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Mol Ecol. 2018 Oct;27(20):3968-3975. doi: 10.1111/mec.14844. Epub 2018 Sep 17.

Why the COI barcode should be the community DNA metabarcode for the metazoa.

Author information

1
Grupo de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain.
2
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
3
School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK.
4
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan, China.
5
Department of Life Sciences, Natural History Museum, London, UK.
6
Department of Life Sciences, Imperial College London, Ascot, UK.

Abstract

Metabarcoding of complex metazoan communities is increasingly being used to measure biodiversity in terrestrial, freshwater and marine ecosystems, revolutionizing our ability to observe patterns and infer processes regarding the origin and conservation of biodiversity. A fundamentally important question is which genetic marker to amplify, and although the mitochondrial cytochrome oxidase subunit I (COI) gene is one of the more widely used markers in metabarcoding for the Metazoa, doubts have recently been raised about its suitability. We argue that (a) the extensive coverage of reference sequence databases for COI; (b) the variation it presents; (c) the comparative advantages for denoising protein-coding genes; and (d) recent advances in DNA sequencing protocols argue in favour of standardizing for the use of COI for metazoan community samples. We also highlight where research efforts should focus to maximize the utility of metabarcoding.

KEYWORDS:

barcoding; eDNA; high-throughput sequencing; metabarcoding; next-generation sequencing

PMID:
30129071
DOI:
10.1111/mec.14844

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