MiFish data from river and sea water concentrated using glass fiber filters, Sterivex, and QuickConc

Environmental DNA (eDNA) analysis is effective for non-invasive biodiversity monitoring, revealing species distribution and abundance without ecosystem disruption. Concentration, extraction, and preservation are three essential steps in the eDNA analysis process. Among these, the concentration of eDNA has gained significant research interest, particularly due to the variability of water samples used in studies. To date, various methods for eDNA concentration have been developed, including glass fiber filtration, Sterivex filters, and passive samplers. However, no single method is universally applicable because of the variability in eDNA presence and water characteristics, such as turbidity. Therefore, the development of alternative eDNA concentration methods is crucial for advancing eDNA research. This research introduces QuickConc, a novel nucleic acid capture method that combines benzalkonium chloride (BAC) with dispersed glass fibers. Our results indicate that this approach enhances ..., To evaluate the effect of different concentration methods on the number of detected species and community composition, metabarcoding analyses were conducted for fish eDNA. Our sampling sites included river and sea, but notably excluded pond samples from the sequencing process. The decision to omit pond samples was grounded in the site’s unique characteristics; originally a rice field situated in a segregated area, the pond exhibited a limited presence of fish species.
After DNA extraction, subsequent procedures of amplicon library preparation and NGS were performed by Bioengineering Lab. Co., Ltd (Kanagawa, Japan). The DNeasy PowerClean Pro Cleanup Kit (Qiagen) was used to remove PCR-inhibitory substances, and the elution of DNA was performed in a final volume of 50 μL. The library construction began with a two-step tailed PCR method using four primer sets (Table S3 in related publication), which were partially modified fish universal PCR primers, “MiFish,” developed by Miya et al. (201..., , # Data from: MiFish data from river and sea water concentrated using glass fiber filters, Sterivex, and QuickConc

[https://doi.org/10.5061/dryad.ttdz08m73](https://doi.org/10.5061/dryad.ttdz08m73)

## Description of the data and file structure

This dataset contains metabarcoding data derived from water samples collected across two aquatic environments in Japan: Kobe port and River Muko. The data includes raw sequence reads and associated metadata. This dataset enables comparative analyses of different eDNA concentration methods (glass fiber filters, Sterivex, and QuickConc) and provides insights into the fish community composition in the investigated environments.

### Files and variables

#### File: sea.zip

**Description:** Contains the MiFish data from the sea water samples. 

#### File: river.zip

**Description:** Contains the MiFish data from the river water samples.

**RawData:** Contains the raw FASTQ files obtained from MiSeq sequencing for each sample. Files are named accordi...,