{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T02:02:52Z","timestamp":1776996172240,"version":"3.51.4"},"reference-count":82,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2023,8,24]],"date-time":"2023-08-24T00:00:00Z","timestamp":1692835200000},"content-version":"vor","delay-in-days":23,"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><jats:p>Chlamydiae like Chlamydia trachomatis and Chlamydia psittaci are well-known human and animal pathogens. Yet, the chlamydiae are a much larger group of evolutionary ancient obligate intracellular bacteria that includes predominantly symbionts of protists and diverse animals. This makes them ideal model organisms to study evolutionary transitions from symbionts in microbial eukaryotes to pathogens of humans. To this end, comparative genome analysis has served as an important tool. Genome sequence data for many chlamydial lineages are, however, still lacking, hampering our understanding of their evolutionary history. Here, we determined the first high-quality draft genome sequence of the fish pathogen \u201cCandidatus Clavichlamydia salmonicola\u201d, representing a separate genus within the human and animal pathogenic Chlamydiaceae. The \u201cCa. Clavichlamydia salmonicola\u201d genome harbors genes that so far have been exclusively found in Chlamydia species suggesting that basic mechanisms important for the interaction with chordate hosts have evolved stepwise in the history of chlamydiae. Thus, the genome sequence of \u201cCa. Clavichlamydia salmonicola\u201d allows to constrain candidate genes to further understand the evolution of chlamydial virulence mechanisms required to infect mammals.<\/jats:p>","DOI":"10.1093\/gbe\/evad147","type":"journal-article","created":{"date-parts":[[2023,8,22]],"date-time":"2023-08-22T14:50:53Z","timestamp":1692715853000},"source":"Crossref","is-referenced-by-count":10,"title":["The Fish Pathogen \u201c<i>Candidatus<\/i>Clavichlamydia salmonicola\u201d\u2014A Missing Link in the Evolution of Chlamydial Pathogens of Humans"],"prefix":"10.1093","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4100-832X","authenticated-orcid":false,"given":"Astrid","family":"Collingro","sequence":"first","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6710-7572","authenticated-orcid":false,"given":"Stephan","family":"K\u00f6stlbacher","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"},{"name":"Doctoral School in Microbiology and Environmental Science, University of Vienna , Vienna , Austria"},{"name":"Laboratory of Microbiology, Wageningen University and Research , Wageningen , The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Siegl","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elena R","family":"Toenshoff","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"},{"name":"Institute of Molecular Biology and Biophysics, Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich (ETH) , Z\u00fcrich , Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederik","family":"Schulz","sequence":"additional","affiliation":[{"name":"Centre for Microbiology and Environmental Systems Science, University of Vienna , Vienna , Austria"},{"name":"DOE Joint Genome Institute , Berkeley, California , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Susan O","family":"Mitchell","sequence":"additional","affiliation":[{"name":"FishVet Group Ireland , Oranmore, Co. Galway , Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Weinmaier","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":"Duncan J","family":"Colquhoun","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Bergen , Bergen , Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8309-5855","authenticated-orcid":false,"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":[[2023,8,24]]},"reference":[{"key":"2023082414015820400_evad147-B1","doi-asserted-by":"crossref","first-page":"D373","DOI":"10.1093\/nar\/gkaa1007","article-title":"OMA Orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more","volume":"49","author":"Altenhoff","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023082414015820400_evad147-B2","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J Comput Biol"},{"key":"2023082414015820400_evad147-B3","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1111\/tbed.12908","article-title":"Epitheliocystis in fish: an emerging aquaculture disease with a global impact","volume":"65","author":"Blandford","year":"2018","journal-title":"Transbound Emerg Dis"},{"key":"2023082414015820400_evad147-B4","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1177\/0300985817751218","article-title":"Chlamydial