Dataset Information

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

ABSTRACT: Chlamydia trachomatis is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the history of the species comprises two phases, and conclude that the currently circulating lineages are the result of evolution in different genomic ecotypes. Temporal analysis indicates these lineages have recently expanded in the space of thousands of years, rather than the millions of years as previously thought, a finding that dramatically changes our understanding of this pathogen's history. Finally, at a time when almost every pathogen is becoming increasingly resistant to antimicrobials, we show that there is no evidence of circulating genomic resistance in C. trachomatis.

SUBMITTER: Hadfield J

PROVIDER: S-EPMC5495073 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Comprehensive global genome dynamics of <i>Chlamydia trachomatis</i> show ancient diversification followed by contemporary mixing and recent lineage expansion.

Hadfield James J Harris Simon R SR Seth-Smith Helena M B HMB Parmar Surendra S Andersson Patiyan P Giffard Philip M PM Schachter Julius J Moncada Jeanne J Ellison Louise L Vaulet María Lucía Gallo MLG Fermepin Marcelo Rodríguez MR Radebe Frans F Mendoza Suyapa S Ouburg Sander S Morré Servaas A SA Sachse Konrad K Puolakkainen Mirja M Korhonen Suvi J SJ Sonnex Chris C Wiggins Rebecca R Jalal Hamid H Brunelli Tamara T Casprini Patrizia P Pitt Rachel R Ison Cathy C Savicheva Alevtina A Shipitsyna Elena E Hadad Ronza R Kari Laszlo L Burton Matthew J MJ Mabey David D Solomon Anthony W AW Lewis David D Marsh Peter P Unemo Magnus M Clarke Ian N IN Parkhill Julian J Thomson Nicholas R NR

Genome research 20170606 7

<i>Chlamydia trachomatis</i> is the world's most prevalent bacterial sexually transmitted infection and leading infectious cause of blindness, yet it is one of the least understood human pathogens, in part due to the difficulties of in vitro culturing and the lack of available tools for genetic manipulation. Genome sequencing has reinvigorated this field, shedding light on the contemporary history of this pathogen. Here, we analyze 563 full genomes, 455 of which are novel, to show that the histo ...[more]

PMID: 28588068

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Project description:BackgroundThe evolution and origin of cave organisms is a recurring issue in evolutionary studies, but analyses are often hindered by the inaccessibility of caves, morphological convergence, and complex colonization processes. Here we investigated the evolutionary history of Nesticella cave spiders, which are mainly distributed in the Yunnan-Guizhou Plateau, China. With comprehensive sampling and phylogenetic and coalescent-based analyses, we investigated the tempo and mode of diversification and the origins of these troglobites. We also aimed to determine which factors have influenced the diversification of this little-known group.ResultsCoalescent-based species delimitation validated the 18 species recognized by morphological inspection and also suggested the existence of cryptic lineages. Divergence time estimates suggested that Nesticella cave spiders in the Yunnan-Guizhou Plateau constituted a monophyletic troglobite clade that originated in the middle Miocene (11.1-18.6 Ma). Although the Yunnan-Guizhou Plateau clade was composed exclusively of troglobite species, suggesting an ancient common subterranean ancestor, we favor multiple, independent cave colonizations during the Pleistocene over a single ancient cave colonization event to explain the origin of these cave faunas. The diversification of plateau Nesticella has been greatly influenced by the sequential uplift of the plateau and likely reflects multiple cave colonizations over time by epigean ancestors during Pleistocene glacial advances.ConclusionsWe concluded that plateau cave Nesticella represent an ancient group of spiders, but with young troglobite lineages that invaded caves only recently. The absence of extant epigean relatives and nearly complete isolation among caves supported their relict status. Our work highlights the importance of comprehensive sampling for studies of subterranean diversity and the evolution of cave organisms. The existence of potentially cryptic species and the relict status of Nesticella highlight the need to conserve these cave spiders.

Dataset Information

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion.

Publications

Comprehensive global genome dynamics of <i>Chlamydia trachomatis</i> show ancient diversification followed by contemporary mixing and recent lineage expansion.

Similar Datasets

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