Environmental DNA metabarcoding dataset of fish communities in Shuikou Reservoir, Fujian, China

Abstract: This dataset contains environmental DNA (eDNA) metabarcoding data of fish communities collected from Shuikou Reservoir, a large subtropical canyon-type reservoir on the main stem of the Min River in Fujian Province, China (118°30′–118°50′E, 26°10′–26°25′N). Water sampling was conducted during July–August 2025 across four longitudinal zones (reservoir head, central basin, reservoir tail, and inflowing tributary), two microhabitats (littoral and pelagic), and three water layers (surface, middle, and bottom), yielding 24 independent sampling units (4 zones × 2 microhabitats × 3 layers). A total of 20 samples passed quality control and were subjected to Illumina sequencing.
Methods: For each sample, 6 L of water was filtered through mixed cellulose acetate membranes (47 mm diameter, 0.45 µm pore size). DNA extraction was performed using the Fast DNA Spin Kit (MP Bio, USA). PCR amplification targeted the mitochondrial 12S rRNA gene (~170 bp) using MiFish-U primers (forward: 5'-GTCGGTAAAACTCGTGCCAGC-3’; reverse: 5'-CATAGTGGGGTATCTAATCCCAGTTTG-3’). Sequencing was conducted on an Illumina MiSeq platform with v2 kit (250 bp paired-end reads), targeting 10,000 reads per sample. Raw sequence data were processed using Cutadapt v.3.4 for adapter trimming, DADA2 v.1.20 for ASV inference, and BLAST+ 2.12.0 against MitoFish v3.85 and GenBank Release 246.0 for taxonomic assignment.