Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding
Abstract Environmental DNA (eDNA)‐based methods of species detection are enabling various applications in ecology and conservation including large‐scale biomonitoring efforts. qPCR is widely used as the standard approach for species‐specific detection, often targeting a fish species of interest from...
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Online Access: | http://dx.doi.org/10.1111/1755-0998.13732 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13732 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13732 |
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crwiley:10.1111/1755-0998.13732 2024-06-02T08:05:22+00:00 Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding McCarthy, Avery Rajabi, Hoda McClenaghan, Beverly Fahner, Nicole A. Porter, Emily Singer, Gregory A. C. Hajibabaei, Mehrdad Petroleum Research Newfoundland and Labrador 2022 http://dx.doi.org/10.1111/1755-0998.13732 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13732 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13732 en eng Wiley http://creativecommons.org/licenses/by/4.0/ Molecular Ecology Resources volume 23, issue 3, page 581-591 ISSN 1755-098X 1755-0998 journal-article 2022 crwiley https://doi.org/10.1111/1755-0998.13732 2024-05-03T11:51:35Z Abstract Environmental DNA (eDNA)‐based methods of species detection are enabling various applications in ecology and conservation including large‐scale biomonitoring efforts. qPCR is widely used as the standard approach for species‐specific detection, often targeting a fish species of interest from aquatic eDNA. However, DNA metabarcoding has the potential to displace qPCR in certain eDNA applications. In this study, we compare the sensitivity of the latest Illumina NovaSeq 6000 NGS platform to qPCR TaqMan assays by measuring limits of detection and by analysing eDNA from water samples collected from Churchill River and Lake Melville, NL, Canada. Species‐specific, targeted next generation sequencing (NGS) assays had significantly higher sensitivity than qPCR, with limits of detection 14‐ to 29‐fold lower. For example, when analysing eDNA, qPCR detected Gadus ogac (Greenland cod) in 21% of samples, but targeted NGS detected this species in 29% of samples. General NGS assays were as sensitive as qPCR, while simultaneously detecting 15 fish species from eDNA samples. With over 34,000 fish species on the planet, parallel and sensitive methods such as NGS will be required to support effective biomonitoring at both regional and global scales. Article in Journal/Newspaper Churchill River Gadus ogac Greenland Greenland cod Wiley Online Library Canada Greenland Lake Melville ENVELOPE(-59.557,-59.557,53.728,53.728) Molecular Ecology Resources 23 3 581 591 |
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Wiley Online Library |
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crwiley |
language |
English |
description |
Abstract Environmental DNA (eDNA)‐based methods of species detection are enabling various applications in ecology and conservation including large‐scale biomonitoring efforts. qPCR is widely used as the standard approach for species‐specific detection, often targeting a fish species of interest from aquatic eDNA. However, DNA metabarcoding has the potential to displace qPCR in certain eDNA applications. In this study, we compare the sensitivity of the latest Illumina NovaSeq 6000 NGS platform to qPCR TaqMan assays by measuring limits of detection and by analysing eDNA from water samples collected from Churchill River and Lake Melville, NL, Canada. Species‐specific, targeted next generation sequencing (NGS) assays had significantly higher sensitivity than qPCR, with limits of detection 14‐ to 29‐fold lower. For example, when analysing eDNA, qPCR detected Gadus ogac (Greenland cod) in 21% of samples, but targeted NGS detected this species in 29% of samples. General NGS assays were as sensitive as qPCR, while simultaneously detecting 15 fish species from eDNA samples. With over 34,000 fish species on the planet, parallel and sensitive methods such as NGS will be required to support effective biomonitoring at both regional and global scales. |
author2 |
Petroleum Research Newfoundland and Labrador |
format |
Article in Journal/Newspaper |
author |
McCarthy, Avery Rajabi, Hoda McClenaghan, Beverly Fahner, Nicole A. Porter, Emily Singer, Gregory A. C. Hajibabaei, Mehrdad |
spellingShingle |
McCarthy, Avery Rajabi, Hoda McClenaghan, Beverly Fahner, Nicole A. Porter, Emily Singer, Gregory A. C. Hajibabaei, Mehrdad Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding |
author_facet |
McCarthy, Avery Rajabi, Hoda McClenaghan, Beverly Fahner, Nicole A. Porter, Emily Singer, Gregory A. C. Hajibabaei, Mehrdad |
author_sort |
McCarthy, Avery |
title |
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding |
title_short |
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding |
title_full |
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding |
title_fullStr |
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding |
title_full_unstemmed |
Comparative analysis of fish environmental DNA reveals higher sensitivity achieved through targeted sequence‐based metabarcoding |
title_sort |
comparative analysis of fish environmental dna reveals higher sensitivity achieved through targeted sequence‐based metabarcoding |
publisher |
Wiley |
publishDate |
2022 |
url |
http://dx.doi.org/10.1111/1755-0998.13732 https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13732 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/1755-0998.13732 |
long_lat |
ENVELOPE(-59.557,-59.557,53.728,53.728) |
geographic |
Canada Greenland Lake Melville |
geographic_facet |
Canada Greenland Lake Melville |
genre |
Churchill River Gadus ogac Greenland Greenland cod |
genre_facet |
Churchill River Gadus ogac Greenland Greenland cod |
op_source |
Molecular Ecology Resources volume 23, issue 3, page 581-591 ISSN 1755-098X 1755-0998 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1111/1755-0998.13732 |
container_title |
Molecular Ecology Resources |
container_volume |
23 |
container_issue |
3 |
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581 |
op_container_end_page |
591 |
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1800750166921183232 |