{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:50:40Z","timestamp":1753876240352,"version":"3.41.2"},"reference-count":91,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2023,7,29]],"date-time":"2023-07-29T00:00:00Z","timestamp":1690588800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Evolution experiments with free-living microbes have radically improved our understanding of genome evolution and how microorganisms adapt. Yet there is a paucity of such research focusing on strictly host-associated bacteria, even though they are widespread in nature. Here, we used the Acanthamoeba symbiont Protochlamydia amoebophila, a distant relative of the human pathogen Chlamydia trachomatis and representative of a large group of protist-associated environmental chlamydiae, as a model to study how obligate intracellular symbionts evolve and adapt to elevated temperature, a prerequisite for the pivotal evolutionary leap from protist to endothermic animal hosts. We established 12 replicate populations under two temperatures (20 \u00b0C, 30 \u00b0C) for 510 bacterial generations (38 months). We then used infectivity assays and pooled whole-genome resequencing to identify any evolved phenotypes and the molecular basis of adaptation in these bacteria. We observed an overall reduction in infectivity of the symbionts evolved at 30 \u00b0C, and we identified numerous nonsynonymous mutations and small indels in these symbiont populations, with several variants persisting throughout multiple time points and reaching high frequencies. This suggests that many mutations may have been beneficial and played an adaptive role. Mutated genes within the same temperature regime were more similar than those between temperature regimes. Our results provide insights into the molecular evolution of intracellular bacteria under the constraints of strict host dependance and highly structured populations and suggest that for chlamydial symbionts of protists, temperature adaptation was facilitated through attenuation of symbiont infectivity as a tradeoff to reduce host cell burden.<\/jats:p>","DOI":"10.1093\/gbe\/evad139","type":"journal-article","created":{"date-parts":[[2023,7,29]],"date-time":"2023-07-29T14:26:16Z","timestamp":1690640776000},"source":"Crossref","is-referenced-by-count":3,"title":["Genome Dynamics and Temperature Adaptation During Experimental Evolution of Obligate Intracellular Bacteria"],"prefix":"10.1093","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6715-8924","authenticated-orcid":false,"given":"Paul","family":"Herrera","sequence":"first","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lisa","family":"Schuster","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Markus","family":"Zojer","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hyunsoo","family":"Na","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jasmin","family":"Schwarz","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Wascher","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Kempinger","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Regner","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0592-7791","authenticated-orcid":false,"given":"Thomas","family":"Rattei","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthias","family":"Horn","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,7,29]]},"reference":[{"key":"2023080908200608100_evad139-B1","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1016\/j.femsre.2005.03.002","article-title":"The chlamydial developmental cycle","volume":"29","author":"Abdelrahman","year":"2005","journal-title":"FEMS Microbiol Rev"},{"key":"2023080908200608100_evad139-B2","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1093\/molbev\/msw035","article-title":"Large-effect beneficial synonymous mutations mediate rapid and parallel adaptation in a bacterium","volume":"33","author":"Agashe","year":"2016","journal-title":"Mol Biol Evol"},{"key":"2023080908200608100_evad139-B3","doi-asserted-by":"crossref","first-page":"6053","DOI":"10.1128\/AEM.01503-08","article-title":"High and low temperatures differently affect infection density and vertical transmission of male-killing Spiroplasma symbionts in Drosophila hosts","volume":"74","author":"Anbutsu","year":"2008","journal-title":"Appl Environ Microbiol"},{"key":"2023080908200608100_evad139-B4","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2205856119","article-title":"Defensive symbiosis against giant viruses in amoebae","volume":"119","author":"Arthofer","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023080908200608100_evad139-B5","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1126\/science.1104816","article-title":"Host-bacterial mutualism in the human intestine","volume":"307","author":"B\u00e4ckhed","year":"2005","journal-title":"Science"},{"key":"2023080908200608100_evad139-B6","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/s004300050071","article-title":"Identification