Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle

When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI’s da...

Descripción completa

Detalles Bibliográficos
Autores principales: Neumann, Guilherme B., Korkuć, Paula, Reißmann, Monika, Wolf, Manuel J., May, Katharina, König, Sven, Brockmann, Gudrun A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Short Report
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10585868/
https://www.ncbi.nlm.nih.gov/pubmed/37853447
http://dx.doi.org/10.1186/s13567-023-01227-0
_version_ 1785123038623170560
author Neumann, Guilherme B.
Korkuć, Paula
Reißmann, Monika
Wolf, Manuel J.
May, Katharina
König, Sven
Brockmann, Gudrun A.
author_facet Neumann, Guilherme B.
Korkuć, Paula
Reißmann, Monika
Wolf, Manuel J.
May, Katharina
König, Sven
Brockmann, Gudrun A.
author_sort Neumann, Guilherme B.
collection PubMed
description When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI’s database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13567-023-01227-0.
format Online
Article
Text
id pubmed-10585868
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-105858682023-10-20 Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle Neumann, Guilherme B. Korkuć, Paula Reißmann, Monika Wolf, Manuel J. May, Katharina König, Sven Brockmann, Gudrun A. Vet Res Short Report When resequencing animal genomes, some short reads cannot be mapped to the reference genome and are usually discarded. In this study, unmapped reads from 302 German Black Pied cattle were analyzed to identify potential pathogenic DNA. These unmapped reads were assembled and blasted against NCBI’s database to identify bacterial and viral sequences. The results provided evidence for the presence of pathogens. We found sequences of Bovine parvovirus 3 and Mycoplasma species. These findings emphasize the information content of unmapped reads for gaining insight into bacterial and viral infections, which is important for veterinarians and epidemiologists. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13567-023-01227-0. BioMed Central 2023-10-18 2023 /pmc/articles/PMC10585868/ /pubmed/37853447 http://dx.doi.org/10.1186/s13567-023-01227-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Short Report
Neumann, Guilherme B.
Korkuć, Paula
Reißmann, Monika
Wolf, Manuel J.
May, Katharina
König, Sven
Brockmann, Gudrun A.
Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
title Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
title_full Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
title_fullStr Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
title_full_unstemmed Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
title_short Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle
title_sort unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in german black pied cattle
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10585868/
https://www.ncbi.nlm.nih.gov/pubmed/37853447
http://dx.doi.org/10.1186/s13567-023-01227-0
work_keys_str_mv AT neumannguilhermeb unmappedshortreadsfromwholegenomesequencingindicatepotentialinfectiouspathogensingermanblackpiedcattle
AT korkucpaula unmappedshortreadsfromwholegenomesequencingindicatepotentialinfectiouspathogensingermanblackpiedcattle
AT reißmannmonika unmappedshortreadsfromwholegenomesequencingindicatepotentialinfectiouspathogensingermanblackpiedcattle
AT wolfmanuelj unmappedshortreadsfromwholegenomesequencingindicatepotentialinfectiouspathogensingermanblackpiedcattle
AT maykatharina unmappedshortreadsfromwholegenomesequencingindicatepotentialinfectiouspathogensingermanblackpiedcattle
AT konigsven unmappedshortreadsfromwholegenomesequencingindicatepotentialinfectiouspathogensingermanblackpiedcattle
AT brockmanngudruna unmappedshortreadsfromwholegenomesequencingindicatepotentialinfectiouspathogensingermanblackpiedcattle

Ejemplares similares