4.5 | eDNA and metabarcoding
In order to explore biodiversity, ecosystem function, and population
genetics, a high-resolution marker with a good reference library is
critical. As of the writing of this manuscript there was COI data
(including mitochondrial genomes) for ~eight species of
ctenophores on GenBank and BOLD databases. The paucity of mitochondrial
sequencing data is mostly a result of the failure of commonly used
‘barcoding’ primers to amplify the highly divergent phylum. In a study
that took 100-meter depth vertical net tows at stations from Monterey
Bay, CA to the Gulf of California, Mexico, Pitz et al. , (2020)
successfully sequenced at least some ctenophores for COI and18S, but was only able to assign taxonomy mostly to the family
level. When net tow data were queried against sequences generated by the
new ctenophore primers, we were able to assign thousands of sequences to
ten distinct species of ctenophores, illuminating how diversity changed
over two important biogeographic barriers, Point Conception and Punta
Eugenia (Figure 6). Common primers only amplify a few groups of
ctenophores and although we had successful taxonomic assignments, there
were certainly more than ten species in the net-tow samples. With the
addition of new primers and sequences, researchers are now able to
redesign common primers to include the full spectrum of diversity of
ctenophores in the world ocean.
In conclusion, the primers designed herein will enable
researchers worldwide to amplify and sequence ctenophores for the
mitochondrial COI locus for quick identification, as a population
genetic marker, and for metabarcoding studies. With the publication of
our sequences amplified from our new primers, researchers can increase
our understanding of processes large and small in the world ocean. As we
continue to sequence a broader diversity of ctenophores, new sequence
information will help with species identification and descriptions, and
will also provide a better understanding of relationships within
Ctenophora.