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A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish

Citation

Zhang, Shan; Zhao, Jindong; Yao, Meng (2020), A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish, Dryad, Dataset, https://doi.org/10.5061/dryad.hdr7sqvfw

Abstract

Accurate assessments of fish species diversity and community composition are essential for understanding fish ecology and conservation management. Environmental DNA (eDNA) metabarcoding has become an integrated method for monitoring fish species. The accuracy and efficacy of eDNA metabarcoding relies heavily on the choice of primers used for PCR amplification. A wide selection of metabarcoding primers for fish has been developed; however, there exists no comprehensive and comparative evaluation of their amplification or taxonomic classification of a rich diversity of fish species, which hinders informed decisions regarding their suitability for different study systems.

Here, we reviewed the literature and compiled a list of 22 primer sets for eDNA-based metabarcoding analysis of teleost fish, the performance of which was compared using in silico PCR, followed by in vitro metabarcoding analysis using eDNA from waterbodies in Beijing, which harbour a high number of freshwater fish species.

We found that the primers showed considerable differences in the amplified taxonomic ranges and proportions, fish taxa richness, species discrimination power, and fish community compositions, both in silico and in vitro. The number of fish taxa detected from eDNA by the primer sets varied from 0 to 66. Primers targeting the 12S rRNA gene generally detected greater fish diversity than those targeting the 16S rRNA or COI genes, while primers targeting the cytochrome b gene amplified the fewest fish taxa in vitro. 4. Regarding target genes, 12S primers generally outperformed other primers in terms of amplified fish diversity. The results of in silico PCR and in vitro tests were not always in agreement, suggesting that primer choice for biodiversity surveys should not be based solely on in silico evaluation. The use of different primers can qualitatively and quantitatively affect the detected biodiversity and these effects should be considered in experimental design and data interpretation. These results will assist with primer selection for eDNA-based fish surveys, and consequently support conservation of freshwater biodiversity.

Usage Notes

01_Krona_files. Interactive versions of the Krona graphs showing the results of in silico PCR using each primer set.

02_ecopcr_all_taxa. Files of the in silico PCR results using the primers to extract all sequences in the EMBL database.

03_ecopcr_Actinopterygii. Files of the in silico PCR results using the primers to extract sequences within Actinopterygii.

04_Obitools_output_rawdata. Summary of sequence abundance data generated by the Obitools program for each primer set.

05_Final_metabarcoding_data_fish_taxa. Files of final metabarcoding data of the primers following bioinformatics processing, showing sequence identity and abundance of fish taxa.