Metabarcoding primers for Indo-Pacific fishes

Environmental DNA (eDNA) metabarcoding offers an effective solution to determine fish species compositions in communities across diverse environments. However, it is not clear how different metabarcoding primers perform in terms of recovering fish species and community diversity in the Indo-Pacific bioregion. In this study, we compared the relative performance of five metabarcoding primers (Berry 16S, Riaz 12S, MiFish E 12S, MiFish U 12S, and Leray CO1) in recovering Indo-Pacific fish taxa. We tested the primers using template DNA from three different environments: (1) a controlled mock community composed of tissue-based DNA extractions from 96 species, (2) a semi-controlled Indo-Pacific reef fish community from a public aquarium tank, and (3) a natural tropical coral reef lagoon. In the mock community sample, each primer recovered a distinct subset of the community, and no single primer recovered all taxa. Of the 65 distinct genera included in the mock community, all but six were recov..., , # Metabarcoding primers for Indo-Pacific fishes

Dataset DOI: [10.5061/dryad.dr7sqvbbf](https://doi.org/10.5061/dryad.dr7sqvbbf)

## Description of the data and file structure

Environmental DNA (eDNA) samples were amplified with various metabarcoding primers. The file archive contains four directories: VW_Berry_Fishes, VW_MiFish_E_Fishes, VW_Riaz_Fishes, VW_CO1_Fishes, VW_MiFish_U_Fishes, each containing the metabarcoding data for the specified primer. Within each directory, you will find subdirectories for each within-primer sample, including: ExtractionBlank, FieldBlank, PCRBlank, MC001-003 (mock community samples), SP004-006 (coral reef lagoon samples), and WA001-003 (Waikīkī Aquarium samples). Each of these directories in turn contains two fastq.gz files representing the forward (R1) and reverse (R2) raw Illumina reads. These are the raw data files that inform the analysis in the paper.

### Files and variables

#### File: Archive.zip

**Description:** Illumina data. See above for ...,