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Background    Chlamydia  ( C. )  gallinacea  is a recently identified bacterium that mainly infects domestic chickens. Demonstration of  C. gallinacea  in human atypical pneumonia suggests its zoonotic potential. Its prevalence in chickens exceeds that of  C. psittaci , but genetic and genomic research on  C. gallinacea  is still at the beginning. In this study, we conducted whole-genome sequencing of  C. gallinacea  strain JX-1 isolated from an asymptomatic chicken, and comparative genomic analysis between  C. gallinacea  strains and related chlamydial species.    Results  The genome of  C. gallinacea  JX-1 was sequenced by single-molecule, real-time technology and is comprised of a 1,059,522-bp circular chromosome with an overall G + C content of 37.93% and sequence similarity of 99.4% to type strain 08-1274/3. In addition, a plasmid designated pJX-1, almost identical to p1274 of the type strain, except for two point mutations, was only found in field strains from chicken, but not in other hosts. In contrast to chlamydial species with notably variable polymorphic membrane protein ( pmp ) genes and plasticity zone (PZ), these regions were conserved in both  C. gallinacea  strains. There were 15 predicted  pmp  genes, but only B, A, E1, H, G1 and G2 were apparently intact in both strains. In comparison to chlamydial species where the PZ may be up to 50 kbp,  C. gallinacea  strains displayed gene content reduction in the PZ (14 kbp), with strain JX-1 having a premature STOP codon in the  cytotoxin  ( tox ) gene, while  tox  gene is intact in the type strain. In multilocus sequence typing (MLST), 15  C. gallinacea  STs were identified among 25 strains based on cognate MLST allelic profiles of the concatenated sequences. The type strain and all Chinese strains belong to two distinct phylogenetic clades. Clade of the Chinese strains separated into 14 genetically distinct lineages, thus revealing considerable genetic diversity of  C. gallinacea  strains in China.    Conclusions  In this first detailed comparative genomic analysis of  C. gallinacea , we have provided evidence for substantial genetic diversity among  C. gallinacea  strains. How these genetic polymorphisms affect  C. gallinacea  biology and pathogenicity should be addressed in future studies that focus on phylogenetics and host adaption of this enigmatic bacterial agent.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4343-9) contains supplementary material, which is available to authorized users.

bmc genomics

From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen