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Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture
BACKGROUND: Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As A. phagocytophilum is difficult to isolate and cultivate, only n...
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/PMC4239370/ https://www.ncbi.nlm.nih.gov/pubmed/25400116 http://dx.doi.org/10.1186/1471-2164-15-973 |
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author | Dugat, Thibaud Loux, Valentin Marthey, Sylvain Moroldo, Marco Lagrée, Anne-Claire Boulouis, Henri-Jean Haddad, Nadia Maillard, Renaud |
author_facet | Dugat, Thibaud Loux, Valentin Marthey, Sylvain Moroldo, Marco Lagrée, Anne-Claire Boulouis, Henri-Jean Haddad, Nadia Maillard, Renaud |
author_sort | Dugat, Thibaud |
collection | PubMed |
description | BACKGROUND: Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As A. phagocytophilum is difficult to isolate and cultivate, only nine genome sequences have been published to date, none of which originate from a bovine strain. Our goals were to; 1/ develop a sequencing methodology which efficiently circumvents the difficulties associated with A. phagocytophilum isolation and culture; 2/ describe the first genome of a bovine strain; and 3/ compare it with available genomes, in order to both explore key genomic features at the species level, and to identify candidate genes that could be specific to bovine strains. RESULTS: DNA was extracted from a bovine blood sample infected by A. phagocytophilum. Following a whole genome capture approach, A. phagocytophilum DNA was enriched 197-fold in the sample and then sequenced using Illumina technology. In total, 58.9% of obtained reads corresponded to the A. phagocytophilum genome, covering 85.3% of the HZ genome. Then by performing comparisons with nine previously-sequenced A. phagocytophilum genomes, we determined the core genome of these ten strains. Following analysis, 1281 coding DNA sequences, including 1001 complete sequences, were detected in the A. phagocytophilum bovine genome, of which four appeared to be unique to the bovine isolate. These four coding DNA sequences coded for "hypothetical proteins of unknown function” and require further analysis. We also identified nine proteins common to both European domestic ruminants tested. CONCLUSION: Using a whole genome capture approach, we have sequenced the first A. phagocytophilum genome isolated from a cow. To the best of our knowledge, this is the first time that this method has been used to selectively enrich pathogenic bacterial DNA from samples also containing host DNA. The four proteins unique to the A. phagocytophilum bovine genome could be involved in host tropism, therefore their functions need to be explored. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-973) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4239370 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-42393702014-11-21 Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture Dugat, Thibaud Loux, Valentin Marthey, Sylvain Moroldo, Marco Lagrée, Anne-Claire Boulouis, Henri-Jean Haddad, Nadia Maillard, Renaud BMC Genomics Research Article BACKGROUND: Anaplasma phagocytophilum is a zoonotic and obligate intracellular bacterium transmitted by ticks. In domestic ruminants, it is the causative agent of tick-borne fever, which causes significant economic losses in Europe. As A. phagocytophilum is difficult to isolate and cultivate, only nine genome sequences have been published to date, none of which originate from a bovine strain. Our goals were to; 1/ develop a sequencing methodology which efficiently circumvents the difficulties associated with A. phagocytophilum isolation and culture; 2/ describe the first genome of a bovine strain; and 3/ compare it with available genomes, in order to both explore key genomic features at the species level, and to identify candidate genes that could be specific to bovine strains. RESULTS: DNA was extracted from a bovine blood sample infected by A. phagocytophilum. Following a whole genome capture approach, A. phagocytophilum DNA was enriched 197-fold in the sample and then sequenced using Illumina technology. In total, 58.9% of obtained reads corresponded to the A. phagocytophilum genome, covering 85.3% of the HZ genome. Then by performing comparisons with nine previously-sequenced A. phagocytophilum genomes, we determined the core genome of these ten strains. Following analysis, 1281 coding DNA sequences, including 1001 complete sequences, were detected in the A. phagocytophilum bovine genome, of which four appeared to be unique to the bovine isolate. These four coding DNA sequences coded for "hypothetical proteins of unknown function” and require further analysis. We also identified nine proteins common to both European domestic ruminants tested. CONCLUSION: Using a whole genome capture approach, we have sequenced the first A. phagocytophilum genome isolated from a cow. To the best of our knowledge, this is the first time that this method has been used to selectively enrich pathogenic bacterial DNA from samples also containing host DNA. The four proteins unique to the A. phagocytophilum bovine genome could be involved in host tropism, therefore their functions need to be explored. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-973) contains supplementary material, which is available to authorized users. BioMed Central 2014-11-17 /pmc/articles/PMC4239370/ /pubmed/25400116 http://dx.doi.org/10.1186/1471-2164-15-973 Text en © Dugat 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 Dugat, Thibaud Loux, Valentin Marthey, Sylvain Moroldo, Marco Lagrée, Anne-Claire Boulouis, Henri-Jean Haddad, Nadia Maillard, Renaud Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture |
title | Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture |
title_full | Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture |
title_fullStr | Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture |
title_full_unstemmed | Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture |
title_short | Comparative genomics of first available bovine Anaplasma phagocytophilum genome obtained with targeted sequence capture |
title_sort | comparative genomics of first available bovine anaplasma phagocytophilum genome obtained with targeted sequence capture |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239370/ https://www.ncbi.nlm.nih.gov/pubmed/25400116 http://dx.doi.org/10.1186/1471-2164-15-973 |
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