and localization of Chlamydia pneumoniae in the Alzheimer's Brain","volume":"187","author":"Balin","year":"1998","journal-title":"Med Microbiol Immunol"},{"key":"2023080908200608100_evad139-B7","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1101\/sqb.2009.74.018","article-title":"Genome-wide mutational diversity in an evolving population of Escherichia coli","volume":"74","author":"Barrick","year":"2009","journal-title":"Cold Spring Harb Symp Quant Biol"},{"key":"2023080908200608100_evad139-B8","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nrg3564","article-title":"Genome dynamics during experimental evolution","volume":"14","author":"Barrick","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2023080908200608100_evad139-B9","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2023080908200608100_evad139-B10","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.meegid.2013.03.035","article-title":"Effect of long-term laboratory propagation on Chlamydia trachomatis genome dynamics","volume":"17","author":"Borges","year":"2013","journal-title":"Infect Genet Evol"},{"key":"2023080908200608100_evad139-B11","doi-asserted-by":"crossref","first-page":"E21","DOI":"10.1371\/journal.pbio.0000021","article-title":"Developmental origin and evolution of bacteriocytes in the aphid-Buchnera symbiosis","volume":"1","author":"Braendle","year":"2003","journal-title":"PLoS Biol"},{"key":"2023080908200608100_evad139-B12","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1093\/genetics\/151.3.921","article-title":"Evolution by small steps and rugged landscapes in the RNA virus phi6","volume":"151","author":"Burch","year":"1999","journal-title":"Genetics"},{"key":"2023080908200608100_evad139-B13","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.idc.2009.10.002","article-title":"Chlamydophila pneumoniae","volume":"24","author":"Burillo","year":"2010","journal-title":"Infect Dis Clin North Am"},{"key":"2023080908200608100_evad139-B14","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/nrmicro796","article-title":"Chlamydia pneumoniae\u2014an infectious risk factor for atherosclerosis?","volume":"2","author":"Campbell","year":"2004","journal-title":"Nat Rev Microbiol"},{"key":"2023080908200608100_evad139-B15","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1016\/j.micinf.2005.12.011","article-title":"Parachlamydia acanthamoebae enters and multiplies within pneumocytes and lung fibroblasts","volume":"8","author":"Casson","year":"2006","journal-title":"Microbes Infect"},{"key":"2023080908200608100_evad139-B16","doi-asserted-by":"crossref","first-page":"eaaw3307","DOI":"10.1126\/sciadv.aaw3307","article-title":"Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex","volume":"5","author":"Chiner-Oms","year":"2019","journal-title":"Sci Adv"},{"key":"2023080908200608100_evad139-B17","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1099\/mic.0.27406-0","article-title":"Recovery of an environmental Chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp","volume":"151","author":"Collingro","year":"2005","journal-title":"Microbiology"},{"key":"2023080908200608100_evad139-B18","doi-asserted-by":"crossref","first-page":"1863","DOI":"10.1099\/ijs.0.63572-0","article-title":"\u2018Candidatus Protochlamydia amoebophila\u2019, an endosymbiont of Acanthamoeba spp","volume":"55","author":"Collingro","year":"2005","journal-title":"Int J Syst Evol Microbiol"},{"key":"2023080908200608100_evad139-B19","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1016\/j.tim.2020.05.020","article-title":"Chlamydiae in the environment","volume":"28","author":"Collingro","year":"2020","journal-title":"Trends Microbiol"},{"key":"2023080908200608100_evad139-B20","doi-asserted-by":"crossref","first-page":"R118","DOI":"10.1186\/gb-2009-10-10-r118","article-title":"Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations","volume":"10","author":"Conrad","year":"2009","journal-title":"Genome Biol"},{"key":"2023080908200608100_evad139-B21","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.vetmic.2011.05.043","article-title":"The Pho regulon and the pathogenesis of Escherichia coli","volume":"153","author":"Cr\u00e9pin","year":"2011","journal-title":"Vet Microbiol."