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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
Metabarcoding for stomach-content analyses of Pygmy devil ray (Mobula kuhlii cf. eregoodootenkee): Comparing tissue and ethanol preservative-derived DNA
Ecology and Evolution, Vol.9(5), pp.2678-2687
03/2019
PMCID: PMC6405894
PMID: 30891208
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Source: InCites
Abstract
The application of high-throughput sequencing to retrieve multi-taxon DNA from different substrates such as water, soil, and stomach contents has enabled species identification without prior knowledge of taxon compositions. Here we used three minibarcodes designed to target mitochondrial COI in plankton, 16S in fish, and 16S in crustaceans, to compare ethanol- and tissue-derived DNA extraction methodologies for metabarcoding. The stomach contents of pygmy devilrays (
cf.
) were used to test whether ethanol-derived DNA would provide a suitable substrate for metabarcoding. The DNA barcoding assays indicated that tissue-derived operational taxonomic units (OTUs) were greater compared to those from extractions performed directly on the ethanol preservative. Tissue-derived DNA extraction is therefore recommended for broader taxonomic coverage. Metabarcoding applications should consider including the following: (i) multiple barcodes, both taxon specific (e.g., 12S or 16S) and more universal (e.g., COI or 18S) to overcome bias and taxon misidentification and (ii) PCR inhibitor removal steps that will likely enhance amplification yields. However, where tissue is limited or no longer available, but the ethanol-preservative medium is still available, metabarcoding directly from ethanol does recover the majority of common OTUs, suggesting the ethanol-retrieval method could be applicable for dietary studies. Metabarcoding directly from preservative ethanol may also be useful where tissue samples are limited or highly valued; bulk samples are collected, such as for rapid species inventories; or mixed-voucher sampling is conducted (e.g., for plankton, insects, and crustaceans).
Details
- Title
- Metabarcoding for stomach-content analyses of Pygmy devil ray (Mobula kuhlii cf. eregoodootenkee): Comparing tissue and ethanol preservative-derived DNA
- Creators
- Matteo Barbato - The University of SydneyToby Kovacs - The University of SydneyMelinda A Coleman - Southern Cross University, National Marine Science CentreMatt K Broadhurst - NSW Department of Primary IndustriesMark de Bruyn - The University of Sydney
- Publication Details
- Ecology and Evolution, Vol.9(5), pp.2678-2687
- Publisher
- John Wiley & Sons Ltd.; England
- Grant note
- MdB acknowledges start-up funds from The University of Sydney and the USyd School of Life and Environmental Sciences. MKB acknowledges funding from NSW DPI. We are thankful to three anonymous referees for their helpful comments to improve the manuscript.
- Identifiers
- 991012925459602368
- Copyright
- This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.
- Academic Unit
- Faculty of Science and Engineering; School of Environment, Science and Engineering; National Marine Science Centre
- Language
- English
- Resource Type
- Journal article