parallel identification of multiple taxa from one complex DNA sample. ![]() Biodiversity assessments of an eDNA sample using a universal primer set fall under the broader term metabarcoding, i.e. filtered from water) can detect the presence of a species or of multiple taxa by targeting a variable gene with either a species-specific or universal primer set, respectively. PCR amplification of eDNA in a sample (e.g. This technique is based on the idea that organisms leave DNA in the environment, and that this DNA can be extracted and sequenced to identify the species from which it originates. The challenges associated with cephalopod sampling, particularly in remote areas such as deep pelagic environments, raise an urgent need for novel monitoring methods.Įnvironmental DNA (eDNA) analysis constitutes a promising tool to study the distribution and diversity of cephalopods. The study of cephalopod remains in the stomachs of predators provides indirect evidence of their presence, but the digested state of cephalopod remains may hamper species identification, and the selectivity of the predators and limited knowledge of their foraging area introduces bias. Video surveys with submersibles and towed cameras require lights that are easily detectable by the well-developed cephalopod eyes, which may result in avoidance behaviour. Additional difficulties in sampling cephalopods result from their possibly patchy distribution and their agility which allows them to avoid or escape sampling gear. The size of trawled cephalopods is biased by the used mesh and net size and specimens often get entangled and damaged in the mesh which may make it difficult to identify them morphologically. One of the reasons for this paucity of information is that cephalopods are difficult to study with traditional sampling methods like net catches or video surveys. ĭeep-sea cephalopods have evolved specialized traits to cope with life in continuous darkness, but basic biological data are still lacking for the majority of species. Cephalopods are among the giants of the ocean (giant squid Architeuthis spp., colossal squid Mesonychoteuthis hamiltoni), and the highest diversity at the family level is found in the deep sea. Their high protein content and large populations make them important in commercial fisheries and food–web interactions as both predator and prey. All sequences obtained with Ceph18S were submitted to GenBank, resulting in new 18S rRNA sequences for 13 cephalopod taxa.Ĭephalopods, the molluscan class to which squids, octopods, cuttlefish and vampire squids belong, occur in all the world's oceans from the intertidal zone to the deep sea. 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. ![]() 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. 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. 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. 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′). Metabarcoding of environmental DNA (eDNA) is a potentially powerful technique to study oceanic cephalopod biodiversity and distribution but has not been applied thus far. ![]() Cephalopods are pivotal components of marine food webs, but biodiversity studies are hampered by challenges to sample these agile marine molluscs.
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