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DOI

  • Rosemary Moorhouse-Gann
    Cardiff University
  • Jenny Dunn
    RSPB Centre for Conservation ScienceCardiff UniversityUniversity of Lincoln
  • Natasha de Vere
    National Botanic Garden of Wales
  • Martine Goder
    Mauritian Wildlife Foundation
  • Nik C. Cole
    Mauritian Wildlife FoundationDurrell Wildlife Conservation Trust
  • Helen Hipperson
    NERC Biomolecular Analysis Facility
  • William Symondson
    Cardiff University
DNA metabarcoding is a rapidly growing technique for obtaining detailed dietary information. Current metabarcoding methods for herbivory, using a single locus, can lack taxonomic resolution for some applications. We present novel primers for the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) designed for dietary studies in Mauritius and the UK, which have the potential to give unrivalled taxonomic coverage and resolution from a short-amplicon barcode. In silico testing used three databases of plant ITS2 sequences from UK and Mauritian floras (native and introduced) totalling 6561 sequences from 1790 species across 174 families. Our primers were well-matched in silico to 88% of species, providing taxonomic resolution of 86.1%, 99.4% and 99.9% at the species, genus and family levels, respectively. In vitro, the primers amplified 99% of Mauritian (n = 169) and 100% of UK (n = 33) species, and co-amplified multiple plant species from degraded faecal DNA from reptiles and birds in two case studies. For the ITS2 region, we advocate taxonomic assignment based on best sequence match instead of a clustering approach. With short amplicons of 187–387 bp, these primers are suitable for metabarcoding plant DNA from faecal samples, across a broad geographic range, whilst delivering unparalleled taxonomic resolution.
Original languageEnglish
Article number8542
JournalScientific Reports
Volume8
DOIs
Publication statusPublished - 4 Jun 2018
Externally publishedYes
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