Background and Significance:Novel families in the Chlamydiales have been associated with epitheliocystis, an under-recognised disease of fish. Phylogenetic analysis using 16S rRNA-based methods placed chlamydial pathogens of fish at the root of the order Chlamydiales, suggesting these organisms may be, or at least share similarity with, the evolutionary ancestors of the family Chlamydiaceae. Due to the lack of culture systems, little is known about the biology of these Chlamydia-like organisms (CLOs).

Objectives: In the absence of culture methods, we aimed to characterise the genome sequences of the novel pathogen, Candidatus. Parilichlamydia carangidicola to better understand host-pathogen interactions, host adaptation mechanisms, and evolutionary relationships between CLOs and traditional Chlamydiae.

Methods: DNA was isolated from gills from two Yellowtail Kingfish presenting with chlamydial epitheliocystis. DNA was enriched for microbial DNA and whole genome amplification was conducted prior to shotgun sequencing on a MiSeq. The resulting reads were assembled using a de novo method (SPAdes). Genome annotation was conducted by RAST and genomes were analysed using a number of tools including Geneious, CLC genomics and DNAplotter.

Results: We used a combined DNA enrichment approach followed by shotgun sequencing to determine the first genome of the first representative of the Candidatus Parilichlamydiaceae species, Ca. Parilichlamydia carangidicola. The draft genome is 2,089,218 bp long, and contains 1933 predicted coding sequences. Preliminary analysis reveals the presence of a number of conserved proteins, such as structural components of the type three secretion system.

Conclusions: The availability of the Ca. Parilichlamydia carangidicola genome provides us with new insights into the evolution of members of the order Chlamydiales, and can be used to inform future characterisation of novel CLOs.