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 (see associated analysis study including the assemblies) 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.