Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum
Nathan L Bachmann1, Tamieka A Fraser2, Claire Bertelli2,3,8, Martina Jelocnik2, Amber Gillett4, Oliver Funnell5, Cheyne Flanagan6, Garry S A Myers7, Peter Timms1,2 and Adam Polkinghorne1,2*
1 Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs 4558, Queensland, Australia.
2 Institute for Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove 4059, Queensland, Australia.
3 SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
4 Australia Zoo Wildlife Hospital, Beerwah, Queensland 4519, Australia.
5 Adelaide Hills Animal Hospital, Stirling, South Australia 5152, Australia.
6 Port Macquarie Koala Hospital, Port Macquarie, NSW 2444, Australia.
7 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore 21201, USA.
8 Current address: Center for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland.
Background Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced.
Results Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the origin of these point mutations.
Conclusions The genomic data revealed that variation between C. pecorum strains were mainly due to the accumulation of SNPs, some of which cause gene inactivation. The identification of these genetic differences will provide the basis for further studies to understand the biology and evolution of this important animal pathogen.