},{"key":"2023080908200608100_evad139-B22","first-page":"73","article-title":"Lymphogranuloma venereum: an old, forgotten re-emerging systemic disease","volume":"56","author":"Dal Conte","year":"2014","journal-title":"Panminerva Med"},{"key":"2023080908200608100_evad139-B23","doi-asserted-by":"crossref","first-page":"E1904","DOI":"10.1073\/pnas.1616132114","article-title":"Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures","volume":"114","author":"Deatherage","year":"2017","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023080908200608100_evad139-B24","doi-asserted-by":"crossref","first-page":"1726","DOI":"10.1128\/JCM.41.4.1726-1729.2003","article-title":"Quantitative detection of Chlamydia psittaci and C. pecorum by high-sensitivity real-time PCR reveals high prevalence of vaginal infection in cattle","volume":"41","author":"DeGraves","year":"2003","journal-title":"J Clin Microbiol"},{"key":"2023080908200608100_evad139-B25","doi-asserted-by":"crossref","first-page":"2725","DOI":"10.1038\/s41396-022-01305-9","article-title":"Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae","volume":"16","author":"Dharamshi","year":"2022","journal-title":"ISME J"},{"key":"2023080908200608100_evad139-B26","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1038\/s41564-022-01284-9","article-title":"Gene gain facilitated endosymbiotic evolution of Chlamydiae","volume":"8","author":"Dharamshi","year":"2023","journal-title":"Nature Microbiol"},{"key":"2023080908200608100_evad139-B27","doi-asserted-by":"crossref","first-page":"7160","DOI":"10.1073\/pnas.88.16.7160","article-title":"A constant rate of spontaneous mutation in DNA-based microbes","volume":"88","author":"Drake","year":"1991","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023080908200608100_evad139-B28","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000520","article-title":"Avoiding dangerous missense: thermophiles display especially low mutation rates","volume":"5","author":"Drake","year":"2009","journal-title":"PLoS Genet"},{"key":"2023080908200608100_evad139-B29","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1128\/jb.151.2.750-755.1982","article-title":"Specific mutator effects of ung (uracil-DNA glycosylase) mutations in Escherichia coli","volume":"151","author":"Duncan","year":"1982","journal-title":"J Bacteriol"},{"key":"2023080908200608100_evad139-B30","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1038\/nrmicro.2016.30","article-title":"Chlamydia cell biology and pathogenesis","volume":"14","author":"Elwell","year":"2016","journal-title":"Nat Rev Microbiol"},{"key":"2023080908200608100_evad139-B31","doi-asserted-by":"crossref","DOI":"10.1111\/cmi.12940","article-title":"Safe haven under constant attack\u2014the Chlamydia-containing vacuole","volume":"20","author":"Fischer","year":"2018","journal-title":"Cell Microbiol"},{"key":"2023080908200608100_evad139-B32","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1101\/gr.3832305","article-title":"Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states","volume":"15","author":"Fong","year":"2005","journal-title":"Genome Res"},{"key":"2023080908200608100_evad139-B33","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1023\/A:1017067816551","article-title":"The fate of competing beneficial mutations in an asexual population","volume":"102\/103","author":"Gerrish","year":"1998","journal-title":"Genetica"},{"key":"2023080908200608100_evad139-B34","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1007\/s10709-005-4012-9","article-title":"Adaptive evolution in a spatially structured asexual population","volume":"127","author":"Gordo","year":"2006","journal-title":"Genetica"},{"key":"2023080908200608100_evad139-B35","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1093\/infdis\/168.5.1231","article-title":"Evidence that Chlamydia pneumoniae causes pneumonia and bronchitis","volume":"168","author":"Grayston","year":"1993","journal-title":"J Infect Dis"},{"key":"2023080908200608100_evad139-B36","doi-asserted-by":"crossref","first-page":"5979","DOI":"10.1128\/IAI.71.10.5979-5985.2003","article-title":"Parachlamydia acanthamoebae enters and multiplies within human macrophages and induces their apoptosis [corrected]","volume":"71","author":"Greub","year":"2003","journal-title":"Infect Immun"},{"key":"2023080908200608100_evad139-B37","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1111\/j.1461-0248.2006.00955.x","article-title":"The effect of population structure on the adaptive radiation of microbial populations evolving in spatially structured environments","volume":"9","author":"Habets","year":"2006","journal-title":"Ecol Lett"},{"key":"2023080908200608100_evad139-B38","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1101\/gr.212647.116","article-title":"Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion","volume":"27","author":"Hadfield","year":"2017","journal-title":"Genome Res"},{"key":"2023080908200608100_evad139-B39","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1146\/annurev.ecolsys.39.110707.173437","article-title":"Spontaneous mutation accumulation studies in evolutionary genetics","volume":"40","author":"Halligan","year":"2009","journal-title":"Ann Rev Ecol Evol Syst"},{"key":"2023080908200608100_evad139-B40","doi-asserted-by":"crossref","first-page":"21658","DOI":"10.1073\/pnas.2005536117","article-title":"Molecular causes of an evolutionary shift along the parasitism\u2013mutualism continuum in a bacterial symbiont","volume":"117","author":"Herrera","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023080908200608100_evad139-B41","doi-asserted-by":"crossref","first-page":"728","DOI":"10.1126\/science.1096330","article-title":"Illuminating