eDNA along Houdong riverine zonation in Taiwan

Description

Enregistrements de données

Les données de cette ressource occurrence ont été publiées sous forme d'une Archive Darwin Core (Darwin Core Archive ou DwC-A), le format standard pour partager des données de biodiversité en tant qu'ensemble d'un ou plusieurs tableurs de données. Le tableur de données du cœur de standard (core) contient 6 297 enregistrements.

1 tableurs de données d'extension existent également. Un enregistrement d'extension fournit des informations supplémentaires sur un enregistrement du cœur de standard (core). Le nombre d'enregistrements dans chaque tableur de données d'extension est illustré ci-dessous.

Cet IPT archive les données et sert donc de dépôt de données. Les données et métadonnées de la ressource sont disponibles pour téléchargement dans la section téléchargements. Le tableau des versions liste les autres versions de chaque ressource rendues disponibles de façon publique et permet de tracer les modifications apportées à la ressource au fil du temps.

Versions

Le tableau ci-dessous n'affiche que les versions publiées de la ressource accessibles publiquement.

Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Hoh D (2023): eDNA along Houdong riverine zonation in Taiwan. v1.7. Taiwan Biodiversity Information Facility (TaiBIF). Dataset/Occurrence. https://ipt.taibif.tw/resource?r=houdongkeng_water_edna&v=1.7

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est Taiwan Biodiversity Information Facility (TaiBIF). Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 2615342d-7349-4e75-ae34-cda6cb403e2e.  Taiwan Biodiversity Information Facility (TaiBIF) publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Taiwan Biodiversity Information Facility.

Mots-clé

SamplingEvent; river ecosystem; species occurrence; metabarcoding; cytochrome c oxidase I gene; Eukaryota

Contacts

Daphne Hoh

• Fournisseur Des Métadonnées ●
• Créateur ●
• Personne De Contact

Postdoctoral Researcher

Taiwan Biodiversity Information Facility

TW

daphnehohzhiwei@gmail.com

https://orcid.org/0000-0002-7810-1034

Min-Chen Wang

• Personne De Contact

Postdoctoral Researcher

Institute of Cellular and Organismic Biology, Academia Sinica

TW

mcwinlab@gmail.com

https://orcid.org/0000-0003-2044-1148

Couverture géographique

Houdong River (猴洞坑), Jiaoxi Township, Yilan County, Taiwan

Couverture taxonomique

We detected eukaryotic organisms in the water samples using the COI mitochondrial gene. A total of 2,736 OTUs were identified and 421 of the OTUs were assigned to at least the kingdom level.

Couverture temporelle

Données sur le projet

Pas de description disponible

Les personnes impliquées dans le projet:

Daphne Hoh

• Publicateur

https://orcid.org/0000-0002-7810-1034

Min-Chen Wang

• Chercheur Principal

https://orcid.org/0000-0003-2044-1148

Méthodes d'échantillonnage

Water samples for eDNA were collected from the near surface of the river. Before the collection, the water containers were rinsed with the local water at each sampling site. 1L of water was collected for eDNA analysis, and 200mL of water was collected for water quality measurements and were measured using multiple handheld probes on-site at each sampling site. Temperature, pH, and dissolved oxygen were measured through a multi-parameter meter (Multiline® Multi 3620 IDS, WTW, Weilheim, Germany) equipped with an IDS pH electrode (SenTix 940, WTW) and an optical IDS dissolved oxygen sensor (FDO® 925, WTW). Turbidity was measured by the turbidity meter (TUB-430, EZDO, Taiwan). Salinity was determined by the sanity refractometer (2491 MASTER-S/Milla Salinity Refractometer, Atago, Japan). Three replicate measurements of each parameter were taken. Water samples were transported and processed through two filtration steps at the Marine Research Station (MRS, Yilan, Taiwan) of the Institute of Cellular and Organismic Biology (Academia Sinica, Taipei, Taiwan). In the first step, the larger particles were removed by a 75µm pore size sieve. Afterward, the 1L water sample from each site was vacuum-filtered with a 0.22µm filter (PC651-0024, GeneDireX, USA). The filter membranes were placed in sterile Petri dishes and stored at -80°C until DNA extraction.

