Comparative genome analysis of 33 Chlamydia strains reveals characteristic features of Chlamydia psittaci and closely related species

To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Besides publicly available data, the genomes of eight field strains (3 C. avium, 4 C. gallinacea, 1 C. abortus) were de novo sequenced and assembled (assemblies available at https://osf.io/j9zas/) and uploaded here. These eight strains were cultured on BGM cells and DNA extracted as described previously (Sachse et al., 2014, Syst Appl Microbiol). Approximately 5 µg of genomic DNA was sent to GATC/Eurofins Genomics for Illumina MiSeq 2x300-bp paired-end sequencing, except for C. abortus 16DC122 were only 2x151 cycles were used. In the case of C. gallinacea strain 12-4358, a genomic library was prepared using 1 ng of genomic DNA and the Nextera XT kit, and sequencing was performed on the MiSeq platform at Anses using a Micro V2 with 2x151 cycles.