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Contrary to what is known for other bacteria, for the obligate intracellular human pathogen Chlamydia trachomatis, the knowledge of the molecular basis underlying serovars\u2019 tissue specificity is scarce. We examined all ~900 genes to evaluate the association between individual phylogenies and cell-appetence or ecological success of C. trachomatis strains. Only ~1% of the genes presented a tree topology showing the segregation of all three disease groups (ocular, urogenital, and lymphatic) into three well-supported clades. Approximately 28% of the genes, which include the majority of the genes encoding putative type III secretion system effectors and Inc proteins, present a phylogenetic tree where only lymphogranuloma venereum strains form a clade. Similarly, an exclusive phylogenetic segregation of the most prevalent genital serovars was observed for 61 proteins. Curiously, these serovars are phylogenetically cosegregated with the lymphogranuloma venereum serovars for ~20% of the genes. Some clade-specific pseudogenes were identified (novel findings include the conserved hypothetical protein CT037 and the predicted \u03b1-hemolysin CT473), suggesting their putative expendability for the infection of particular niches. Approximately 3.5% of the genes revealed a significant overrepresentation of nonsynonymous mutations, and the majority encode proteins that directly interact with the host. Overall, this in silico scrutiny of genes whose phylogeny is congruent with clinical prevalence or tissue specificity of C. trachomatis strains may constitute an important database of putative targets for future functional studies to evaluate their biological role in chlamydial infections.<\/jats:p>","DOI":"10.1534\/g3.114.015354","type":"journal-article","created":{"date-parts":[[2017,1,25]],"date-time":"2017-01-25T19:50:18Z","timestamp":1485373818000},"page":"9-19","source":"Crossref","is-referenced-by-count":15,"title":["<i>In Silico<\/i>Scrutiny of Genes Revealing Phylogenetic Congruence with Clinical Prevalence or Tropism Properties of<i>Chlamydia trachomatis<\/i>Strains"],"prefix":"10.1093","volume":"5","author":[{"given":"Rita","family":"Ferreira","sequence":"first","affiliation":[{"name":"Reference Laboratory of Sexually Transmitted Bacterial Infections, Department of Infectious Diseases, National Institute of Health, Av. 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