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A real-time PCR assay to accurately quantify polar bear DNA in fecal extracts

Lookup NU author(s): Dr Evelyn JensenORCiD

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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).


Abstract

© 2020 Hayward et al. DNA extracted from fecal samples contains DNA from the focal species, food, bacteria and pathogens. Most DNA quantification methods measure total DNA and cannot differentiate among sources. Despite the desirability of noninvasive fecal sampling for studying wildlife populations, low amounts of focal species DNA make it difficult to use for next-generation sequencing (NGS), where accurate DNA quantification is critical for normalization. Two factors are required prior to using fecal samples in NGS libraries: (1) an accurate quantification method for the amount of target DNA and (2) a determination of the relative amount of target DNA needed for successful single nucleotide polymorphism genotyping assays. Here, we address these needs by developing primers to amplify a 101 bp region of the nuclear F2 gene and a quantitative PCR (qPCR) assay that allows the accurate quantification of the amount of polar bear (Ursus maritimus) DNA in fecal extracts. We test the assay on pure polar bear DNA extracted from muscle tissue and find a high correlation between fluorometric and qPCR quantifications. The qPCR assay was also successfully used to quantify the amount of DNA derived from polar bears in fecal extractions. Orthologs of the F2 gene have been identified across vertebrates; thus, similar qPCR assays could be developed for other species to enable noninvasive studies.


Publication metadata

Author(s): Hayward KM, Harwood MP, Lougheed SC, Sun Z, Van Coeverden de Groot P, Jensen EL

Publication type: Article

Publication status: Published

Journal: PeerJ

Year: 2020

Volume: 8

Online publication date: 07/04/2020

Acceptance date: 11/03/2020

Date deposited: 03/03/2022

ISSN (electronic): 2167-8359

Publisher: PeerJ Inc.

URL: https://doi.org/10.7717/peerj.8884

DOI: 10.7717/peerj.8884


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Funding

Funder referenceFunder name
NSERC
OGI-123

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