DOI: 10.5061/dryad.dr7sqvbbf
title: Metabarcoding primers for Indo-Pacific fishes

description: 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 recovered by at
 least one primer, representing 91% of genera. Fifty-nine of the 96
 included species (61%) were identified to species-level using at least one
 primer set. From the aquarium community, 17 of the 20 known genera were
 recovered (85%), and 13 out of 24 (54%) censused species were identified
 by at least one primer. In the coral reef lagoon 48 genera were
 identified, and 47 species-level identifications were made, including 87%
 endemic and established species. Overall, we find Riaz 12S performed
 better than other fish-specific markers although there were differences in
 the specific fish taxa recovered. While all markers performed well in the
 mock community in terms of the relative proportion of fish sequences
 recovered, this did not accurately predict how they would perform under
 natural conditions. Caution is therefore urged in using a mock community
 alone to evaluate metabarcoding primer performance for studies in natural
 environments.
description: # 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 description of files. ## Code/software Please see paper for
 details. ## Access information Other publicly accessible locations of the
 data: * NCBI PRJNA1241309 Data was derived from the following sources: *
 n/a