{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T01:36:02Z","timestamp":1772156162834,"version":"3.50.1"},"reference-count":26,"publisher":"Microbiology Society","issue":"2","license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"unspecified","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":[[2025,1,1]]},"abstract":"\n Recently discovered obligate intracellular bacteria belonging to the genus\n Chlamydiifrater<\/jats:italic>\n with the species of\n Chlamydiifrater phoenicopteri<\/jats:italic>\n and\n Chlamydiifrater volucris<\/jats:italic>\n were studied to explore the composition of their genomes and their relatedness to\n Chlamydia<\/jats:italic>\n , the other genus of the family\n Chlamydiaceae<\/jats:italic>\n . We investigated 4 isolates of\n Cf. volucris<\/jats:italic>\n , 2 of them newly sequenced, and one of\n Cf. phoenicopteri<\/jats:italic>\n alongside 12 representatives of the\n Chlamydia<\/jats:italic>\n species. Our study uncovers previously unrecognized genomic structures within\n Chlamydiifrater<\/jats:italic>\n using a hybrid sequencing approach and advanced annotation pipelines, providing insights into species-specific adaptations and evolutionary dynamics. The integration of long-read sequencing data, comprehensive re-annotation strategies and pan-genomics enabled the localization of the unique plasticity zone and the identification of novel gene clusters in\n Chlamydiifrater<\/jats:italic>\n strains, which improves our understanding of chlamydial genome architecture and plasticity in the family\n Chlamydiaceae<\/jats:italic>\n . Our analysis revealed that 761 CDS (~80%) are shared among members of both genera. We further identified 158 unique genes of\n Chlamydiifrater<\/jats:italic>\n species, but their annotation remains challenging because of the absence of functionally annotated orthologs in public databases. A full-length\n ompA<\/jats:italic>\n gene encoding the major outer membrane porin was seen in all\n Chlamydiifrater<\/jats:italic>\n strains. We also describe the localization and structure of multiple truncated CDS of\n ompA<\/jats:italic>\n family members, representing one of this study\u2019s most interesting findings. While genome analysis of\n Chlamydiifrater<\/jats:italic>\n spp. confirmed numerous common features shared with representatives of the genus\n Chlamydia,<\/jats:italic>\n many unique genomic elements were identified that underpin the distinct phenotype and separate genetic position of these new microorganisms.\n <\/jats:p>","DOI":"10.1099\/acmi.0.000936.v3","type":"journal-article","created":{"date-parts":[[2025,2,3]],"date-time":"2025-02-03T04:16:41Z","timestamp":1738556201000},"source":"Crossref","is-referenced-by-count":2,"title":["Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs"],"prefix":"10.1099","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7090-8717","authenticated-orcid":false,"given":"Martin","family":"H\u00f6lzer","sequence":"first","affiliation":[{"name":"Bioinformatics and Translational Research, Genome Competence 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