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.