Environmental DNA (eDNA) Metabarcoding Dataset from Urban and Protected Coastal Waters in Jakarta Bay, Indonesia
Description
This dataset contains raw and filtered read sequences generated through environmental DNA (eDNA) metabarcoding of marine water samples collected from four sites in Jakarta Bay, Indonesia. These include two urban-impacted locations (Tanjung Priok Port and Untung Jawa Island) and two sites within the Seribu Islands National Marine Park (Pramuka and Harapan Islands). Water samples were collected in triplicate at each site, and eDNA was extracted using the Qiagen DNeasy Blood and Tissue Kit protocol. PCR amplification targeted the mitochondrial cytochrome c oxidase subunit I (COI) gene using universal primers. Sequencing was performed on the Illumina MiSeq platform, and sequence processing followed the MBRAVE pipeline with taxonomic assignment referencing BOLD and NCBI databases. This dataset supports the manuscript entitled "Urbanization Reshapes Marine Biodiversity: eDNA Insights from Jakarta Bay", submitted to Scientific Reports.
Files
Steps to reproduce
Site Selection & Sampling Four coastal sites in Jakarta Bay, Indonesia were selected: Urban-impacted: Tanjung Priok Port and Untung Jawa Island Protected areas: Pramuka Island and Harapan Island (within Seribu Islands National Marine Park) At each site, three replicates of surface water (1 L each) were collected using sterile techniques. Filtration & DNA Extraction Water samples were filtered on-site using 0.45 µm cellulose nitrate membranes. Filters were preserved in 95% ethanol and stored at –20°C. DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit following a modified protocol for eDNA recovery. PCR Amplification The mitochondrial COI gene was amplified using universal metazoan primers (mlCOIintF/jgHCO2198). PCR conditions followed a 35-cycle program, with successful amplification confirmed via gel electrophoresis. High-Throughput Sequencing Amplicons were pooled and sequenced on the Illumina MiSeq platform (2 × 300 bp, paired-end), using the MiSeq v2 kit. Sequence Processing Raw reads were uploaded to the MBRAVE platform. Reads were quality filtered, paired, denoised, and clustered into OTUs. Taxonomic assignment was conducted using the BOLD and NCBI databases. Data Filtering and Compilation Only sequences identified within Kingdom Animalia were retained for downstream analysis. Final datasets include raw sequences, processed OTU tables, and associated site metadata.
Institutions
- Universitas Padjadjaran
- Institut Pertanian Bogor