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

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