Reference sequence database for eDNA metabarcoding of San Francisco estuary fishes and invertebrates

Environmental DNA (eDNA) methods complement traditional monitoring and can
be configured to detect multiple species simultaneously. One such
approach, eDNA metabarcoding, uses high-throughput DNA sequencing to
indirectly detect many different organisms, spanning broad taxonomic
boundaries, from water samples. We are optimizing a non-invasive, low cost
eDNA metabarcoding protocol to be used in conjunction with existing
monitoring programs. One resource that is currently lacking for
metabarcoding studies in general, including those in the San Francisco
Estuary (SFE), is a comprehensive database of DNA barcode reference
sequences. Without this foundational data, many species go undetected or
misidentified in metabarcoding studies. To meet this need, we generated a
custom barcode sequence database for the SFE by DNA sequencing and mining
of public DNA seqeunce data for estuarine and freshwater species of
interest to monitoring programs and ecological studies. Here we present
custom reference sequence databases for three barcodes: Cytochrome C
Oxidase I (COI), 12S MiFish and 16S.