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A high-resolution view of genome-wide pneumococcal transformation.

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD - PLoS Pathog. (2012)

Bottom Line: Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes.However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA.The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1).

View Article: PubMed Central - PubMed

Affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. nc3@sanger.ac.uk

ABSTRACT
Transformation is an important mechanism of microbial evolution through which bacteria have been observed to rapidly adapt in response to clinical interventions; examples include facilitating vaccine evasion and the development of penicillin resistance in the major respiratory pathogen Streptococcus pneumoniae. To characterise the process in detail, the genomes of 124 S. pneumoniae isolates produced through in vitro transformation were sequenced and recombination events detected. Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes. However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA. The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1). This distribution of recombination sizes, coupled with an observed under representation of large insertions within transferred sequence, suggests transformation has the potential to reduce the size of bacterial genomes, and is unlikely to act as an efficient mechanism for the uptake of accessory genomic loci.

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Related in: MedlinePlus

Distribution of secondary recombinations with respect to sequence divergence between the donor and recipient strains.The red line represents the proportion of non-overlapping windows of the recipient sequence, containing at least one marker SNP, that have a mean SNP sequence identity of, or greater than, the threshold marked on the x axis. The blue line represents the same statistic for the subset of windows that overlap with at least one detected secondary RSS. The two lines are very similar, suggesting that recombinations are not concentrated in a subset of windows that have a relatively high level of sequence identity between the donor and recipient. A hypergeometric test for enrichment of recombinations in windows with high levels of sequence similarity was performed at 0.1% intervals; the calculated p values are displayed as a black dashed line relative to the y axis on the right side, confirming the lack of a significant relationship.
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ppat-1002745-g005: Distribution of secondary recombinations with respect to sequence divergence between the donor and recipient strains.The red line represents the proportion of non-overlapping windows of the recipient sequence, containing at least one marker SNP, that have a mean SNP sequence identity of, or greater than, the threshold marked on the x axis. The blue line represents the same statistic for the subset of windows that overlap with at least one detected secondary RSS. The two lines are very similar, suggesting that recombinations are not concentrated in a subset of windows that have a relatively high level of sequence identity between the donor and recipient. A hypergeometric test for enrichment of recombinations in windows with high levels of sequence similarity was performed at 0.1% intervals; the calculated p values are displayed as a black dashed line relative to the y axis on the right side, confirming the lack of a significant relationship.

Mentions: Being distributed around the chromosome, the secondary RSSs provided an opportunity to test whether sequence similarity between the donor and recipient affects the positioning of genetic exchanges in this system. Dividing the entire recipient genome into 1,000 equally-sized non-overlapping windows produced 890 outside the primary locus that were found to contain at least one marker SNP, and therefore had the potential to contain a detectable recombination. Comparing the distribution of mean SNP sequence identities (calculated using 50 bp of aligned sequence on each side) of all such windows against the subset of 168 that were found to overlap with secondary RSSs (Figure 5) provided no evidence for the enrichment of imported sequence in regions of the genome with greater sequence identity between donor and recipient. A ‘walking hypergeometric test’ performed at different sequence identity thresholds confirmed the absence of a statistically significant relationship, which concurred with a more detailed sliding window analysis (see Text S1).


A high-resolution view of genome-wide pneumococcal transformation.

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD - PLoS Pathog. (2012)

Distribution of secondary recombinations with respect to sequence divergence between the donor and recipient strains.The red line represents the proportion of non-overlapping windows of the recipient sequence, containing at least one marker SNP, that have a mean SNP sequence identity of, or greater than, the threshold marked on the x axis. The blue line represents the same statistic for the subset of windows that overlap with at least one detected secondary RSS. The two lines are very similar, suggesting that recombinations are not concentrated in a subset of windows that have a relatively high level of sequence identity between the donor and recipient. A hypergeometric test for enrichment of recombinations in windows with high levels of sequence similarity was performed at 0.1% intervals; the calculated p values are displayed as a black dashed line relative to the y axis on the right side, confirming the lack of a significant relationship.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3375284&req=5

ppat-1002745-g005: Distribution of secondary recombinations with respect to sequence divergence between the donor and recipient strains.The red line represents the proportion of non-overlapping windows of the recipient sequence, containing at least one marker SNP, that have a mean SNP sequence identity of, or greater than, the threshold marked on the x axis. The blue line represents the same statistic for the subset of windows that overlap with at least one detected secondary RSS. The two lines are very similar, suggesting that recombinations are not concentrated in a subset of windows that have a relatively high level of sequence identity between the donor and recipient. A hypergeometric test for enrichment of recombinations in windows with high levels of sequence similarity was performed at 0.1% intervals; the calculated p values are displayed as a black dashed line relative to the y axis on the right side, confirming the lack of a significant relationship.
Mentions: Being distributed around the chromosome, the secondary RSSs provided an opportunity to test whether sequence similarity between the donor and recipient affects the positioning of genetic exchanges in this system. Dividing the entire recipient genome into 1,000 equally-sized non-overlapping windows produced 890 outside the primary locus that were found to contain at least one marker SNP, and therefore had the potential to contain a detectable recombination. Comparing the distribution of mean SNP sequence identities (calculated using 50 bp of aligned sequence on each side) of all such windows against the subset of 168 that were found to overlap with secondary RSSs (Figure 5) provided no evidence for the enrichment of imported sequence in regions of the genome with greater sequence identity between donor and recipient. A ‘walking hypergeometric test’ performed at different sequence identity thresholds confirmed the absence of a statistically significant relationship, which concurred with a more detailed sliding window analysis (see Text S1).

Bottom Line: Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes.However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA.The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1).

View Article: PubMed Central - PubMed

Affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. nc3@sanger.ac.uk

ABSTRACT
Transformation is an important mechanism of microbial evolution through which bacteria have been observed to rapidly adapt in response to clinical interventions; examples include facilitating vaccine evasion and the development of penicillin resistance in the major respiratory pathogen Streptococcus pneumoniae. To characterise the process in detail, the genomes of 124 S. pneumoniae isolates produced through in vitro transformation were sequenced and recombination events detected. Those recombinations importing the selected marker were independent of unselected events elsewhere in the genome, the positions of which were not significantly affected by local sequence similarity between donor and recipient or mismatch repair processes. However, both types of recombinations were sometimes mosaic, with multiple non-contiguous segments originating from the same molecule of donor DNA. The lengths of the unselected events were exponentially distributed with a mean of 2.3 kb, implying that recombinations are stochastically resolved with a fixed per base probability of 4.4×10(-4) bp(-1). This distribution of recombination sizes, coupled with an observed under representation of large insertions within transferred sequence, suggests transformation has the potential to reduce the size of bacterial genomes, and is unlikely to act as an efficient mechanism for the uptake of accessory genomic loci.

Show MeSH
Related in: MedlinePlus