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In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses.

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Title: In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses.
Authors: Tournayre, Orianne1 (AUTHOR) orianne.tournayre@supagro.fr, Leuchtmann, Maxime2 (AUTHOR), Filippi‐Codaccioni, Ondine3,4 (AUTHOR), Trillat, Marine1 (AUTHOR), Piry, Sylvain1 (AUTHOR), Pontier, Dominique3,4 (AUTHOR), Charbonnel, Nathalie1 (AUTHOR), Galan, Maxime1 (AUTHOR)
Source: Ecology & Evolution (20457758). Jul2020, Vol. 10 Issue 13, p6310-6332. 23p.
Subject Terms: *Animal nutrition, *Arthropoda, DNA primers, Horseshoe bats, Bats, Predation, Unmarried couples
Abstract: During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo‐mock community (33 arthropod taxa from 16 orders), and guano‐based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano‐based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one‐third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints. [ABSTRACT FROM AUTHOR]
Copyright of Ecology & Evolution (20457758) is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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Items – Name: Title
  Label: Title
  Group: Ti
  Data: In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses.
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  Data: <searchLink fieldCode="AR" term="%22Tournayre%2C+Orianne%22">Tournayre, Orianne</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> orianne.tournayre@supagro.fr</i><br /><searchLink fieldCode="AR" term="%22Leuchtmann%2C+Maxime%22">Leuchtmann, Maxime</searchLink><relatesTo>2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Filippi‐Codaccioni%2C+Ondine%22">Filippi‐Codaccioni, Ondine</searchLink><relatesTo>3,4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Trillat%2C+Marine%22">Trillat, Marine</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Piry%2C+Sylvain%22">Piry, Sylvain</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Pontier%2C+Dominique%22">Pontier, Dominique</searchLink><relatesTo>3,4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Charbonnel%2C+Nathalie%22">Charbonnel, Nathalie</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Galan%2C+Maxime%22">Galan, Maxime</searchLink><relatesTo>1</relatesTo> (AUTHOR)
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  Data: <searchLink fieldCode="JN" term="%22Ecology+%26+Evolution+%2820457758%29%22">Ecology & Evolution (20457758)</searchLink>. Jul2020, Vol. 10 Issue 13, p6310-6332. 23p.
– Name: Subject
  Label: Subject Terms
  Group: Su
  Data: *<searchLink fieldCode="DE" term="%22Animal+nutrition%22">Animal nutrition</searchLink><br />*<searchLink fieldCode="DE" term="%22Arthropoda%22">Arthropoda</searchLink><br /><searchLink fieldCode="DE" term="%22DNA+primers%22">DNA primers</searchLink><br /><searchLink fieldCode="DE" term="%22Horseshoe+bats%22">Horseshoe bats</searchLink><br /><searchLink fieldCode="DE" term="%22Bats%22">Bats</searchLink><br /><searchLink fieldCode="DE" term="%22Predation%22">Predation</searchLink><br /><searchLink fieldCode="DE" term="%22Unmarried+couples%22">Unmarried couples</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo‐mock community (33 arthropod taxa from 16 orders), and guano‐based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano‐based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one‐third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Ecology & Evolution (20457758) is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1002/ece3.6362
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      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 23
        StartPage: 6310
    Subjects:
      – SubjectFull: Animal nutrition
        Type: general
      – SubjectFull: Arthropoda
        Type: general
      – SubjectFull: DNA primers
        Type: general
      – SubjectFull: Horseshoe bats
        Type: general
      – SubjectFull: Bats
        Type: general
      – SubjectFull: Predation
        Type: general
      – SubjectFull: Unmarried couples
        Type: general
    Titles:
      – TitleFull: In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses.
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            NameFull: Tournayre, Orianne
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            – D: 01
              M: 07
              Text: Jul2020
              Type: published
              Y: 2020
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