diseases in animals: still a challenge for pathologists?","volume":"55","author":"Borel","year":"2018","journal-title":"Vet Pathol"},{"key":"2023082414015820400_evad147-B5","doi-asserted-by":"crossref","first-page":"9","DOI":"10.3354\/dao004009","article-title":"Epitheliocystis associated with massive mortalities of cultured lake trout Saivelinus namaycush","volume":"4","author":"Bradley","year":"1988","journal-title":"Dis Aquat Organ"},{"key":"2023082414015820400_evad147-B6","doi-asserted-by":"crossref","first-page":"e0210403","DOI":"10.1371\/journal.pone.0210403","article-title":"CPN0572, the C. pneumoniae ortholog of TarP, reorganizes the actin cytoskeleton via a newly identified F-actin binding domain and recruitment of vinculin","volume":"14","author":"Braun","year":"2019","journal-title":"PLoS One"},{"key":"2023082414015820400_evad147-B7","doi-asserted-by":"crossref","first-page":"414","DOI":"10.15698\/mic2019.09.691","article-title":"The multiple functions of the numerous Chlamydia trachomatis secreted proteins: the tip of the iceberg","volume":"6","author":"Bugalh\u00e3o","year":"2019","journal-title":"Microb Cell."},{"key":"2023082414015820400_evad147-B8","doi-asserted-by":"crossref","first-page":"e99315","DOI":"10.1371\/journal.pone.0099315","article-title":"Chlamydia pneumoniae CopD translocator protein plays a critical role in type III secretion (T3S) and infection","volume":"9","author":"Bulir","year":"2014","journal-title":"PLoS One"},{"key":"2023082414015820400_evad147-B9","author":"Bushnell"},{"key":"2023082414015820400_evad147-B10","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"key":"2023082414015820400_evad147-B11","doi-asserted-by":"crossref","first-page":"90","DOI":"10.3390\/ijms21010090","article-title":"Pathogenic puppetry: manipulation of the host actin cytoskeleton by Chlamydia trachomatis","volume":"21","author":"Caven","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2023082414015820400_evad147-B12","doi-asserted-by":"crossref","first-page":"21406","DOI":"10.1038\/s41598-022-25786-y","article-title":"Chlamydia trachomatis suppresses host cell store-operated Ca2 + entry and inhibits NFAT\/calcineurin signaling","volume":"12:","author":"Chamberlain","year":"2022","journal-title":"Sci Rep"},{"key":"2023082414015820400_evad147-B13","doi-asserted-by":"crossref","DOI":"10.1101\/2022.07.11.499243","article-title":"CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","author":"Chklovski","year":"2022"},{"key":"2023082414015820400_evad147-B14","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":"2023082414015820400_evad147-B15","doi-asserted-by":"crossref","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"Upsetr: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"2023082414015820400_evad147-B16","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.1016\/j.cub.2020.02.016","article-title":"Marine sediments illuminate chlamydiae diversity and evolution","volume":"30","author":"Dharamshi","year":"2020","journal-title":"Curr Biol"},{"key":"2023082414015820400_evad147-B17","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":"2023082414015820400_evad147-B18","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":"Nat Microbiol"},{"key":"2023082414015820400_evad147-B19","doi-asserted-by":"crossref","first-page":"ftaa035","DOI":"10.1093\/femspd\/ftaa035","article-title":"Comprehensive genome analysis and comparisons of the swine pathogen, Chlamydia suis reveals unique ORFs and candidate host-specificity factors","volume":"79","author":"Dimond","year":"2021","journal-title":"Pathog Dis"},{"key":"2023082414015820400_evad147-B20","doi-asserted-by":"crossref","first-page":"2890","DOI":"10.1093\/molbev\/msu227","article-title":"Massive expansion of ubiquitination-related gene families within the Chlamydiae","volume":"31","author":"Domman","year":"2014","journal-title":"Mol Biol Evol"},{"key":"2023082414015820400_evad147-B21","first-page":"3035","article-title":"Following the footsteps of chlamydial gene regulation","volume":"32","author":"Domman","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2023082414015820400_evad147-B22","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":"2023082414015820400_evad147-B23","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"Orthofinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol"},{"key":"2023082414015820400_evad147-B24","doi-asserted-by":"crossref","first-page":"e74535","DOI":"10.7554\/eLife.74535","article-title":"Phosphoregulation