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Genomic signatures of distributive conjugal transfer among mycobacteria.

Mortimer TD, Pepperell CS - Genome Biol Evol (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Microbiology Doctoral Training Program, University of Wisconsin-Madison.

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Distribution of recombinant fragments across M. canettii chromosomes. Mycobacterium canettii recombinant fragments identified by BRATNextGen are shown as colored blocks. Genomic positions are in reference to M. canettii STB-A (CIPT 140010059). Mycobacterium canettii strain identifiers in order from outermost circle to innermost circle are STB-A (light blue), STB-D (medium blue), STB-E (dark blue), STB-L (light green), STB-G (dark green), STB-I (light purple), STB-H (dark purple), STB-K (gray), STB-J (black). Thin gray circles divide genomes into groups defined by phylogenetic analysis (supplementary fig. S5, Supplementary Material online). Prior to identification of recombinant fragments, regions prone to homoplasy such as PE/PPE genes and transposons were removed from the alignment. Plot made with Circos (Krzywinski et al. 2009). Recombinant DNA sequences are shared by closely related strains of M. canettii, which suggests that they are maintained in situ by clonal evolution following LGT events. This pattern is distinct from hot spots (see supplementary fig. S4, Supplementary Material online), which are shared across all strains. The frequency of recombination appears to vary among bacterial isolates, with two of the nine isolates (STB-K and STB-J) exhibiting little evidence of LGT.
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evu175-F3: Distribution of recombinant fragments across M. canettii chromosomes. Mycobacterium canettii recombinant fragments identified by BRATNextGen are shown as colored blocks. Genomic positions are in reference to M. canettii STB-A (CIPT 140010059). Mycobacterium canettii strain identifiers in order from outermost circle to innermost circle are STB-A (light blue), STB-D (medium blue), STB-E (dark blue), STB-L (light green), STB-G (dark green), STB-I (light purple), STB-H (dark purple), STB-K (gray), STB-J (black). Thin gray circles divide genomes into groups defined by phylogenetic analysis (supplementary fig. S5, Supplementary Material online). Prior to identification of recombinant fragments, regions prone to homoplasy such as PE/PPE genes and transposons were removed from the alignment. Plot made with Circos (Krzywinski et al. 2009). Recombinant DNA sequences are shared by closely related strains of M. canettii, which suggests that they are maintained in situ by clonal evolution following LGT events. This pattern is distinct from hot spots (see supplementary fig. S4, Supplementary Material online), which are shared across all strains. The frequency of recombination appears to vary among bacterial isolates, with two of the nine isolates (STB-K and STB-J) exhibiting little evidence of LGT.

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.—


Genomic signatures of distributive conjugal transfer among mycobacteria.

Mortimer TD, Pepperell CS - Genome Biol Evol (2014)

Distribution of recombinant fragments across M. canettii chromosomes. Mycobacterium canettii recombinant fragments identified by BRATNextGen are shown as colored blocks. Genomic positions are in reference to M. canettii STB-A (CIPT 140010059). Mycobacterium canettii strain identifiers in order from outermost circle to innermost circle are STB-A (light blue), STB-D (medium blue), STB-E (dark blue), STB-L (light green), STB-G (dark green), STB-I (light purple), STB-H (dark purple), STB-K (gray), STB-J (black). Thin gray circles divide genomes into groups defined by phylogenetic analysis (supplementary fig. S5, Supplementary Material online). Prior to identification of recombinant fragments, regions prone to homoplasy such as PE/PPE genes and transposons were removed from the alignment. Plot made with Circos (Krzywinski et al. 2009). Recombinant DNA sequences are shared by closely related strains of M. canettii, which suggests that they are maintained in situ by clonal evolution following LGT events. This pattern is distinct from hot spots (see supplementary fig. S4, Supplementary Material online), which are shared across all strains. The frequency of recombination appears to vary among bacterial isolates, with two of the nine isolates (STB-K and STB-J) exhibiting little evidence of LGT.
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evu175-F3: Distribution of recombinant fragments across M. canettii chromosomes. Mycobacterium canettii recombinant fragments identified by BRATNextGen are shown as colored blocks. Genomic positions are in reference to M. canettii STB-A (CIPT 140010059). Mycobacterium canettii strain identifiers in order from outermost circle to innermost circle are STB-A (light blue), STB-D (medium blue), STB-E (dark blue), STB-L (light green), STB-G (dark green), STB-I (light purple), STB-H (dark purple), STB-K (gray), STB-J (black). Thin gray circles divide genomes into groups defined by phylogenetic analysis (supplementary fig. S5, Supplementary Material online). Prior to identification of recombinant fragments, regions prone to homoplasy such as PE/PPE genes and transposons were removed from the alignment. Plot made with Circos (Krzywinski et al. 2009). Recombinant DNA sequences are shared by closely related strains of M. canettii, which suggests that they are maintained in situ by clonal evolution following LGT events. This pattern is distinct from hot spots (see supplementary fig. S4, Supplementary Material online), which are shared across all strains. The frequency of recombination appears to vary among bacterial isolates, with two of the nine isolates (STB-K and STB-J) exhibiting little evidence of LGT.
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.

View Article: PubMed Central - PubMed

Affiliation: Department of Medical Microbiology and Immunology, University of Wisconsin-Madison Microbiology Doctoral Training Program, University of Wisconsin-Madison.

Show MeSH
Related in: MedlinePlus