Genomes of Chlamydiifrater species contain multiple truncated CDS of the major outer membrane porin (MOMP), more than 150 unique genes and an ortholog of the chlamydial plasticity zone
Recently discovered obligateObligate intracellular bacteria belonging to the genus Chlamydiifrater (Cf.) and the species of Cf. phoenicopteri and Cf. volucris were only recently discovered. This study studied to explore explored the composition of these their genomes and their relatedness to Chlamydia, the other genus of the family Chlamydiaceae.  Results: FourIn this study, we investigated four isolates of Cf. volucris, including two  of them newly sequenced and de novo assembled in this studyisolates, as well as and one isolate of Cf. phoenicopteri, were investigated alongside 12 representatives of the Chlamydia species. Our study reveals previously unrecognized genomic structures within Cf. usingutilized state-of-the-art bioinformatics techniques, including a hybrid sequencing approach and advanced annotation pipelines, to reveal previously unrecognized genomic structures within Cf.thus providing This provides insights into species-specific adaptations and evolutionary dynamics. The integration of long-read sequencing data, comprehensive re-annotation strategies, and pan-genomics has enabled the localization of the unique plasticity zone and identification of novel gene clusters in Chlamydiifrater strains. This, which improves our understanding of chlamydial genome architecture and plasticity in the family Chlamydiaceae. Our analysis revealed that approximately 80% of the761 CDS are shared among members of both genera, (approx. 80 %) which amounts to 761 CDS. We further identified 158 110 unique genes of in the Cf. speciesgenus , but their annotation remains challenging because ofdue to the absence of functionally annotated orthologs in public databases. All Cf. strains contained aA full-length ompA gene encoding the major outer membrane porin (MOMP) was seen in all Cf. strains. One of the most interesting findings is the presence in Cf. of multiple truncated CDS of members of the ompA family in Cf., whose localization and structure we describe here. Conclusions: While gGenome analysis of Chlamydiifrater spp. confirmed numerous common features shared with representatives of the genus Chlamydia. , However, many unique genomic elements were also identified that can underpin the distinct phenotype and separate genetic position of these new microorganisms.