Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems

Abstract Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring of organisms is becoming easier and promises a revolution in our approaches to detect changes in biodiversity over space and time. A cornerstone of eDNA approach is the development of primer pairs that all...

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Autores principales:	Andrea Polanco F., Eilísh Richards, Benjamin Flück, Alice Valentini, Florian Altermatt, Sébastien Brosse, Jean‐Claude Walser, David Eme, Virginie Marques, Stéphanie Manel, Camille Albouy, Tony Dejean, Loïc Pellissier
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	biodiversity biomonitoring environmental DNA fishes in silico PCR neural network Environmental sciences GE1-350 Microbial ecology QR100-130
Acceso en línea:	https://doaj.org/article/0ba3cd649eb844f893fe43655131e7ae
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spelling	oai:doaj.org-article:0ba3cd649eb844f893fe43655131e7ae2021-11-23T16:15:24ZComparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems2637-494310.1002/edn3.232https://doaj.org/article/0ba3cd649eb844f893fe43655131e7ae2021-11-01T00:00:00Zhttps://doi.org/10.1002/edn3.232https://doaj.org/toc/2637-4943Abstract Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring of organisms is becoming easier and promises a revolution in our approaches to detect changes in biodiversity over space and time. A cornerstone of eDNA approach is the development of primer pairs that allow amplifying the DNA of specific taxonomic groups, which is then used to link the DNA sequence to taxonomic identification. Here, we propose a framework for comparing primer pairs regarding (a) their capacity to bind and amplify a broad coverage of species within the target clade using in silico PCR, (b) their capacity to not only discriminate between species but also genera or families, and (c) their in situ specificity and efficiency across a variety of environments. As a case study, we focus on two mitochondrial 12S primer pairs, MiFish‐U and teleo, which were designed to amplify fishes. We found that the performance of in silico PCRs were high for both primer pairs, but teleo amplified more genera across Actinopterygii, Chondrichthyes, and Petromyzontomorphi than MiFish‐U. In contrast, the discriminatory power for species, genera, and families were higher for MiFish‐U than teleo, likely associated with the greater length of the amplified DNA fragments. The evaluation of their in situ efficiency showed a higher recovered species richness of teleo compared to MiFish‐U in tropical and temperate freshwater environments, but that generally both teleo and MiFish‐U primers pairs perform well to monitor fish species. Since more species were detected when used together, those primer pairs are best used in combination to increase the ability of species detection.Andrea Polanco F.Eilísh RichardsBenjamin FlückAlice ValentiniFlorian AltermattSébastien BrosseJean‐Claude WalserDavid EmeVirginie MarquesStéphanie ManelCamille AlbouyTony DejeanLoïc PellissierWileyarticlebiodiversitybiomonitoringenvironmental DNAfishesin silico PCRneural networkEnvironmental sciencesGE1-350Microbial ecologyQR100-130ENEnvironmental DNA, Vol 3, Iss 6, Pp 1113-1127 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	biodiversity biomonitoring environmental DNA fishes in silico PCR neural network Environmental sciences GE1-350 Microbial ecology QR100-130
spellingShingle	biodiversity biomonitoring environmental DNA fishes in silico PCR neural network Environmental sciences GE1-350 Microbial ecology QR100-130 Andrea Polanco F. Eilísh Richards Benjamin Flück Alice Valentini Florian Altermatt Sébastien Brosse Jean‐Claude Walser David Eme Virginie Marques Stéphanie Manel Camille Albouy Tony Dejean Loïc Pellissier Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
description	Abstract Through the development of environmental DNA (eDNA) metabarcoding, in situ monitoring of organisms is becoming easier and promises a revolution in our approaches to detect changes in biodiversity over space and time. A cornerstone of eDNA approach is the development of primer pairs that allow amplifying the DNA of specific taxonomic groups, which is then used to link the DNA sequence to taxonomic identification. Here, we propose a framework for comparing primer pairs regarding (a) their capacity to bind and amplify a broad coverage of species within the target clade using in silico PCR, (b) their capacity to not only discriminate between species but also genera or families, and (c) their in situ specificity and efficiency across a variety of environments. As a case study, we focus on two mitochondrial 12S primer pairs, MiFish‐U and teleo, which were designed to amplify fishes. We found that the performance of in silico PCRs were high for both primer pairs, but teleo amplified more genera across Actinopterygii, Chondrichthyes, and Petromyzontomorphi than MiFish‐U. In contrast, the discriminatory power for species, genera, and families were higher for MiFish‐U than teleo, likely associated with the greater length of the amplified DNA fragments. The evaluation of their in situ efficiency showed a higher recovered species richness of teleo compared to MiFish‐U in tropical and temperate freshwater environments, but that generally both teleo and MiFish‐U primers pairs perform well to monitor fish species. Since more species were detected when used together, those primer pairs are best used in combination to increase the ability of species detection.
format	article
author	Andrea Polanco F. Eilísh Richards Benjamin Flück Alice Valentini Florian Altermatt Sébastien Brosse Jean‐Claude Walser David Eme Virginie Marques Stéphanie Manel Camille Albouy Tony Dejean Loïc Pellissier
author_facet	Andrea Polanco F. Eilísh Richards Benjamin Flück Alice Valentini Florian Altermatt Sébastien Brosse Jean‐Claude Walser David Eme Virginie Marques Stéphanie Manel Camille Albouy Tony Dejean Loïc Pellissier
author_sort	Andrea Polanco F.
title	Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
title_short	Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
title_full	Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
title_fullStr	Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
title_full_unstemmed	Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems
title_sort	comparing the performance of 12s mitochondrial primers for fish environmental dna across ecosystems
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/0ba3cd649eb844f893fe43655131e7ae
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Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems

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