{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T13:18:57Z","timestamp":1762521537685},"reference-count":88,"publisher":"American Society for Microbiology","issue":"22","license":[{"start":{"date-parts":[[2012,11,15]],"date-time":"2012-11-15T00:00:00Z","timestamp":1352937600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Bacteriol"],"published-print":{"date-parts":[[2012,11,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            On behalf of the host-pathogen \u201carms race,\u201d a cutting-edge approach for elucidating genotype-phenotype relationships relies on the identification of positively selected loci involved in pathoadaptation. We studied the obligate intracellular bacterium\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Chlamydia trachomatis<\/jats:named-content>\n            , for which same-species strains display a nearly identical core and pan genome, while presenting a wide range of tissue tropism and ecological success. We sought to evaluate the evolutionary patterns underlying species separation (divergence) and\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">C. trachomatis<\/jats:named-content>\n            serovar radiation (polymorphism) and to establish genotype-phenotype associations. By analyzing 60\n            <jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Chlamydia<\/jats:named-content>\n            strains, we detected traces of Muller's ratchet as a result of speciation and identified positively selected genes and codons hypothetically involved in the infection of different human cell types (e.g., columnar epithelial cells of ocular or genital mucosae and mononuclear phagocytes) and also events likely driving pathogenic and ecological success dissimilarities. In general, these genes code for proteins involved in immune response elicitation, proteolysis, and the subversion of host-cell functions, and also for proteins with unknown function(s). Several genes are potentially involved in more than one adaptive process, suggesting multiple functions or a distinct\n            <jats:italic>modus operandi<\/jats:italic>\n            for a specific function, and thus should be considered as crucial research targets. In addition, six of the nine genes encoding the putative antigen\/adhesin polymorphic membrane proteins seem to be under positive selection along specific serovars, which sustains an essential biological role of this extra-large paralogue family in chlamydial pathobiology. This study provides insight into how evolutionary inferences illuminate ecological processes such as adaptation to different niches, pathogenicity, or ecological success driven by arms races.\n          <\/jats:p>","DOI":"10.1128\/jb.01291-12","type":"journal-article","created":{"date-parts":[[2012,9,8]],"date-time":"2012-09-08T04:02:48Z","timestamp":1347076968000},"page":"6143-6153","update-policy":"http:\/\/dx.doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":43,"title":["Directional Evolution of Chlamydia trachomatis towards Niche-Specific Adaptation"],"prefix":"10.1128","volume":"194","author":[{"given":"V\u00edtor","family":"Borges","sequence":"first","affiliation":[{"name":"Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal"}]},{"given":"Alexandra","family":"Nunes","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal"}]},{"given":"Rita","family":"Ferreira","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal"}]},{"given":"Maria J.","family":"Borrego","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal"}]},{"given":"Jo\u00e3o P.","family":"Gomes","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-9-2"},{"key":"e_1_3_3_3_2","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1073\/pnas.93.2.906","article-title":"Muller's ratchet decreases fitness of a DNA-based microbe","volume":"93","author":"Andersson DI","year":"1996","unstructured":"AnderssonDI HughesD. 1996. 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