the evolutionary history of chlamydiae","volume":"304","author":"Horn","year":"2004","journal-title":"Science"},{"key":"2023080908200608100_evad139-B42","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1146\/annurev.micro.62.081307.162818","article-title":"Chlamydiae as symbionts in eukaryotes","volume":"62","author":"Horn","year":"2008","journal-title":"Annu Rev Microbiol"},{"key":"2023080908200608100_evad139-B43","doi-asserted-by":"crossref","first-page":"D309","DOI":"10.1093\/nar\/gky1085","article-title":"eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses","volume":"47","author":"Huerta-Cepas","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023080908200608100_evad139-B44","doi-asserted-by":"crossref","first-page":"699","DOI":"10.1093\/genetics\/156.2.699","article-title":"Male-killing Wolbachia in Drosophila: a temperature-sensitive trait with a threshold bacterial density","volume":"156","author":"Hurst","year":"2000","journal-title":"Genetics"},{"key":"2023080908200608100_evad139-B45","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/35084545","article-title":"The role of selfish genetic elements in eukaryotic evolution","volume":"2","author":"Hurst","year":"2001","journal-title":"Nat Rev Genet"},{"key":"2023080908200608100_evad139-B46","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1023\/A:1024875232511","article-title":"Excess non-synonymous substitutions suggest that positive selection episodes occurred during the evolution of DNA-binding domains in the Arabidopsis R2R3-MYB gene family","volume":"52","author":"Jia","year":"2003","journal-title":"Plant Mol Biol"},{"key":"2023080908200608100_evad139-B47","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1186\/1471-2180-9-218","article-title":"A novel inhibitor of Chlamydophila pneumoniae protein kinase D (PknD) inhibits phosphorylation of CdsD and suppresses bacterial replication","volume":"9","author":"Johnson","year":"2009","journal-title":"BMC Microbiol"},{"key":"2023080908200608100_evad139-B48","doi-asserted-by":"crossref","first-page":"3933","DOI":"10.1093\/molbev\/mss198","article-title":"Population genomics of Chlamydia trachomatis: insights on drift, selection, recombination, and population structure","volume":"29","author":"Joseph","year":"2012","journal-title":"Mol Biol Evol"},{"key":"2023080908200608100_evad139-B49","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/j.tree.2012.06.001","article-title":"Experimental evolution","volume":"27","author":"Kawecki","year":"2012","journal-title":"Trends Ecol Evol"},{"key":"2023080908200608100_evad139-B50","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1111\/j.1574-695X.2011.00856.x","article-title":"Permissivity of fish cell lines to three Chlamydia-related bacteria: Waddlia chondrophila, Estrella lausannensis and Parachlamydia acanthamoebae","volume":"63","author":"Kebbi-Beghdadi","year":"2011","journal-title":"FEMS Immunol Med Microbiol"},{"key":"2023080908200608100_evad139-B51","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00202-16","article-title":"Biphasic metabolism and host interaction of a chlamydial symbiont","volume":"2","author":"K\u00f6nig","year":"2017","journal-title":"mSystems"},{"key":"2023080908200608100_evad139-B52","doi-asserted-by":"crossref","first-page":"9037","DOI":"10.1073\/pnas.91.19.9037","article-title":"Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat","volume":"91","author":"Korona","year":"1994","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023080908200608100_evad139-B53","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"key":"2023080908200608100_evad139-B54","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.45952","article-title":"The distribution of fitness effects among synonymous mutations in a gene under directional selection","volume":"8","author":"Lebeuf-Taylor","year":"2019","journal-title":"eLife"},{"key":"2023080908200608100_evad139-B55","doi-asserted-by":"crossref","first-page":"4158","DOI":"10.1128\/AEM.00373-10","article-title":"Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a nonnative carbon source, L-1,2-propanediol","volume":"76","author":"Lee","year":"2010","journal-title":"Appl Environ Microbiol"},{"key":"2023080908200608100_evad139-B56","doi-asserted-by":"crossref","first-page":"E2774","DOI":"10.1073\/pnas.1210309109","article-title":"Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing","volume":"109","author":"Lee","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023080908200608100_evad139-B57","doi-asserted-by":"crossref","first-page":"S57","DOI":"10.1086\/691209","article-title":"Convergence and divergence in a long-term experiment with Bacteria","volume":"190","author":"Lenski","year":"2017","journal-title":"Am Nat"},{"key":"2023080908200608100_evad139-B58","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023080908200608100_evad139-B59","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2023080908200608100_evad139-B60","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/S0079-6603(08)60800-4","article-title":"DNA