FishCARD: Fish 12S California Current Specific Reference Database for
Enhanced Metabarcoding Efforts
Abstract
DNA metabarcoding is an important tool for molecular ecology. However,
metabarcoding effectiveness hinges on the quality of reference databases
for taxa and loci of interest. This limitation is true for metabarcoding
of marine fishes in the California Current Large Marine Ecosystem where
there is a paucity of reference 12S barcodes. Here we present FishCARD,
a California Current-specific fish 12S-specific reference barcode
database. We barcoded 612 species using the MiFish metabarcoding
primers; an addition of 258 species to the 459 California Current fish
species with existing 12S barcodes from GenBank. The resulting FishCARD
database covers 82.7% of California Current fishes, and it includes
virtually all fishes sampled by large marine monitoring programs such as
the Partnership for Interdisciplinary Studies of Coastal Oceans and
California Cooperative Oceanic Fisheries Investigation. To demonstrate
the importance of complete reference databases for eDNA metabarcoding,
we compared species and reads identified from three 1L seawater samples
collected off Santa Cruz Island, CA using GenBank sequences with and
without our generated barcodes, as well as the FishCARD database curated
here. The inclusion of our generated barcodes allowed the additional
identification of 15 native taxa and 21.8% of total reads from eDNA
samples. However, we found that half of all amplicon sequence variants
(ASVs) generated by MiFish 12S primers were of non-vertebrate 16S
origin, demonstrating a clear limitation of a widely employed fish
metabarcoding primers. Despite these limitations, FishCARD provides an
important genetic resource to enhance the effectiveness of marine
metabarcoding efforts in the California Current Large Marine Ecosystem.