Description des étapes de la méthode:

1. Wet lab process: The DNA was extracted at the Biodiversity Research Center (Academia Sinica, Taipei, Taiwan). Each filtered membrane was cut into quarters. 3 of 4 pieces of filtered membranes were used in the study as 3 experimental replicates. The final quarter was saved as the sample backup. DNA from each quarter membrane piece was extracted using the Presto™ Stool DNA Extraction Kit (STLD100, Geneaid Biotech Ltd., Taiwan) following the manufacturer's instructions (Instruction Manual Ver. 10.21.17). The quality and quantity of the extracted DNA was assessed using a Nanodrop 2000 (Thermo Fisher Scientific Inc., USA) and the Qubit 4 dsDNA High Sensitivity Assay Kit (Thermo Fisher Scientific Inc., USA). The MinibarF1 (5'TCCACTAATCACAARGATATTGGTAC) and MinibarR1 (5'GAAAATCATAATGAAGGCATGAGC) primers that were designed by Meusnier et al. (2008), were used to amplify the 5' region (ca. 120-150bp) of the mitochondrial Cytochrome c oxidase I (COI) gene. The universality of the primers was recommended for distinguishing the highly diverse DNA from the environmental mixture. We conducted PCR using a one-step single-indexed approach, with a 13bp tag attached to the MinibarR1 primer. The PCR reaction volume was 16μl, which included 8μl KAPA HiFi HotStart ReadyMix (KK2602, Roche Molecular Systems Inc., USA), 5μl ddH20, 1μl of each primer (10μM), and 1μl of DNA template. To optimize the protocol, we performed a preliminary PCR using an annealing temperature gradient and found that 54°C gave the best results. The PCR mixture was denatured at 95°C for 15 minutes, followed by 35 cycles of 94°C for 30 seconds, 54°C for 30 seconds, and a final elongation at 72°C for 10 minutes. The PCR products were checked on a 1.5% agarose gel and quantified with the Invitrogen Qubit 4 fluorometer (Thermo Fisher Scientific Inc., USA). Afterwards, all the PCR products were pooled in one tube for next-generation sequencing. Sequencing was performed on the Illumina NovaSeq 6000 platform with 2*150 paired-end reads by Genomics Co., Taipei, Taiwan.
2. Data processing and analyzing: The Illumina raw reads were demultiplexed by Genomics Co., Taipei, Taiwan. FastQC (v0.11.9; https://github.com/s-andrews/FastQC) was used to the quality-checked. The forward and reverse primers of the demultiplexed reads were trimmed using Cutadapt (version 4.2; Martin 2011). The USEARCH platform (v11.0.667; Edgar 2010) was used to verify if the primer sequences were completely removed from the demultiplexed reads. The "denoised-paired" function was used to create an amplicon sequence variant (ASV) data output from the demultiplexed reads. The "denoise-paired" function in QIIME2 (v2023.2.0; Bolyen et al. 2019) can automatically trim, filter, denoise, merge reads, and remove chimeric reads in one step. The maximum expected error of forward and reverse reads was set to 1.0. The reads with a quality score of less than 20 were truncated. The minimum overlap length for the forward and reverse reads merger was set to 16 bp. Other parameters followed the default settings in the "denoise-paired" function. No reads were trimmed or truncated during the ASV creation process. The ASV output was then further clustered through the "cluster-features-de-novo" function provided by QIIME 2. ASVs with more than 97% sequence identity were clustered into one operational taxonomic unit (OTU). The sequences that were shorter than 100bp in the ASV and OTU results were discarded. Taxonomic assignments were conducted using Constax (v2.0.18; Liber et al. 2021) against the MIDORI database (vGB250; Machida et al. 2017). The R package phyloseq was used to analyze the preprocessed sequencing data (v1.40.0; McMurdie and Holmes 2013). The pie chart figure was produced with ggplot2 (v3.4.2; Villanueva and Chen 2019). Lowest taxon level-annotation of each OTU was extracted to perform a secondary species mapping to the GBIF Backbone Taxonomy (GBIF Secretariat 2011) using the "name_backbone_checklist" function in R package rgbif (v3.7.7; Chamberlain et al. 2022) in R (R Core Team 2023).
3. Open data and code: DNA sequence data have been deposited on ENA at EMBL-EBI under accession number PRJEB60905. We converted the occurrence data into Darwin Core Archive standard (Darwin Core Task Group 2009) and validated data in the event and occurrence data sheets using the GBIF Data Validator (Global Biodiversity Information Facility 2017). We then published the dataset containing one event core and four extensions following GBIF registered extensions: occurrence, DNA-derived data, measurement or facts, and resource relationship using the Integrated Publishing Toolkit (IPT) of GBIF installed under the Taiwan Biodiversity Information Facility (TaiBIF). All source code used in the project can be found in the project's GitHub repository.

Citations bibliographiques

1. European Nucleotide Archive EMBL-EBI Project. https://www.ebi.ac.uk/ena/browser/view/PRJEB60905
2. Chamberlain S, Barve V, Mcglinn D, Oldoni D, Desmet P, Geffert L, Ram K (2023). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.7.7. https://CRAN.R-project.org/package=rgbif
3. R Core Team (2022). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/

Métadonnées additionnelles