glycosylases, endonucleases for apurinic\/apyrimidinic sites, and base excision-repair","volume":"22","author":"Lindahl","year":"1979","journal-title":"Prog Nucleic Acid Res Mol Biol"},{"key":"2023080908200608100_evad139-B61","doi-asserted-by":"crossref","first-page":"17878","DOI":"10.1073\/pnas.0804445105","article-title":"Whole-genome mutational biases in bacteria","volume":"105","author":"Lind","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023080908200608100_evad139-B62","doi-asserted-by":"crossref","first-page":"1920","DOI":"10.1126\/science.1106442","article-title":"Immunity, inflammation, and allergy in the gut","volume":"307","author":"Macdonald","year":"2005","journal-title":"Science"},{"key":"2023080908200608100_evad139-B63","doi-asserted-by":"crossref","first-page":"3065","DOI":"10.1128\/AAC.46.9.3065-3067.2002","article-title":"Antibiotic susceptibilities of Parachlamydia acanthamoeba in amoebae","volume":"46","author":"Maurin","year":"2002","journal-title":"Antimicrob Agents Chemother"},{"key":"2023080908200608100_evad139-B64","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1126\/science.285.5434.1745","article-title":"Clonal interference and the evolution of RNA viruses","volume":"285","author":"Miralles","year":"1999","journal-title":"Science"},{"key":"2023080908200608100_evad139-B65","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1128\/AEM.71.1.20-28.2005","article-title":"Amoebae as training grounds for intracellular bacterial pathogens","volume":"71","author":"Molmeret","year":"2005","journal-title":"Appl Environ Microbiol"},{"key":"2023080908200608100_evad139-B66","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1146\/annurev.genet.41.110306.130119","article-title":"Genomics and evolution of heritable bacterial symbionts","volume":"42","author":"Moran","year":"2008","journal-title":"Annu Rev Genet"},{"key":"2023080908200608100_evad139-B67","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1111\/1574-6976.12059","article-title":"Chlamydial metabolism revisited: interspecies metabolic variability and developmental stage-specific physiologic activities","volume":"38","author":"Omsland","year":"2014","journal-title":"FEMS Microbiol Rev"},{"key":"2023080908200608100_evad139-B68","doi-asserted-by":"crossref","first-page":"935","DOI":"10.2307\/2411226","article-title":"The population genetics of adaptation: the distribution of factors fixed during adaptive evolution","volume":"52","author":"Orr","year":"1998","journal-title":"Evolution"},{"key":"2023080908200608100_evad139-B69","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2164-12-238","article-title":"Escherichia coli genome-wide promoter analysis: identification of additional AtoC binding target elements","volume":"12","author":"Pilalis","year":"2011","journal-title":"BMC Genomics"},{"key":"2023080908200608100_evad139-B70","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.vetmic.2008.09.034","article-title":"Molecular evidence for chlamydial infections in the eyes of sheep","volume":"135","author":"Polkinghorne","year":"2009","journal-title":"Vet Microbiol"},{"key":"2023080908200608100_evad139-B71","doi-asserted-by":"crossref","first-page":"4081","DOI":"10.1128\/AEM.68.8.4081-4089.2002","article-title":"Detection and differentiation of chlamydiae by fluorescence in situ hybridization","volume":"68","author":"Poppert","year":"2002","journal-title":"Appl Environ Microbiol"},{"key":"2023080908200608100_evad139-B72","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/27900","article-title":"Adaptive radiation in a heterogeneous environment","volume":"394","author":"Rainey","year":"1998","journal-title":"Nature"},{"key":"2023080908200608100_evad139-B73","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nrmicro2112","article-title":"Life on the inside: the intracellular lifestyle of cytosolic bacteria","volume":"7","author":"Ray","year":"2009","journal-title":"Nat Rev Microbiol"},{"volume-title":"R: A language and environment for statistical computing","year":"2019","author":"R Core Team","key":"2023080908200608100_evad139-B74"},{"key":"2023080908200608100_evad139-B75","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1016\/j.tim.2012.10.009","article-title":"Chlamydia pneumoniae: modern insights into an ancient pathogen","volume":"21","author":"Roulis","year":"2013","journal-title":"Trends Microbiol"},{"key":"2023080908200608100_evad139-B76","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1297-9716-42-29","article-title":"Chlamydiaceae infections in pig","volume":"42","author":"Schautteet","year":"2011","journal-title":"Vet Res"},{"key":"2023080908200608100_evad139-B77","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/bioinformatics\/btr026","article-title":"Quality control and preprocessing of metagenomic