Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs.

Recently discovered obligate intracellular bacteria belonging to the genus with the species of and were studied to explore the composition of their genomes and their relatedness to , the other genus of the family . We investigated 4 isolates of , 2 of them newly sequenced, and one of alongside 12 representatives of the species. Our study uncovers previously unrecognized genomic structures within 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 strains, which improves our understanding of chlamydial genome architecture and plasticity in the family . Our analysis revealed that 761 CDS (~80%) are shared among members of both genera. We further identified 158 unique genes of species, but their annotation remains challenging because of the absence of functionally annotated orthologs in public databases. A full-length gene encoding the major outer membrane porin was seen in all strains. We also describe the localization and structure of multiple truncated CDS of family members, representing one of this study's most interesting findings. While genome analysis of spp. confirmed numerous common features shared with representatives of the genus many unique genomic elements were identified that underpin the distinct phenotype and separate genetic position of these new microorganisms.