Bottom Line:
Distributive conjugal transfer (DCT) is a newly described mechanism of lateral gene transfer (LGT) that results in a mosaic transconjugant structure, similar to the products of meiosis.We found that DCT results in transfer of larger chromosomal segments, that these segments are distributed more broadly around the chromosome, and that a greater proportion of the chromosome is affected by DCT than by other mechanisms of LGT.Based on the proportion of recombinant sites, the size of recombinant fragments, their spatial distribution and lack of association with MGE, as well as unidirectionality of DNA transfer, we conclude that DCT is the predominant mechanism of LGT among M. canettii.

Mentions:
In order to investigate bias in the location of recombinant fragments, we divided genomes into windows of 100 kb and calculated the number of recombination events for each window. We find for all bacterial species in our sample that there are more windows with no recombination events than expected if the fragments were placed at randomly selected locations throughout the genome. This suggests that there are genomic regions in which transferred fragments of DNA are infrequently inserted due to impacts on fitness, structural barriers to recombination or other reasons (i.e., recombination “cold spots”) (table 3). We also looked for evidence of recombination “hot spots.” We performed pairwise comparisons of all strains in each data set and calculated the proportion of recombinant regions that were shared. In the presence of hot spots, we expect strains to have more overlapping areas of recombination than observed when fragments are randomly placed. We found evidence of hot spots in all species, relative to a distribution in which recombinant fragments were placed at randomly chosen locations (table 4). This positive spatial bias was less marked in M. canettii and M. smegmatis than in the other species of bacteria. LGT hot spots in Str. pneumoniae, Sta. aureus, and E. faecium are easily observed when recombinant fragments are plotted; they are less evident in data from M. smegmatis and M. canettii (fig. 3 and supplementary fig. S3, Supplementary Material online; Gray et al. 2013). In M. canettii, overlapping fragments tend to be shared between subsets of isolates that cluster together on the phylogeny rather than being shared across all strains.Fig. 3.—

Mentions:
In order to investigate bias in the location of recombinant fragments, we divided genomes into windows of 100 kb and calculated the number of recombination events for each window. We find for all bacterial species in our sample that there are more windows with no recombination events than expected if the fragments were placed at randomly selected locations throughout the genome. This suggests that there are genomic regions in which transferred fragments of DNA are infrequently inserted due to impacts on fitness, structural barriers to recombination or other reasons (i.e., recombination “cold spots”) (table 3). We also looked for evidence of recombination “hot spots.” We performed pairwise comparisons of all strains in each data set and calculated the proportion of recombinant regions that were shared. In the presence of hot spots, we expect strains to have more overlapping areas of recombination than observed when fragments are randomly placed. We found evidence of hot spots in all species, relative to a distribution in which recombinant fragments were placed at randomly chosen locations (table 4). This positive spatial bias was less marked in M. canettii and M. smegmatis than in the other species of bacteria. LGT hot spots in Str. pneumoniae, Sta. aureus, and E. faecium are easily observed when recombinant fragments are plotted; they are less evident in data from M. smegmatis and M. canettii (fig. 3 and supplementary fig. S3, Supplementary Material online; Gray et al. 2013). In M. canettii, overlapping fragments tend to be shared between subsets of isolates that cluster together on the phylogeny rather than being shared across all strains.Fig. 3.—

Bottom Line:
Distributive conjugal transfer (DCT) is a newly described mechanism of lateral gene transfer (LGT) that results in a mosaic transconjugant structure, similar to the products of meiosis.We found that DCT results in transfer of larger chromosomal segments, that these segments are distributed more broadly around the chromosome, and that a greater proportion of the chromosome is affected by DCT than by other mechanisms of LGT.Based on the proportion of recombinant sites, the size of recombinant fragments, their spatial distribution and lack of association with MGE, as well as unidirectionality of DNA transfer, we conclude that DCT is the predominant mechanism of LGT among M. canettii.