New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones

Moorhouse-Gann, Rosemary J. and Dunn, Jenny and de Vere, Natasha and Goder, Martine and Cole, Nik and Hipperson, Helen and Symondson, William O. C. (2018) New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones. Scientific Reports, 8 . p. 8542. ISSN 2045-2322

Full content URL: https://doi.org/10.1038/s41598-018-26648-2

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New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones
https://doi.org/10.1038/s41598-018-26648
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Abstract

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.

Keywords:metebarcoding, herbivory, universal primers, ITS2
Subjects:C Biological Sciences > C210 Applied Botany
C Biological Sciences > C181 Biodiversity
C Biological Sciences > C180 Ecology
C Biological Sciences > C410 Applied Genetics
C Biological Sciences > C300 Zoology
Divisions:College of Science > School of Life Sciences
ID Code:32124
Deposited On:27 Jun 2018 21:50

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