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Article

Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala (Phascolarctos cinereus) Pathogen

1
Genecology Research Centre, University of the Sunshine Coast, Sippy Downs, Sunshine Coast, QLD 4557, Australia
2
Asia Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010, Australia
3
Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
4
Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia
*
Author to whom correspondence should be addressed.
Academic Editor: Guangming Zhong
Pathogens 2021, 10(12), 1543; https://doi.org/10.3390/pathogens10121543 (registering DOI)
Received: 3 November 2021 / Revised: 17 November 2021 / Accepted: 24 November 2021 / Published: 25 November 2021
(This article belongs to the Special Issue Animal Chlamydiae: A Concern for Human and Veterinary Medicine)
Chlamydia pecorum, an obligate intracellular pathogen, causes significant morbidity and mortality in livestock and the koala (Phascolarctos cinereus). A variety of C. pecorum gene-centric molecular studies have revealed important observations about infection dynamics and genetic diversity in both koala and livestock hosts. In contrast to a variety of C. pecorum molecular studies, to date, only four complete and 16 draft genomes have been published. Of those, only five draft genomes are from koalas. Here, using whole-genome sequencing and a comparative genomics approach, we describe the first two complete C. pecorum genomes collected from diseased koalas. A de novo assembly of DBDeUG_2018 and MC/MarsBar_2018 resolved the chromosomes and chlamydial plasmids each as single, circular contigs. Robust phylogenomic analyses indicate biogeographical separation between strains from northern and southern koala populations, and between strains infecting koala and livestock hosts. Comparative genomics between koala strains identified new, unique, and shared loci that accumulate single-nucleotide polymorphisms and separate between northern and southern, and within northern koala strains. Furthermore, we predicted novel type III secretion system effectors. This investigation constitutes a comprehensive genome-wide comparison between C. pecorum from koalas and provides improvements to annotations of a C. pecorum reference genome. These findings lay the foundations for identifying and understanding host specificity and adaptation behind chlamydial infections affecting koalas. View Full-Text
Keywords: Chlamydia pecorum; comparative genomics; recombination; phylogenetics; strain DBDeUG_2018; strain MC/MarsBar_2018 Chlamydia pecorum; comparative genomics; recombination; phylogenetics; strain DBDeUG_2018; strain MC/MarsBar_2018
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MDPI and ACS Style

White, R.T.; Legione, A.R.; Taylor-Brown, A.; Fernandez, C.M.; Higgins, D.P.; Timms, P.; Jelocnik, M. Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala (Phascolarctos cinereus) Pathogen. Pathogens 2021, 10, 1543. https://doi.org/10.3390/pathogens10121543

AMA Style

White RT, Legione AR, Taylor-Brown A, Fernandez CM, Higgins DP, Timms P, Jelocnik M. Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala (Phascolarctos cinereus) Pathogen. Pathogens. 2021; 10(12):1543. https://doi.org/10.3390/pathogens10121543

Chicago/Turabian Style

White, Rhys T., Alistair R. Legione, Alyce Taylor-Brown, Cristina M. Fernandez, Damien P. Higgins, Peter Timms, and Martina Jelocnik. 2021. "Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala (Phascolarctos cinereus) Pathogen" Pathogens 10, no. 12: 1543. https://doi.org/10.3390/pathogens10121543

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