Interplay of recombination and selection in the genomes of <it>Chlamydia trachomatis</it>
<p>Abstract</p> <p>Background</p> <p><it>Chlamydia trachomatis </it>is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published <it...
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| Format: | Article |
| Language: | English |
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BMC
2011-05-01
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| Series: | Biology Direct |
| Online Access: | http://www.biology-direct.com/content/6/1/28 |
| _version_ | 1818569540634673152 |
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| author | Dean Deborah Gandhi Khanjan Didelot Xavier Joseph Sandeep J Read Timothy D |
| author_facet | Dean Deborah Gandhi Khanjan Didelot Xavier Joseph Sandeep J Read Timothy D |
| author_sort | Dean Deborah |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Chlamydia trachomatis </it>is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published <it>C. trachomatis </it>genomes to assess the contribution of recombination and selection in this pathogen and to understand the major evolutionary forces acting on the genome of this bacterium.</p> <p>Results</p> <p>The conserved core genes of <it>C. trachomatis </it>are a large proportion of the pan-genome: we identified 836 core genes in <it>C. trachomatis </it>out of a range of 874-927 total genes in each genome. The ratio of recombination events compared to mutation (ρ/θ) was 0.07 based on ancestral reconstructions using the ClonalFrame tool, but recombination had a significant effect on genetic diversification (r/m = 0.71). The distance-dependent decay of linkage disequilibrium also indicated that <it>C. trachomatis </it>populations behaved intermediately between sexual and clonal extremes. Fifty-five genes were identified as having a history of recombination and 92 were under positive selection based on statistical tests. Twenty-three genes showed evidence of being under both positive selection and recombination, which included genes with a known role in virulence and pathogencity (e.g., <it>ompA, pmps, tarp</it>). Analysis of inter-clade recombination flux indicated non-uniform currents of recombination between clades, which suggests the possibility of spatial population structure in <it>C. trachomatis </it>infections.</p> <p>Conclusions</p> <p><it>C. trachomatis </it>is the archetype of a bacterial species where recombination is relatively frequent yet gene gains by horizontal gene transfer (HGT) and losses (by deletion) are rare. Gene conversion occurs at sites across the whole <it>C. trachomatis </it>genome but may be more often fixed in genes that are under diversifying selection. Furthermore, genome sequencing will reveal patterns of serotype specific gene exchange and selection that will generate important research questions for understanding <it>C. trachomatis </it>pathogenesis.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Jeremy Selengut, Dr. Lee S. Katz (nominated by Dr. I. King Jordan) and Dr. Arcady Mushegian.</p> |
| first_indexed | 2024-12-14T06:49:22Z |
| format | Article |
| id | doaj.art-1c8c5e09dda84c4291f8c7a64e5ed56a |
| institution | Directory Open Access Journal |
| issn | 1745-6150 |
| language | English |
| last_indexed | 2024-12-14T06:49:22Z |
| publishDate | 2011-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Biology Direct |
| spelling | doaj.art-1c8c5e09dda84c4291f8c7a64e5ed56a2022-12-21T23:12:56ZengBMCBiology Direct1745-61502011-05-01612810.1186/1745-6150-6-28Interplay of recombination and selection in the genomes of <it>Chlamydia trachomatis</it>Dean DeborahGandhi KhanjanDidelot XavierJoseph Sandeep JRead Timothy D<p>Abstract</p> <p>Background</p> <p><it>Chlamydia trachomatis </it>is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published <it>C. trachomatis </it>genomes to assess the contribution of recombination and selection in this pathogen and to understand the major evolutionary forces acting on the genome of this bacterium.</p> <p>Results</p> <p>The conserved core genes of <it>C. trachomatis </it>are a large proportion of the pan-genome: we identified 836 core genes in <it>C. trachomatis </it>out of a range of 874-927 total genes in each genome. The ratio of recombination events compared to mutation (ρ/θ) was 0.07 based on ancestral reconstructions using the ClonalFrame tool, but recombination had a significant effect on genetic diversification (r/m = 0.71). The distance-dependent decay of linkage disequilibrium also indicated that <it>C. trachomatis </it>populations behaved intermediately between sexual and clonal extremes. Fifty-five genes were identified as having a history of recombination and 92 were under positive selection based on statistical tests. Twenty-three genes showed evidence of being under both positive selection and recombination, which included genes with a known role in virulence and pathogencity (e.g., <it>ompA, pmps, tarp</it>). Analysis of inter-clade recombination flux indicated non-uniform currents of recombination between clades, which suggests the possibility of spatial population structure in <it>C. trachomatis </it>infections.</p> <p>Conclusions</p> <p><it>C. trachomatis </it>is the archetype of a bacterial species where recombination is relatively frequent yet gene gains by horizontal gene transfer (HGT) and losses (by deletion) are rare. Gene conversion occurs at sites across the whole <it>C. trachomatis </it>genome but may be more often fixed in genes that are under diversifying selection. Furthermore, genome sequencing will reveal patterns of serotype specific gene exchange and selection that will generate important research questions for understanding <it>C. trachomatis </it>pathogenesis.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Jeremy Selengut, Dr. Lee S. Katz (nominated by Dr. I. King Jordan) and Dr. Arcady Mushegian.</p>http://www.biology-direct.com/content/6/1/28 |
| spellingShingle | Dean Deborah Gandhi Khanjan Didelot Xavier Joseph Sandeep J Read Timothy D Interplay of recombination and selection in the genomes of <it>Chlamydia trachomatis</it> Biology Direct |
| title | Interplay of recombination and selection in the genomes of <it>Chlamydia trachomatis</it> |
| title_full | Interplay of recombination and selection in the genomes of <it>Chlamydia trachomatis</it> |
| title_fullStr | Interplay of recombination and selection in the genomes of <it>Chlamydia trachomatis</it> |
| title_full_unstemmed | Interplay of recombination and selection in the genomes of <it>Chlamydia trachomatis</it> |
| title_short | Interplay of recombination and selection in the genomes of <it>Chlamydia trachomatis</it> |
| title_sort | interplay of recombination and selection in the genomes of it chlamydia trachomatis it |
| url | http://www.biology-direct.com/content/6/1/28 |
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