{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T10:35:47Z","timestamp":1770287747363,"version":"3.49.0"},"reference-count":67,"publisher":"MDPI AG","issue":"23","license":[{"start":{"date-parts":[[2024,11,26]],"date-time":"2024-11-26T00:00:00Z","timestamp":1732579200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The Chlamydiaceae are a family of obligate intracellular bacteria known for their unique biphasic developmental cycle. Chlamydial are associated with various host organisms, including humans, and have been proposed as emerging pathogens. Genomic studies have significantly enhanced our understanding of chlamydial biology, host adaptation, and evolutionary processes. In this study, we conducted a complete pangenome association analysis (pan-GWAS) using 101 genomes from the Chlamydiaceae family to identify differentially represented genes in Chlamydia and Chlamydophila, revealing their distinct evolutionary strategies for interacting with eukaryotic hosts. Our analysis identified 289 genes with differential abundance between the two clades: 129 showed a strong association with Chlamydia and 160 with Chlamydophila. Most genes in Chlamydia were related to the type III secretion system, while Chlamydophila genes corresponded to various functional categories, including translation, replication, transport, and metabolism. These findings suggest that Chlamydia has developed a high dependence on mammalian cells for replication, facilitated by a complex T3SS for intracellular manipulation. In contrast, the metabolic and functional diversity in Chlamydophila allows it to colonize a broad range of hosts, such as birds, reptiles, amphibians, and mammals, making it a less specialized clade.<\/jats:p>","DOI":"10.3390\/ijms252312671","type":"journal-article","created":{"date-parts":[[2024,11,26]],"date-time":"2024-11-26T04:02:18Z","timestamp":1732593738000},"page":"12671","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pangenome-Wide Association Study in the Chlamydiaceae Family Reveals Key Evolutionary Aspects of Their Relationship with Their Hosts"],"prefix":"10.3390","volume":"25","author":[{"given":"Rosalba","family":"Salgado-Morales","sequence":"first","affiliation":[{"name":"Laboratorio de Estudios Ecogen\u00f3micos, Centro de Investigaci\u00f3n en Biotecnolog\u00eda, Universidad Aut\u00f3noma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca CP 62210, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2263-4409","authenticated-orcid":false,"given":"Karla","family":"Barba-Xochipa","sequence":"additional","affiliation":[{"name":"Facultad de Ciencias de la Salud, Universidad Aut\u00f3noma de Tlaxcala, Universidad 1, Tlaxcala de Xicoht\u00e9ncatl CP 90000, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fernando","family":"Mart\u00ednez-Ocampo","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Din\u00e1mica Celular, Universidad Aut\u00f3noma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca CP 62210, Mexico"},{"name":"Programa de Estancias Posdoctorales por M\u00e9xico 2022(3), Modalidad Acad\u00e9mica-Inicial, Consejo Nacional de Humanidades, Ciencias y Tecnolog\u00edas, Av. Insurgentes Sur 1582, Col. Cr\u00e9dito Constructor, Alcald\u00eda Benito Ju\u00e1rez CP 03940, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3973-1244","authenticated-orcid":false,"given":"Edgar","family":"Dant\u00e1n-Gonz\u00e1lez","sequence":"additional","affiliation":[{"name":"Laboratorio de Estudios Ecogen\u00f3micos, Centro de Investigaci\u00f3n en Biotecnolog\u00eda, Universidad Aut\u00f3noma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca CP 62210, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7809-6888","authenticated-orcid":false,"given":"Armando","family":"Hern\u00e1ndez-Mendoza","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Din\u00e1mica Celular, Universidad Aut\u00f3noma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca CP 62210, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuel","family":"Quiterio-Trenado","sequence":"additional","affiliation":[{"name":"Centro de Investigaci\u00f3n en Salud Poblacional, Instituto Nacional de Salud P\u00fablica, Av. Universidad 655, Cuernavaca CP 62100, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Magdalena","family":"Rodr\u00edguez-Santiago","sequence":"additional","affiliation":[{"name":"Facultad de Ciencias de la Salud, Universidad Aut\u00f3noma de Tlaxcala, Universidad 1, Tlaxcala de Xicoht\u00e9ncatl CP 90000, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7155-740X","authenticated-orcid":false,"given":"Abraham","family":"Rivera-Ram\u00edrez","sequence":"additional","affiliation":[{"name":"Laboratorio de Estudios Ecogen\u00f3micos, Centro de Investigaci\u00f3n en Biotecnolog\u00eda, Universidad Aut\u00f3noma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca CP 62210, Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,11,26]]},"reference":[{"key":"ref_1","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":"ref_2","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1007\/s10482-017-0962-z","article-title":"The Paradigms They Are a-Changin\u2019: Past, present and future of PVC bacteria research","volume":"111","author":"Devos","year":"2018","journal-title":"Antonie Leeuwenhoek"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1016\/j.tim.2014.04.013","article-title":"Chlamydia genomics: Providing novel insights into chlamydial biology","volume":"22","author":"Bachmann","year":"2014","journal-title":"Trends Microbiol."},{"key":"ref_4","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. 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