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Strategies for sample labelling and library preparation in DNA metabarcoding studies

Bohmann, Kristine and Elbrecht, Vasco and Caroe, Christian and Bista, Iliana and Leese, Florian and Bunce, Michael and Yu, Douglas W. and Seymour, Mathew and Dumbrell, Alex J. and Creer, Simon (2022). Strategies for sample labelling and library preparation in DNA metabarcoding studies. Molecular Ecology Resources. 22 :4 , 1231-1246
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Abstract

Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.

Authors/Creators:Bohmann, Kristine and Elbrecht, Vasco and Caroe, Christian and Bista, Iliana and Leese, Florian and Bunce, Michael and Yu, Douglas W. and Seymour, Mathew and Dumbrell, Alex J. and Creer, Simon
Title:Strategies for sample labelling and library preparation in DNA metabarcoding studies
Series Name/Journal:Molecular Ecology Resources
Year of publishing :2022
Volume:22
Number:4
Page range:1231-1246
Number of Pages:16
Publisher:WILEY
ISSN:1755-098X
Language:English
Publication Type:Article Review/Survey
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Ecology
Keywords:amplicon sequencing, biodiversity assessment, eDNA, environmental DNA, high-throughput sequencing, Illumina sequencing, library preparation
URN:NBN:urn:nbn:se:slu:epsilon-p-114159
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-114159
Additional ID:
Type of IDID
DOI10.1111/1755-0998.13512
Web of Science (WoS)000706646800001
ID Code:27568
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Ecology
(S) > Dept. of Ecology
Deposited By: SLUpub Connector
Deposited On:19 Apr 2022 08:15
Metadata Last Modified:19 Apr 2022 08:21

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