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

Neumann, Guilherme B.; Korkuc, Paula; Reißmann, Monika; Wolf, Manuel J.; May, Katharina; König, Sven and Brockmann, Gudrun A. (2023) Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German black Pied cattle. Veterinary Research, 54 (95), pp. 1-7.

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Document available online at: https://veterinaryresearch.biomedcentral.com/articles/10.1186/s13567-023-01227-0


Summary

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.


EPrint Type:Journal paper
Type of presentation:Paper
Keywords:BLE, BÖL, BOEL, FKZ 15NA010, DSN – Deutsches Schwarzbuntes Niederungsrind, Milchvieh, Doppelnutzungsrind, Genreserve, Erhaltungszucht, Sequenzierung
Agrovoc keywords:
Language
Value
URI
English
cattle
http://aims.fao.org/aos/agrovoc/c_1391
English
genotypes
http://aims.fao.org/aos/agrovoc/c_3225
English
genetic markers
http://aims.fao.org/aos/agrovoc/c_24030
Subjects: Animal husbandry > Production systems > Dairy cattle
Animal husbandry > Production systems > Beef cattle
Animal husbandry > Breeding and genetics
Research affiliation: Germany > Federal Organic Farming Scheme - BOEL > Animals > Tierzucht
Germany > University of Berlin - HU
Germany > University of Gießen > Institute of Animal Breeding and Genetics
DOI:10.1186/s13567-023-01227-0
Related Links:https://www.bundesprogramm.de, https://orgprints.org/id/eprint/30261/, https://www.ble.de/DE/Projektfoerderung/projektfoerderung_node.html
Deposited By: Korkuc, Dr. Paula
ID Code:52435
Deposited On:19 Jan 2024 10:04
Last Modified:19 Jan 2024 13:56
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted
Additional Publishing Information:Gefördert durch das Bundesministerium für Ernährung und Landwirtschaft aufgrund eines Beschlusses des Deutschen Bundestages im Rahmen des Bundesprogramms Ökologischer Landbau und andere Formen nachhaltiger Landwirtschaft.

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