Lin Chieh-Ping, Huang Chung-Hsin, Padgett Trevor, Bucay Mark Angelo C, Chen Cheng-Wei, Shen Zong-Yu, Chiu Ling, Tseng Yung-Che, Yu Jr-Kai, Wang John, Wang Min-Chen, Hoh Daphne Z
Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University Taipei Taiwan.
Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Biodiversity Research Center, Academia Sinica Taipei Taiwan.
Biodivers Data J. 2024 Apr 23;12:e116921. doi: 10.3897/BDJ.12.e116921. eCollection 2024.
This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 , accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios.
The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.
本文描述了两个数据集：物种出现情况，由环境DNA（eDNA）宏条形码分析确定，以及其相关的DNA序列，这些数据源自台湾宜兰礁溪乡后东溪开展的一个研究项目。后东溪发源于海拔860米处，流经约9公里后注入太平洋。这条短河蜿蜒穿过山脉、丘陵、平原和冲积河谷，是台湾河流系统的代表。本研究的主要目的是通过eDNA分析确定河流生态系统中的真核生物物种出现情况。第二个目标是基于当前数据集，建立一个宏条形码eDNA数据模板，该模板对所有用户，特别是台湾地区的用户有用且可复制。物种出现数据可在全球生物多样性信息设施（GBIF）门户网站获取，其相关的DNA序列已分别存入欧洲分子生物学实验室-欧洲生物信息研究所（EMBL-EBI）的欧洲核苷酸档案馆（ENA）。该研究共采集了12个水样，平均产生了150万个读数。随后从采集的样本中进行物种鉴定，在总共2734个分类单元中分类出432个可操作分类单元（OTU）。此外，在GBIF中记录了总共1356次与分类单元匹配的出现情况（不包括2023年12月5日访问的4941次）。这些数据对于未来这条短河中的物种和栖息地监测至关重要，例如评估不同海拔、分区和时间段的生物多样性模式及其与水质、土地利用和人为活动的相关性。此外，这些数据集对于区域生态研究也很重要，特别是淡水生态系统及其在当前全球变化情景下的状况。
这些数据集是首次使用eDNA或传统监测方法对后东溪系统进行的物种多样性描述。
