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Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum
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 conjunct...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137089/ https://www.ncbi.nlm.nih.gov/pubmed/25106440 http://dx.doi.org/10.1186/1471-2164-15-667 |
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author | Bachmann, Nathan L Fraser, Tamieka A Bertelli, Claire Jelocnik, Martina Gillett, Amber Funnell, Oliver Flanagan, Cheyne Myers, Garry S A Timms, Peter Polkinghorne, Adam |
author_facet | Bachmann, Nathan L Fraser, Tamieka A Bertelli, Claire Jelocnik, Martina Gillett, Amber Funnell, Oliver Flanagan, Cheyne Myers, Garry S A Timms, Peter Polkinghorne, Adam |
author_sort | Bachmann, Nathan L |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-667) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4137089 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41370892014-08-19 Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum Bachmann, Nathan L Fraser, Tamieka A Bertelli, Claire Jelocnik, Martina Gillett, Amber Funnell, Oliver Flanagan, Cheyne Myers, Garry S A Timms, Peter Polkinghorne, Adam BMC Genomics Research Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-667) contains supplementary material, which is available to authorized users. BioMed Central 2014-08-08 /pmc/articles/PMC4137089/ /pubmed/25106440 http://dx.doi.org/10.1186/1471-2164-15-667 Text en © Bachmann et al.; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Bachmann, Nathan L Fraser, Tamieka A Bertelli, Claire Jelocnik, Martina Gillett, Amber Funnell, Oliver Flanagan, Cheyne Myers, Garry S A Timms, Peter Polkinghorne, Adam Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum |
title | Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum |
title_full | Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum |
title_fullStr | Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum |
title_full_unstemmed | Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum |
title_short | Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum |
title_sort | comparative genomics of koala, cattle and sheep strains of chlamydia pecorum |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137089/ https://www.ncbi.nlm.nih.gov/pubmed/25106440 http://dx.doi.org/10.1186/1471-2164-15-667 |
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