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. 2011 Apr;157(Pt 4):1066-1074.
doi: 10.1099/mic.0.045153-0. Epub 2011 Jan 6.

Introgression in the Genus Campylobacter: Generation and Spread of Mosaic Alleles

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Free PMC article

Introgression in the Genus Campylobacter: Generation and Spread of Mosaic Alleles

Samuel K Sheppard et al. Microbiology. .
Free PMC article

Abstract

Horizontal genetic exchange strongly influences the evolution of many bacteria, substantially contributing to difficulties in defining their position in taxonomic groups. In particular, how clusters of related bacterial genotypes - currently classified as microbiological species - evolve and are maintained remains controversial. The nature and magnitude of gene exchange between two closely related (approx. 15 % nucleotide divergence) microbiologically defined species, Campylobacter jejuni and Campylobacter coli, was investigated by the examination of mosaic alleles, those with some ancestry from each population. A total of 1738 alleles from 2953 seven-locus housekeeping gene sequence types (STs) were probabilistically assigned to each species group with the model-based clustering algorithm structure. Alleles with less than 75 % assignment probability to one of the populations were confirmed as mosaics using the structure linkage model. For each of these, the putative source of the recombinant region was determined and the allele was mapped onto a clonalframe genealogy derived from concatenated ST sequences. This enabled the direction and frequency of introgression between the two populations to be established, with 8.3 % of C. coli clade 1 alleles having acquired C. jejuni sequence, compared to 0.5 % for the reciprocal process. Once generated, mosaic genes spread within C. coli clade 1 by a combination of clonal expansion and lateral gene transfer, with some evidence of erosion of the mosaics by reacquisition of C. coli sequence. These observations confirm previous analyses of the exchange of complete housekeeping alleles and extend this work by describing the processes of horizontal gene transfer and subsequent spread within recipient species.

Figures

Fig. 1.
Fig. 1.
Identification of mosaic alleles: cluster analysis using structure inferring the probability-based genetic ancestry for allelic variants of the seven MLST loci (aspAuncA). Each unique allele sequence is represented with vertical lines, divided into two shaded regions indicative of genetic ancestry to C. jejuni (light grey) or C. coli (dark grey). From this information inter-specific recombination between these species can be inferred. Alleles not assigned to a single genetic ancestry (P≥0.95), and with assignment probability ≤0.75, are considered inter-genomic recombinants (r). The analyses were carried out with k=2.
Fig. 2.
Fig. 2.
Distribution of mosaic alleles: consensus trees from clonalframe analysis of concatenated sequences of 275 STs from a combined C. coli and C. jejuni population, including 81 STs containing one or more inter-genomic mosaic alleles. Lines connect the mosaic alleles to the STs in which they occur. Alleles located in (a) closely related and (b) distant clades are indicated in separate trees. Site-by-site nucleotide ancestry, inferred using a linkage model in structure, is given for mosaic alleles describing putative origin within C. jejuni (light grey shading) and C. coli (dark grey shading). Background population structure (k=2) was defined using non-recombinant STs. The number of founding introductions was estimated from shared patterns of mosaicism among alleles and the clustering of mosaic alleles on the tree.
Fig. 3.
Fig. 3.
Major mosaic allele clusters: enlarged clonalframe tree topologies and mosaic allele intra-allelic recombinant regions from the four largest ST clusters containing mosaic alleles of the aspA (a), gltA (b) and tkt [tkt1 (c) and tkt2 (d)] loci. Site-by-site putative nucleotide ancestry is given for the numbered mosaic alleles (C. jejuni, light grey shading, C. coli, dark grey shading), and the approximate terminal positions of recombinant fragments are indicated with broken lines.

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