DOI: 10.57760/sciencedb.07058
title: A dataset of environmental DNA metabarcoding to detect the jellyfish taxa in Yantai Sishili bay, China 2022
title: A dataset of environmental DNA metabarcoding to detect the jellyfish taxa in Yantai Sishili bay, China 2022

description: Two cruises were carried out in YSB on 18-21 July and 16-18 August, respectively. Eighteen stations were surveyed in July and 17 stations in August (except station YT-14). In each station, 1 L of surface and bottom layer seawater were collected by water sampler in sterile 1 L plastic bottles. Each water sample (1 L) was filtered through a 0.7 μm GF/F filter membrane (Whatman, Maidstone, UK). In total, membrane samples of surface (n = 35) and bottom (n = 35) layer seawater were obtained in two cruises. Sediments were collected from each station using a bottom sampler, and a tube (about 50 ml in volume) of sediments was dug with a sterile disposable syringe on board and placed in a 50 ml sterile centrifuge tube. A total of 35 sediment samples were obtained in two cruises. Samples were temporarily placed in liquid nitrogen until they were brought back to the laboratory and quickly transferred to -80 ℃ refrigerator. The eDNA extraction of GF/F filter membranes from field collection (n = 70) and laboratory experiment (n = 9) was performed using DNeasy Blood & Tissue Kits (Qiagen, Hilden, Germany). The eDNA extraction of sediments from field collection (n = 35) was performed using a DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany).PCR amplification was performed using a 20 μl reaction system from TransStart Fastpfu DNA Polymerase (TransGen AP221-02) including 4 μl 5× FastPfu Buffer, 2 μl 2.5 mM dNTPs, 0.8 μl each of forward and reverse primers with barcodes (5 µM), 0.4μl FastPfu Polymerase, 0.2 μl BSA, 2μl template DNA, and 9.8 μl ddH2O. The following programs were run on the ABI GeneAmp® 9700 PCR instrument: initial denaturation at 95℃ for 3min; 37 cycles of 95℃ 30s, 60℃ 30s and 72℃ 45s; followed by a final extension executed at 72℃ for 10min. Three replicates were used for each sample. The PCR products from the same sample were mixed and detected by electrophoresis in a 2% (w/v) agarose gel. Subsequently, the PCR products were recovered with the AxyPrepDNA gel recovery kit (AXYGEN), eluted with Tris-HCl buffer, and detected again on 2% agarose gel electrophoresis. The PCR amplicons of each sample were quantified by the QuantiFluorTM-ST blue fluorescence quantification system (Promega), and then normalized to equimolar amounts. The amplicon libraries were generated using TruSeqTM DNA Sample Prep Kit (Illumina) and paired-end sequenced (2×300bp) on a MiSeq platform at Majorbio Bio-Pharm Technology Co., Ltd (Shanghai, China). The paired-end (PE) reads obtained from Miseq high-throughput sequencing of 48 eDNA samples were merged into consensus sequences with Flash (version 1.2.11) and then treated to remove sequences with mismatch ratio above 0.2. The merged sequences were quality-filtered to obtain optimized sequences using QIIME v1.9.1 with the following criteria: Exact barcode matching and 2 nucleotides mismatch in primer matching. Operational taxonomic units (OTUs) were clustered with 97% sequence similarity cutoff using UPARSE, and chimeric sequences were identified and removed using UCHIME. The taxonomy of each sequence was analyzed by BLAST (E-value = 10-5) against the Nucleotide Sequence Database (nt_v20210917) of NCBI database. Singleton OTUs and OTUs being classified as other domains (except for Eukaryota) or kingdom (except for Metazoa) were removed because of the non-specific amplication of primers. This dataset contains sequence information for OTU clustering and species annotation.
description: Two cruises were carried out in YSB on 18-21 July and 16-18 August, respectively. Eighteen stations were surveyed in July and 17 stations in August (except station YT-14). In each station, 1 L of surface and bottom layer seawater were collected by water sampler in sterile 1 L plastic bottles. Each water sample (1 L) was filtered through a 0.7 μm GF/F filter membrane (Whatman, Maidstone, UK). In total, membrane samples of surface (n = 35) and bottom (n = 35) layer seawater were obtained in two cruises. Sediments were collected from each station using a bottom sampler, and a tube (about 50 ml in volume) of sediments was dug with a sterile disposable syringe on board and placed in a 50 ml sterile centrifuge tube. A total of 35 sediment samples were obtained in two cruises. Samples were temporarily placed in liquid nitrogen until they were brought back to the laboratory and quickly transferred to -80 ℃ refrigerator. The eDNA extraction of GF/F filter membranes from field collection (n = 70) and laboratory experiment (n = 9) was performed using DNeasy Blood & Tissue Kits (Qiagen, Hilden, Germany). The eDNA extraction of sediments from field collection (n = 35) was performed using a DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany).PCR amplification was performed using a 20 μl reaction system from TransStart Fastpfu DNA Polymerase (TransGen AP221-02) including 4 μl 5× FastPfu Buffer, 2 μl 2.5 mM dNTPs, 0.8 μl each of forward and reverse primers with barcodes (5 µM), 0.4μl FastPfu Polymerase, 0.2 μl BSA, 2μl template DNA, and 9.8 μl ddH2O. The following programs were run on the ABI GeneAmp® 9700 PCR instrument: initial denaturation at 95℃ for 3min; 37 cycles of 95℃ 30s, 60℃ 30s and 72℃ 45s; followed by a final extension executed at 72℃ for 10min. Three replicates were used for each sample. The PCR products from the same sample were mixed and detected by electrophoresis in a 2% (w/v) agarose gel. Subsequently, the PCR products were recovered with the AxyPrepDNA gel recovery kit (AXYGEN), eluted with Tris-HCl buffer, and detected again on 2% agarose gel electrophoresis. The PCR amplicons of each sample were quantified by the QuantiFluorTM-ST blue fluorescence quantification system (Promega), and then normalized to equimolar amounts. The amplicon libraries were generated using TruSeqTM DNA Sample Prep Kit (Illumina) and paired-end sequenced (2×300bp) on a MiSeq platform at Majorbio Bio-Pharm Technology Co., Ltd (Shanghai, China). The paired-end (PE) reads obtained from Miseq high-throughput sequencing of 48 eDNA samples were merged into consensus sequences with Flash (version 1.2.11) and then treated to remove sequences with mismatch ratio above 0.2. The merged sequences were quality-filtered to obtain optimized sequences using QIIME v1.9.1 with the following criteria: Exact barcode matching and 2 nucleotides mismatch in primer matching. Operational taxonomic units (OTUs) were clustered with 97% sequence similarity cutoff using UPARSE, and chimeric sequences were identified and removed using UCHIME. The taxonomy of each sequence was analyzed by BLAST (E-value = 10-5) against the Nucleotide Sequence Database (nt_v20210917) of NCBI database. Singleton OTUs and OTUs being classified as other domains (except for Eukaryota) or kingdom (except for Metazoa) were removed because of the non-specific amplication of primers. This dataset contains sequence information for OTU clustering and species annotation.