accommodates type III secretion and assembly of a tether of ER-Chlamydia inclusion membrane contact sites","volume":"11","author":"Ende","year":"2022","journal-title":"Elife"},{"key":"2023082414015820400_evad147-B25","doi-asserted-by":"crossref","DOI":"10.1128\/IAI.00841-19","article-title":"Fluorescence-reported allelic exchange mutagenesis-mediated gene deletion indicates a requirement for Chlamydia trachomatis TarP during in vivo infectivity and reveals a specific role for the C terminus during cellular invasion","author":"Ghosh","year":"2020"},{"key":"2023082414015820400_evad147-B26","doi-asserted-by":"crossref","first-page":"2329","DOI":"10.3389\/fmicb.2019.02329","article-title":"Chlamydial infection from outside to inside","volume":"10","author":"Gitsels","year":"2019","journal-title":"Front Microbiol"},{"key":"2023082414015820400_evad147-B27","doi-asserted-by":"crossref","first-page":"131","DOI":"10.3389\/fphys.2016.00131","article-title":"Epitheliocystis distribution and characterization in brown trout (Salmo trutta) from the headwaters of two major European rivers, the Rhine and Rhone","volume":"7","author":"Guevara Soto","year":"2016","journal-title":"Front Physiol"},{"key":"2023082414015820400_evad147-B28","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1007\/s00203-016-1192-x","article-title":"The emergence of epitheliocystis in the upper Rhone region: evidence for Chlamydiae in wild and farmed salmonid populations","volume":"198","author":"Guevara Soto","year":"2016","journal-title":"Arch Microbiol"},{"key":"2023082414015820400_evad147-B29","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1111\/jfd.12562","article-title":"Investigations into the temporal development of epitheliocystis infections in brown trout: a histological study","volume":"40","author":"Guevara Soto","year":"2017","journal-title":"J Fish Dis"},{"key":"2023082414015820400_evad147-B30","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1093\/sysbio\/syq010","article-title":"New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0","volume":"59","author":"Guindon","year":"2010","journal-title":"Syst Biol"},{"key":"2023082414015820400_evad147-B31","doi-asserted-by":"crossref","first-page":"2334","DOI":"10.1093\/bioinformatics\/btq413","article-title":"Genoplotr: comparative gene and genome visualization in R","volume":"26","author":"Guy","year":"2010","journal-title":"Bioinformatics"},{"key":"2023082414015820400_evad147-B32","doi-asserted-by":"crossref","first-page":"26784","DOI":"10.1073\/pnas.2005389117","article-title":"The Chlamydia effector CT622\/TaiP targets a nonautophagy related function of ATG16L1","volume":"117","author":"Hamaoui","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023082414015820400_evad147-B33","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: improving the ultrafast bootstrap approximation","volume":"35","author":"Hoang","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2023082414015820400_evad147-B34","doi-asserted-by":"crossref","first-page":"899","DOI":"10.3390\/pathogens9110899","article-title":"Comparative genome analysis of 33 chlamydia strains reveals characteristic features of Chlamydia psittaci and closely related species","volume":"9","author":"H\u00f6lzer","year":"2020","journal-title":"Pathogens"},{"key":"2023082414015820400_evad147-B35","doi-asserted-by":"crossref","first-page":"15599","DOI":"10.1073\/pnas.0603044103","article-title":"Chlamydial TarP is a bacterial nucleator of actin","volume":"103","author":"Jewett","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023082414015820400_evad147-B36","doi-asserted-by":"crossref","first-page":"e1000997","DOI":"10.1371\/journal.ppat.1000997","article-title":"The conserved tarp actin binding domain is important for chlamydial invasion","volume":"6","author":"Jewett","year":"2010","journal-title":"PLoS Pathog"},{"key":"2023082414015820400_evad147-B37","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"Modelfinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"2023082414015820400_evad147-B38","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1111\/j.1462-2920.2007.01445.x","article-title":"Characterization of \u2018Candidatus clavochlamydia salmonicola\u2019: an intracellular bacterium infecting salmonid fish","volume":"10","author":"Karlsen","year":"2008","journal-title":"Environ Microbiol"},{"key":"2023082414015820400_evad147-B39","doi-asserted-by":"crossref","first-page":"17609","DOI":"10.1038\/srep17609","article-title":"Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp","volume":"5","author":"Katharios","year":"2015","journal-title":"Sci