YZFishDB: A curated DNA reference database for the fishes of the Yangtze River Basin

The utility and precision of DNA metabarcoding are heavily dependent on the quality of the corresponding reference database, especially in understudied ecosystems. Public databases are often relied upon, especially for studies in species-rich ecosystems, despite potential issues of accuracy and reliability. We developed a curated DNA reference database (YZFishDB) by combining four public reference databases and representative sequences of underrepresented taxa for ray-finned fishes of the Yangtze River Basin (YRB), to improve taxonomic identification, particularly for environmental DNA (eDNA) metabarcoding. We compared taxonomic assignment results for a set of eDNA data from the YRB using YZFishDB and the MitoFish reference database to test their utility. YZFishDB included 54,546 unique sequences covering 503 taxa. The taxonomic assignment comparison showed that both reference databases (YZFishDB and MitoFish) identified 118 shared taxa, while YZFishDB identified 16 additional taxa and MitoFish identified 7 additional taxa. All ASVs assigned to unique taxa by MitoFish were assigned to other taxa by YZFishDB, with better BLAST quality metrics. The development of YZFishDB provides a valuable resource towards improving DNA metabarcoding results as eDNA surveys continue to increase in popularity in the YRB.