eDNA along Houdong riverine zonation in Taiwan

Descrição

Registros de Dados

Os dados deste recurso de ocorrência foram publicados como um Darwin Core Archive (DwC-A), que é o formato padronizado para compartilhamento de dados de biodiversidade como um conjunto de uma ou mais tabelas de dados. A tabela de dados do núcleo contém 6.297 registros.

Também existem 4 tabelas de dados de extensão. Um registro de extensão fornece informações adicionais sobre um registro do núcleo. O número de registros em cada tabela de dados de extensão é ilustrado abaixo.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Lembre-se, esta é uma versão antiga do dataset.  Pesquisadores deveriam citar esta obra da seguinte maneira:

Hoh D (2023): eDNA along Houdong riverine zonation in Taiwan. v1.2. Taiwan Biodiversity Information Facility (TaiBIF). Dataset/Samplingevent. https://ipt.taibif.tw/resource?r=houdongkeng_water_edna&v=1.2

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é Taiwan Biodiversity Information Facility (TaiBIF). This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 2615342d-7349-4e75-ae34-cda6cb403e2e.  Taiwan Biodiversity Information Facility (TaiBIF) publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Taiwan Biodiversity Information Facility.

Palavras-chave

SamplingEvent

Contatos

Daphne Hoh

• Provedor Dos Metadados ●
• Originador ●
• Ponto De Contato

Postdoctoral Researcher

Taiwan Biodiversity Information Facility

TW

daphnehohzhiwei@gmail.com

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

Min-Chen Wang

• Ponto De Contato

Postdoctoral Researcher

Institute of Cellular and Organismic Biology, Academia Sinica

TW

mcwinlab@gmail.com

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

Cobertura Geográfica

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

Cobertura Taxonômica

We detected eukaryotic organisms in the water samples using the cytochrome oxidase subunit 1 (COI) mitochondrial gene. A total of 2,736 operational taxonomic units (OTUs) were identified, but only 421 of these could be successfully assigned to a taxonomic group at (at least) the kingdom level.

Cobertura Temporal

Dados Sobre o Projeto

Nenhuma descrição disponível

O pessoal envolvido no projeto:

Daphne Hoh

• Processador

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

Chieh-Ping Lin

• Autor

http://orcid.org/0009-0006-4210-1063

Yung-Che Tseng

• Autor

http://orcid.org/0000-0001-7489-0403

Cheng-Wei Chen

• Autor

http://orcid.org/0000-0001-9709-6739

John Wang

• Autor

Chung-Hsin Huang

• Autor

Mao-Ning Tuanmu

• Autor

http://orcid.org/0000-0002-8233-2935

Min-Chen Wang

• Pesquisador Principal

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

Mark Angelo Bucay

• Autor

http://orcid.org/0000-0002-8769-9592

Métodos de Amostragem

Surface water was collected from each site on the same day, and various water quality parameters were measured on site, including temperature, pH, dissolved oxygen (DO) content, turbidity, and salinity, with three replicate measurements taken for each parameter. Samples were processed at the Marine Research Station of the Institute of Cellular and Organismic Biology and the Biodiversity Research Centre at Academia Sinica in Taiwan. To prepare the samples for eDNA metabarcoding analysis, each water sample was filtered twice. The first filtration step involved using a 75 µm pore size sieve to remove larger materials, such as debris. Next, a 0.22 μm PES filter membrane with a vacuum pump was used to collect eDNA from the filtered water. Two PES filter membranes were used at each site and each membrane was used to filter 2 L of water. The filtered membranes were then placed in sterile petri dishes and stored at -80 °C until DNA extraction.

Descrição dos passos do método:

1. Wet lab process description: pending.
2. Dry lab process description: pending.
3. Lowest taxon level-annotation of each OTU was extracted to perform a secondary species mapping to GBIF Backbone using the rgbif package (Chamberlain et al., 2023; version 3.7.7) in R (R Core Team, 2022; version 4.2.2).
4. Open data and code: We converted the occurrence data into Darwin Core Archive standard and validated data in both event and occurrence data sheets using the Data Validator developed by GBIF (Global Biodiversity Information Facility, 2017). We then published the dataset containing one event core and four extensions: occurrence, DNA derived data, extended measurement or facts, and resource relationship using The Integrated Publishing Toolkit (IPT) of GBIF installed under the Taiwan Biodiversity Information Facility (TaiBIF). DNA sequence data was submitted to European Nucleotide Archive under project accession PRJEB60905. All source codes used in the project can be found in the project GitHub repository (tbc link).

Citações bibliográficas

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/

Metadados Adicionais