Reference Database Comparisons
Samples processed using the CRUX-12S reference database assigned 89.5% (154/172) of vertebrate ASVs to Family-level and 84.3% (145/172) of vertebrate ASVs to species-level (Supplemental Table 5). Examining merged reads only, the CRUX-12S reference database assigned 94.8% (55/58) of all vertebrate ASVs to Family-level and 87.9% (51/58) of all vertebrate ASVs to species-level (Supplemental Table 6). Examining only forward-reads, the CRUX-12S database assigned 87.9% (94/107) of all vertebrate ASVs to Family-level and 83.2% (89/107) of all vertebrate ASVs to species-level. Across all vertebrate ASVs, the CRUX-12S database produced 31 unique Family-level assignments, 39 unique genus-level assignments, and 38 unique species-level assignments of which only 25 were species native to the California Current Large Marine Ecosystem. Across all vertebrate ASVs, the CRUX-12S database failed to resolve 1.7% (3/172) of vertebrate ASVs to a vertebrate Class, 7% (12/172) of vertebrate ASVs below Class-level, and 1.7% (3/172) of vertebrate ASVs below Order-level.
We then conducted taxonomic assignments using the combined database comprised of both CRUX -12S reference barcodes supplemented with the additional 757 barcodes generated in this study. Samples processed using the combined reference database assigned 100% (172/172) of vertebrate ASVs to Family-level and 88.4% (152/172) of vertebrate ASVs to species-level. For merged reads only, the combined database assigned 100% (58/58) of all vertebrate ASVs to Family -level and 93.1% (54/58) of all vertebrate ASVs to species-level. For forward-only reads, the combined database assigned 100% (107/107) of all vertebrate ASVs to Family-level and 87.9% (94/107) of all vertebrate ASVs to species-level. Across all vertebrate ASVs, the combined database produced 28 unique Family-level assignments, 38 unique genus-level assignments, and 37 unique species-level assignments of which 36 were species native to the California Current Large Marine Ecosystem. No ASVs were assigned to only the Class- or Order-level.
Lastly, we assigned taxonomy using the curated FishCARD reference database comprised of only California Current fish 12S reference barcodes. Samples processed using the curated FishCARD reference database resulted in 99.4% (171/172) of all ASVs assigned to Family -level and 90.7% (156/172) of all ASVs assigned to species-level. For merged reads only, the FishCARD database assigned 100% (58/58) of all vertebrate ASVs to Family-level and 95% (55/58) of all vertebrate ASVs to species-level. For forward-only reads, the FishCARD database assigned 100% (107/107) of all vertebrate ASVs to Family-level and 86.0% (92/107) of all vertebrate ASVs to species-level.
Across all vertebrate ASVs, the FishCARD database produced 27 Family-level assignments, 39 genus-level assignments, and 37 species-level assignments of which all were native CA species. The FishCARD database failed to assign one vertebrate ASV which was assigned to the Family Delphinidae by both the CRUX-12S and combined databases.