison of homologous recombination rates in bacteria and archaea

Abstract

It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate.

Contrasting recombination patterns and demographic histories of the plant pathogen Ralstonia solanacearum inferred from MLSA

“…Considering the entire R. solanacearum population, the standardized index of association, I a s (Maynard Smith et al, 1993;Haubold et al, 1998), was significantly different from 0, indicating a high level of linkage disequilibrium and a clonal genetic structure (Table 4). R. solanacearum as a whole had an intermediate relative effect of recombination and mutation (r/m ¼ 1.6), confirming previous results (Vos and Didelot, 2008). However, when calculated on the different phylotypes, I a s indicated that phylotype I population was in linkage equilibrium Gene exchanges are represented with arrows and orientated from the donor (minor parent) to the recombinant.…”

“…Among the recombination processes, the evolutionary importance of horizontal gene transfer has been highlighted by the tremendously increasing number of whole-genome sequences available (Martin and Beiko, 2010), and has mainly been studied on animal or human pathogenic bacteria (Achtman, 2008;Didelot and Maiden, 2010). Although some recent studies address this question on Pseudomonas syringae (Yan et al, 2008) or Xanthomonas campestris (Fargier et al, 2011), data are far less numerous on plant-associated bacteria, and more specifically plant pathogenic bacteria (Vos and Didelot, 2008).…”

“…NS, not significant (P40.05); *0.054PX0.01; **0.014 PX0.001; ***Po0.001 (parametric and Monte Carlo methods, 1000 random resamplings). c Values of r/m (95% credibility interval), the ratio of rates at which nucleotides become substituted as a result of recombination and mutation (Vos and Didelot, 2008), were calculated with ClonalFrame (Didelot and Falush, 2007). d r and y, the ratios of absolute numbers of recombination and mutation events, were calculated by ClonalFrame.…”

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype

“…However, we attributed this to the SAGs being incomplete and fragmented, because when the SAGs were compared with other SAR11 genomes, syntenic genes were a characteristically high percentage of the total shared genes. High amounts of local synteny may seem unlikely given predicted SAR11 recombination rates are among the highest measured for prokaryotes (Vergin et al, 2007;Vos and Didelot, 2009), however, it was shown previously that much of the rearrangement within genomes occurs at operon boundaries, and thus local synteny is not disrupted . Further, the rates in Vergin et al (2007) were restricted to closely related organisms within subclade Ia.…”

Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology

“…The rate of homologous recombination (r) in C. difficile is estimated to be relatively low, and is estimated to have effect ~4 times lower than point mutation (m), (r/m=0.25) (Dingle et al, 2011;Vos and Didelot, 2009). This rate could be an underestimation, however, if barriers between lineages existed, such as geographical separation.…”