Rep"},{"key":"2023082414015820400_evad147-B40","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2023082414015820400_evad147-B41","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1038\/ismej.2017.113","article-title":"Uncultivated microbes in need of their own taxonomy","volume":"11","author":"Konstantinidis","year":"2017","journal-title":"ISME J"},{"key":"2023082414015820400_evad147-B42","doi-asserted-by":"crossref","first-page":"4021","DOI":"10.1038\/s41467-021-24294-3","article-title":"Pangenomics reveals alternative environmental lifestyles among chlamydiae","volume":"12","author":"K\u00f6stlbacher","year":"2021","journal-title":"Nat Commun"},{"key":"2023082414015820400_evad147-B43","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1016\/j.cub.2020.10.030","article-title":"Coevolving plasmids drive gene flow and genome plasticity in host-associated intracellular bacteria","volume":"31","author":"K\u00f6stlbacher","year":"2021","journal-title":"Curr Biol"},{"key":"2023082414015820400_evad147-B44","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1093\/molbev\/msn067","article-title":"An improved general amino acid replacement matrix","volume":"25","author":"Le","year":"2008","journal-title":"Mol Biol Evol"},{"key":"2023082414015820400_evad147-B45","doi-asserted-by":"crossref","first-page":"e0117921","DOI":"10.1128\/mBio.01179-21","article-title":"A chlamydial plasmid-dependent secretion system for the delivery of virulence factors to the host cytosol","volume":"12","author":"Lei","year":"2021","journal-title":"mBio"},{"key":"2023082414015820400_evad147-B46","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2023082414015820400_evad147-B47","doi-asserted-by":"crossref","first-page":"2746","DOI":"10.1128\/JB.01479-09","article-title":"Structure and protein-protein interaction studies on Chlamydia trachomatis protein CT670 (YscO homolog)","volume":"192","author":"Lorenzini","year":"2010","journal-title":"J Bacteriol"},{"key":"2023082414015820400_evad147-B48","doi-asserted-by":"crossref","first-page":"3678","DOI":"10.1128\/IAI.00515-10","article-title":"Phylogenetic analysis of Chlamydia trachomatis TarP and correlation with clinical phenotype","volume":"78","author":"Lutter","year":"2010","journal-title":"Infect Immun"},{"key":"2023082414015820400_evad147-B49","doi-asserted-by":"crossref","first-page":"W276","DOI":"10.1093\/nar\/gkac240","article-title":"Search and sequence analysis tools services from EMBL-EBI in 2022","volume":"50","author":"Madeira","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023082414015820400_evad147-B50","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1111\/j.1742-4658.2010.07974.x","article-title":"Membrane targeting and pore formation by the type III secretion system translocon","volume":"278","author":"Matte\u00ef","year":"2011","journal-title":"FEBS J"},{"key":"2023082414015820400_evad147-B51","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1111\/j.1365-2761.2010.01171.x","article-title":"Epitheliocystis in Atlantic salmon, Salmo salar L., farmed in fresh water in Ireland is associated with \u2018Candidatus Clavochlamydia salmonicola\u2019 infection","volume":"33","author":"Mitchell","year":"2010","journal-title":"J Fish Dis"},{"key":"2023082414015820400_evad147-B52","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1128\/IAI.00917-13","article-title":"New frontiers in type III secretion biology: the Chlamydia perspective","volume":"82","author":"Mueller","year":"2014","journal-title":"Infect Immun"},{"key":"2023082414015820400_evad147-B53","doi-asserted-by":"crossref","first-page":"e1006911","DOI":"10.1371\/journal.ppat.1006911","article-title":"Chlamydia trachomatis inclusion membrane protein MrcA interacts with the inositol 1,4,5-trisphosphate receptor type 3 (ITPR3) to regulate extrusion formation","volume":"14","author":"Nguyen","year":"2018","journal-title":"PLoS Pathog"},{"key":"2023082414015820400_evad147-B54","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"2023082414015820400_evad147-B55","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.meegid.2014.01.029","article-title":"Evolution, phylogeny, and molecular epidemiology of Chlamydia. Infection","volume":"23","author":"Nunes","year":"2014","journal-title":"Genet Evol"},{"key":"2023082414015820400_evad147-B56","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"Checkm: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res"},{"key":"2023082414015820400_evad147-B57","doi-asserted-by":"crossref","first-page":"84","DOI":"10.3389\/fcimb.2016.00084","article-title":"Targeted