datasets","volume":"27","author":"Schmieder","year":"2011","journal-title":"Bioinformatics"},{"key":"2023080908200608100_evad139-B78","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1128\/JB.01379-09","article-title":"The genome of the amoeba symbiont \u2018Candidatus Amoebophilus asiaticus\u2019 reveals common mechanisms for host cell interaction among amoeba-associated bacteria","volume":"192","author":"Schmitz-Esser","year":"2010","journal-title":"J Bacteriol"},{"key":"2023080908200608100_evad139-B79","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1016\/j.tcb.2015.01.002","article-title":"Intranuclear bacteria: inside the cellular control center of eukaryotes","volume":"25","author":"Schulz","year":"2015","journal-title":"Trends Cell Biol"},{"key":"2023080908200608100_evad139-B80","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1007\/s00430-010-0162-1","article-title":"Chlamydia pneumoniae infection and Alzheimer's Disease: a connection to remember?","volume":"199","author":"Shima","year":"2010","journal-title":"Med Microbiol Immunol"},{"key":"2023080908200608100_evad139-B81","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0029565","article-title":"Lack of effective anti-apoptotic activities restricts growth of Parachlamydiaceae in insect cells","volume":"7","author":"Sixt","year":"2012","journal-title":"PLoS One"},{"key":"2023080908200608100_evad139-B82","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003553","article-title":"Metabolic features of Protochlamydia amoebophila elementary bodies\u2014a link between activity and infectivity in Chlamydiae","volume":"9","author":"Sixt","year":"2013","journal-title":"PLoS Pathog"},{"key":"2023080908200608100_evad139-B83","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.2002460","article-title":"Ancient bacteria\u2013amoeba relationships and pathogenic animal bacteria","volume":"15","author":"Strassmann","year":"2017","journal-title":"PLoS Biol"},{"key":"2023080908200608100_evad139-B84","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.tplants.2013.10.005","article-title":"Tracing the primordial Chlamydiae: extinct parasites of plants?","volume":"19","author":"Subtil","year":"2014","journal-title":"Trends Plant Sci"},{"key":"2023080908200608100_evad139-B85","doi-asserted-by":"crossref","first-page":"18488","DOI":"10.1073\/pnas.1216223109","article-title":"Drift-barrier hypothesis and mutation-rate evolution","volume":"109","author":"Sung","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023080908200608100_evad139-B86","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/femspd\/ftu009","article-title":"Twenty years of research into Chlamydia-like organisms: a revolution in our understanding of the biology and pathogenicity of members of the phylum Chlamydiae","volume":"73","author":"Taylor-Brown","year":"2015","journal-title":"Pathog Dis"},{"key":"2023080908200608100_evad139-B87","first-page":"429","volume-title":"Chlamydia biology: from genome to disease","author":"Taylor-Brown","year":"2020"},{"key":"2023080908200608100_evad139-B88","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/S1369-5274(03)00054-7","article-title":"Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes","volume":"6","author":"Wagner","year":"2003","journal-title":"Curr Opin Microbiol"},{"key":"2023080908200608100_evad139-B89","doi-asserted-by":"crossref","first-page":"16923","DOI":"10.1038\/srep16923","article-title":"Efficient test and visualization of multi-set intersections","volume":"5","author":"Wang","year":"2015","journal-title":"Sci Rep"},{"key":"2023080908200608100_evad139-B90","doi-asserted-by":"crossref","first-page":"1945","DOI":"10.1016\/S0140-6736(08)60836-3","article-title":"Trachoma","volume":"371","author":"Wright","year":"2008","journal-title":"Lancet"},{"key":"2023080908200608100_evad139-B91","doi-asserted-by":"crossref","first-page":"e2997","DOI":"10.7717\/peerj.2997","article-title":"Variant profiling of evolving prokaryotic populations","volume":"5","author":"Zojer","year":"2017","journal-title":"Peer J"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gbe\/advance-article-pdf\/doi\/10.1093\/gbe\/evad139\/51004648\/evad139.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/15\/8\/evad139\/51045598\/evad139.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/15\/8\/evad139\/51045598\/evad139.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,9]],"date-time":"2023-08-09T08:21:25Z","timestamp":1691569285000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/doi\/10.1093\/gbe\/evad139\/7233596"}},"subtitle":[],"editor":[{"given":"Laura","family":"Eme","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,7,29]]},"references-count":91,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2023,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evad139","relation":{},"ISSN":["1759-6653"],"issn-type":[{"type":"electronic","value":"1759-6653"}],"subject":[],"published-other":{"date-parts":[[2023,8]]},"published":{"date-parts":[[2023,7,29]]},"article-number":"evad139"}}