A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region
de Jonge, D.S.W.; Merten, V.; Bayer, T.; Puebla, O.; Reusch, Th.B.H.; Hoving, H.-J.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): 201388. https://dx.doi.org/10.1098/rsos.201388
In: Royal Society Open Science. The Royal Society: London. ISSN 2054-5703; e-ISSN 2054-5703, more
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| Keywords |
Cephalopoda [WoRMS]
Marine/Coastal |
| Author keywords |
Cephalopoda, metabarcoding, environmental DNA, universal primer |
| Authors | | Top |
- de Jonge, D.S.W.
- Merten, V.
- Bayer, T.
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- Puebla, O.
- Reusch, Th.B.H.
- Hoving, H.-J.T.
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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. |
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