disruption of Chlamydia trachomatis invasion by in trans expression of dominant negative tarp effectors","volume":"6","author":"Parrett","year":"2016","journal-title":"Front Cell Infect Microbiol"},{"key":"2023082414015820400_evad147-B58","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1007\/s13353-015-0303-8","article-title":"Characteristics of chlamydia-like organisms pathogenic to fish","volume":"57","author":"Pawlikowska-Warych","year":"2016","journal-title":"J Appl Genet"},{"key":"2023082414015820400_evad147-B59","doi-asserted-by":"crossref","first-page":"14763","DOI":"10.1074\/jbc.RA120.015219","article-title":"A post-invasion role for chlamydia type III effector TarP in modulating the dynamics and organization of host cell focal adhesions","volume":"295","author":"Pedrosa","year":"2020","journal-title":"J Biol Chemistry"},{"key":"2023082414015820400_evad147-B60","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.tim.2007.04.005","article-title":"Type III secretion \u00e0 la Chlamydia","volume":"15","author":"Peters","year":"2007","journal-title":"Trends Microbiol"},{"key":"2023082414015820400_evad147-B61","doi-asserted-by":"crossref","first-page":"79","DOI":"10.3389\/fmicb.2018.00079","article-title":"Environmental metagenomic assemblies reveal seven new highly divergent chlamydial lineages and hallmarks of a conserved intracellular lifestyle","volume":"9","author":"Pillonel","year":"2018","journal-title":"Front Microbiol"},{"key":"2023082414015820400_evad147-B62","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1093\/bioinformatics\/bts252","article-title":"SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes","volume":"28","author":"Pruesse","year":"2012","journal-title":"Bioinformatics"},{"key":"2023082414015820400_evad147-B63","doi-asserted-by":"crossref","first-page":"2317","DOI":"10.1093\/bioinformatics\/btn445","article-title":"Empirical profile mixture models for phylogenetic reconstruction","volume":"24","author":"Quang","year":"2008","journal-title":"Bioinformatics"},{"key":"2023082414015820400_evad147-B64","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/bioinformatics\/btv681","article-title":"JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison","volume":"32","author":"Richter","year":"2016","journal-title":"Bioinformatics"},{"key":"2023082414015820400_evad147-B65","first-page":"e1900v1","article-title":"The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes","volume":"4","author":"Rodriguez-R","year":"2016","journal-title":"PeerJ Preprints"},{"key":"2023082414015820400_evad147-B66","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1111\/j.1365-2761.1984.tb00935.x","article-title":"A light and electron microscope study of epitheliocystis in juvenile steelhead trout, Salmo gairdneri Richardson","volume":"7","author":"Rourke","year":"1984","journal-title":"J Fish Dis"},{"key":"2023082414015820400_evad147-B67","doi-asserted-by":"crossref","first-page":"2048","DOI":"10.1111\/j.1462-2920.2011.02670.x","article-title":"A natural freshwater origin for two chlamydial species, Candidatus piscichlamydia salmonis and Candidatus Clavochlamydia salmonicola, causing mixed infections in wild brown trout (Salmo trutta)","volume":"14","author":"Schmidt-Posthaus","year":"2012","journal-title":"Environ Microbiol"},{"key":"2023082414015820400_evad147-B68","doi-asserted-by":"crossref","first-page":"1791","DOI":"10.1038\/ismej.2015.223","article-title":"Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular \u03b2-proteobacteria","volume":"10","author":"Seth-Smith","year":"2016","journal-title":"ISME J"},{"key":"2023082414015820400_evad147-B69","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.bbrc.2021.05.057","article-title":"The Chlamydia trachomatis TarP effector targets the Hippo pathway","volume":"562","author":"Shehat","year":"2021","journal-title":"Biochem Biophys Res Commun"},{"key":"2023082414015820400_evad147-B70","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.vetmic.2014.03.022","article-title":"Chlamydial infections of fish: diverse pathogens and emerging causes of disease in aquaculture species","volume":"171","author":"Stride","year":"2014","journal-title":"Vet Microbiol"},{"key":"2023082414015820400_evad147-B71","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1111\/1462-2920.13694","article-title":"Culture-independent genomics of a novel chlamydial pathogen of fish provides new insight into host-specific adaptations utilized by