Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter

Abstract

An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human and animal enteric pathogens, with genome sequence data available for eight species. We estimate the Campylobacter core genome at 647 genes, with 92.5% of the nonrecombinant core genome loci under positive selection in at least one lineage and the same gene frequently under positive selection in multiple lineages. Tests are provided that reject recombination, saturation, and variation in codon usage bias as factors contributing to this high level of selection. We suggest this genome-wide adaptive evolution may result from a Red Queen macroevolutionary dynamic, in which species are involved in competition for resources within the mammalian and/or vertebrate gastrointestinal tract. Much reduced levels of positive selection evident in Streptococcus, as reported by the authors in an earlier work, may be a consequence of these taxa inhabiting less species-rich habitats, and more unique niches. Despite many common loci under positive selection in multiple Campylobacter lineages, we found no evidence for molecular adaptive convergence at the level of the same or adjacent codons, or even protein domains. Taken collectively, these results describe the diversification of a bacterial genus that involves pervasive natural selection pressure across virtually the entire genome, with this adaptation occurring in different ways in different lineages, despite the species tendency toward a common gastrointestinal habitat.

Outcome of infection of C57BL/6 IL-10−/− mice with Campylobacter jejuni strains is correlated with genome content of open reading frames up- and down-regulated in vivo

“…Campylobacter jejuni genes not present in strain 11168 [25] were identified using procedures described in Lefebure and Stanhope [26]. Fifteen Campylobacter genomes were used; these genomes were available at NCBI in June, 2007, and included ten C. jejuni subsp.…”

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

“…The large amounts of sequence data generated in the past few years have led to a burst in studies examining important open questions about protein evolution Chen et al 2006;Savard et al 2006;Anisimova et al 2007; Drosophila 12 Genomes Consortium 2007; Heger and Ponting 2007;Kawahara and Imanishi 2007;Vieira et al 2007;Kosiol et al 2008;Larracuente et al 2008;Studer et al 2008;Lefebure and Stanhope 2009;Dickson et al 2010;Kunstner et al 2010). Many of these studies use as a basic premise the alignment of nucleotide and amino acid sequences obtained from different species.…”

“…At the same time these are among the most exciting studies, as they can uncover mechanisms difficult to detect at a smaller scale and can lead to important and highly influential conclusions. They are also becoming increasingly common (Bakewell et al 2007; Drosophila 12 Genomes Consortium 2007; Kosiol et al 2008; Lefebure and Stanhope 2009;Kunstner et al 2010). It is therefore crucial to understand the prevalence and impact of any existing alignment problems in such studies and to ensure that they do not significantly affect the conclusions.…”

Molecular diagnostic protocols for bovine genital campylobacteriosis using comparative genomics and virulence studies

“…Campylobacter core genome while 82 and 35 core genes were found to be unique to C. coli and C. jejuni, respectively (Lefébure and Stanhope, 2009;Lefébure et al, 2010). Further analysis of fully sequenced and completely annotated C. fetus genomes is needed to confirm if the seven new putative PCR targets are in fact part of the C. fetus subsp.…”

“…genomes, reported that it contains 552 gene families (Ali et al, 2012;Lefébure and Stanhope, 2009). This latest study included only one C. fetus subsp.…”