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A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes
Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challen...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5891936/ https://www.ncbi.nlm.nih.gov/pubmed/29643938 http://dx.doi.org/10.1186/s13099-018-0242-0 |
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author | Gopinath, G. R. Cinar, H. N. Murphy, H. R. Durigan, M. Almeria, M. Tall, B. D. DaSilva, A. J. |
author_facet | Gopinath, G. R. Cinar, H. N. Murphy, H. R. Durigan, M. Almeria, M. Tall, B. D. DaSilva, A. J. |
author_sort | Gopinath, G. R. |
collection | PubMed |
description | Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mitochondrial genome assembly to be used as a reference genome by applying bioinformatic analyses. Using this reference genome, three new mitochondrial genome assemblies were built starting with metagenomic reads generated by sequencing DNA extracted from oocysts present in stool samples from cyclosporiasis patients. Nucleotide variants were identified in the new and other publicly available genomes in comparison with the mitochondrial reference genome. A consolidated workflow, presented here, to generate new mitochondrion genomes using our reference-guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, and in their application for subtyping C. cayetanensis strains during foodborne outbreak investigations. |
format | Online Article Text |
id | pubmed-5891936 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-58919362018-04-11 A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes Gopinath, G. R. Cinar, H. N. Murphy, H. R. Durigan, M. Almeria, M. Tall, B. D. DaSilva, A. J. Gut Pathog Short Report Cyclospora cayetanensis is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mitochondrial genome assembly to be used as a reference genome by applying bioinformatic analyses. Using this reference genome, three new mitochondrial genome assemblies were built starting with metagenomic reads generated by sequencing DNA extracted from oocysts present in stool samples from cyclosporiasis patients. Nucleotide variants were identified in the new and other publicly available genomes in comparison with the mitochondrial reference genome. A consolidated workflow, presented here, to generate new mitochondrion genomes using our reference-guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, and in their application for subtyping C. cayetanensis strains during foodborne outbreak investigations. BioMed Central 2018-04-10 /pmc/articles/PMC5891936/ /pubmed/29643938 http://dx.doi.org/10.1186/s13099-018-0242-0 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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 | Short Report Gopinath, G. R. Cinar, H. N. Murphy, H. R. Durigan, M. Almeria, M. Tall, B. D. DaSilva, A. J. A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes |
title | A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes |
title_full | A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes |
title_fullStr | A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes |
title_full_unstemmed | A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes |
title_short | A hybrid reference-guided de novo assembly approach for generating Cyclospora mitochondrion genomes |
title_sort | hybrid reference-guided de novo assembly approach for generating cyclospora mitochondrion genomes |
topic | Short Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5891936/ https://www.ncbi.nlm.nih.gov/pubmed/29643938 http://dx.doi.org/10.1186/s13099-018-0242-0 |
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