these intracellular bacteria","volume":"19","author":"Taylor-Brown","year":"2017","journal-title":"Environ Microbiol"},{"key":"2023082414015820400_evad147-B72","doi-asserted-by":"crossref","first-page":"2614","DOI":"10.1093\/gbe\/evy195","article-title":"Metagenomic analysis of fish-associated Ca. Parilichlamydiaceae reveals striking metabolic similarities to the terrestrial Chlamydiaceae","volume":"10","author":"Taylor-Brown","year":"2018","journal-title":"Genome Biol Evol"},{"key":"2023082414015820400_evad147-B73","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":"2023082414015820400_evad147-B74","doi-asserted-by":"crossref","first-page":"30426","DOI":"10.1074\/jbc.M114.604876","article-title":"The Chlamydia effector TarP mimics the mammalian leucine-aspartic acid motif of paxillin to subvert the focal adhesion kinase during invasion","volume":"289","author":"Thwaites","year":"2014","journal-title":"J Biol Chem"},{"key":"2023082414015820400_evad147-B75","doi-asserted-by":"crossref","first-page":"88","DOI":"10.3389\/fcimb.2015.00088","article-title":"Vinculin interacts with the Chlamydia effector tarP via a tripartite vinculin binding domain to mediate actin recruitment and assembly at the plasma membrane","volume":"5","author":"Thwaites","year":"2015","journal-title":"Front Cell Infect Microbiol"},{"key":"2023082414015820400_evad147-B76","doi-asserted-by":"crossref","first-page":"e32696","DOI":"10.1371\/journal.pone.0032696","article-title":"A novel betaproteobacterial agent of gill epitheliocystis in seawater farmed atlantic salmon (Salmo salar)","volume":"7","author":"Toenshoff","year":"2012","journal-title":"PLoS One"},{"key":"2023082414015820400_evad147-B77","doi-asserted-by":"crossref","first-page":"126200","DOI":"10.1016\/j.syapm.2021.126200","article-title":"Evidence for the existence of a new genus Chlamydiifrater gen. nov. inside the family Chlamydiaceae with two new species isolated from flamingo (Phoenicopterus roseus): Chlamydiifrater phoenicopteri sp. nov. and Chlamydiifrater volucris sp. nov","volume":"44","author":"Vorimore","year":"2021","journal-title":"Syst Appl Microbiol"},{"key":"2023082414015820400_evad147-B78","doi-asserted-by":"crossref","first-page":"123","DOI":"10.3389\/fcimb.2016.00123","article-title":"The DUF582 proteins of Chlamydia trachomatis bind to components of the ESCRT machinery, which is dispensable for bacterial growth in vitro","volume":"6","author":"Vromman","year":"2016","journal-title":"Front Cell Infect Microbiol"},{"key":"2023082414015820400_evad147-B79","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1093\/sysbio\/syx068","article-title":"Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation","volume":"67","author":"Wang","year":"2018","journal-title":"Syst Biol"},{"key":"2023082414015820400_evad147-B80","doi-asserted-by":"crossref","first-page":"3327","DOI":"10.1093\/bioinformatics\/btw393","article-title":"Conspred: a rule-based (re-)annotation framework for prokaryotic genomes","volume":"32","author":"Weinmaier","year":"2016","journal-title":"Bioinformatics"},{"key":"2023082414015820400_evad147-B81","doi-asserted-by":"crossref","first-page":"8206","DOI":"10.1128\/JB.01082-06","article-title":"In silico prediction and functional validation of \u03c328-regulated genes in Chlamydia and Escherichia coli","volume":"188","author":"Yu","year":"2006","journal-title":"J Bacteriol"},{"key":"2023082414015820400_evad147-B82","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1128\/aem.62.2.316-322.1996","article-title":"DNA recovery from soils of diverse composition","volume":"62","author":"Zhou","year":"1996","journal-title":"Appl Environ Microbiol"}],"container-title":["Genome Biology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/15\/8\/evad147\/51244456\/evad147.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gbe\/article-pdf\/15\/8\/evad147\/51244456\/evad147.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T14:24:05Z","timestamp":1702995845000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gbe\/article\/doi\/10.1093\/gbe\/evad147\/7249936"}},"subtitle":[],"editor":[{"suffix":"Dr","given":"Tal","family":"Dagan","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2023,8,1]]},"references-count":82,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2023,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gbe\/evad147","relation":{},"ISSN":["1759-6653"],"issn-type":[{"value":"1759-6653","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,8]]},"published":{"date-parts":[[2023,8,1]]},"article-number":"evad147"}}