A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region.

de Jonge, Daniëlle S. W. , Merten, Veronique , Bayer, Till , Puebla, Oscar , Reusch, Thorsten B. H. and Hoving, Henk-Jan T. (2021) A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. Open Access Royal Society Open Science, 8 (2). Art.Nr. 201388. DOI 10.1098/rsos.201388.

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Abstract

Cephalopods are pivotal components of marine food webs, but biodiversity studies are hampered by challenges to sample these agile marine molluscs. Metabarcoding of environmental DNA (eDNA) is a potentially powerful technique to study oceanic cephalopod biodiversity and distribution but has not been applied thus far. We present a novel universal primer pair for metabarcoding cephalopods from eDNA, Ceph18S (Forward: 5′-CGC GGC GCT ACA TAT TAG AC-3′, Reverse: 5′-GCA CTT AAC CGA CCG TCG AC-3′). The primer pair targets the hypervariable region V2 of the nuclear 18S rRNA gene and amplifies a relatively short target sequence of approximately 200 bp in order to allow the amplification of degraded DNA. In silico tests on a reference database and empirical tests on DNA extracts from cephalopod tissue estimate that 44-66% of cephalopod species, corresponding to about 310-460 species, can be amplified and identified with this primer pair. A multi-marker approach with the novel Ceph18S and two previously published cephalopod mitochondrial 16S rRNA primer sets targeting the same region (Jarman et al. 2006 Mol. Ecol. Notes. 6, 268-271; Peters et al. 2015 Mar. Ecol. 36, 1428-1439) is estimated to amplify and identify 89% of all cephalopod species, of which an estimated 19% can only be identified by Ceph18S. All sequences obtained with Ceph18S were submitted to GenBank, resulting in new 18S rRNA sequences for 13 cephalopod taxa

Document Type: Article
Keywords: metabarcodin, universal primer; environmental DNA; Cephalopoda
Dewey Decimal Classification: 500 Natural Sciences and Mathematics > 570 Life sciences; biology
Research affiliation: OceanRep > GEOMAR > FB3 Marine Ecology > FB3-EV Marine Evolutionary Ecology
Main POF Topic: PT6: Marine Life
Refereed: Yes
Open Access Journal?: Yes
Publisher: The Royal Society
Projects: OCEANS
Date Deposited: 13 Apr 2021 11:22
Last Modified: 07 Feb 2024 15:31
URI: https://oceanrep.geomar.de/id/eprint/52269

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