de Jonge, Danielle SW, Merten, Véronique, Bayer, Till, Puebla, Oscar, Reusch, Thorsten BH and Hoving, Henk-Jan T (2021) A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. Royal Society Open Science, 8 (2). pp. 1-16. DOI https://doi.org/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
Programme Area (enter as: PA1/PA2/PA3/PA4/PA5): PA1
Research affiliation: Affiliations > Not ZMT
Ecology > Fish Ecology and Evolution
Refereed: Yes
Open Access Journal?: Yes
DOI etc.: https://doi.org/10.1098/rsos.201388
Date Deposited: 10 Feb 2021 16:37
Last Modified: 10 Feb 2021 16:37
URI: http://cris.leibniz-zmt.de/id/eprint/4525

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