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Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding

SIMPLE SUMMARY: The Taibai stream salamander (Batrachuperus taibaiensis) is a protected species endemic to the Zhouzhi Heihe River. Few traditional studies have been conducted on the distribution of B. taibaiensis, leading to irregular discoveries. Environmental DNA (eDNA) is an ideal species detect...

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Autores principales: Ma, Hongying, Zhang, Han, Deng, Jie, Zhao, Hu, Kong, Fei, Jiang, Wei, Zhang, Hongxing, Dong, Xianggui, Wang, Qijun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9099721/
https://www.ncbi.nlm.nih.gov/pubmed/35565532
http://dx.doi.org/10.3390/ani12091105
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author Ma, Hongying
Zhang, Han
Deng, Jie
Zhao, Hu
Kong, Fei
Jiang, Wei
Zhang, Hongxing
Dong, Xianggui
Wang, Qijun
author_facet Ma, Hongying
Zhang, Han
Deng, Jie
Zhao, Hu
Kong, Fei
Jiang, Wei
Zhang, Hongxing
Dong, Xianggui
Wang, Qijun
author_sort Ma, Hongying
collection PubMed
description SIMPLE SUMMARY: The Taibai stream salamander (Batrachuperus taibaiensis) is a protected species endemic to the Zhouzhi Heihe River. Few traditional studies have been conducted on the distribution of B. taibaiensis, leading to irregular discoveries. Environmental DNA (eDNA) is an ideal species detection technique that can increase accuracy and decrease the cost of population surveys. Here, we have established an optimal method for obtaining the eDNA of B. taibaiensis from water samples, which provides a theoretical basis and reference for resource investigation and protection of B. taibaiensis. Moreover, this study highlights the detection of a rare species in a river for use in further research. ABSTRACT: The Taibai stream salamander (Batrachuperus taibaiensis) is a recently described species of the genus Batrachuperus that occurs in the Zhouzhi Heihe River and is endangered in its native range. Here, we have established a method for water environmental DNA (eDNA) analysis of Batrachuperus using a series of optimizations. We have designed a specific set of primers for the genus Batrachuperus to amplify a 160 bp fragment of Cytb. The sequences were obtained from nested PCR on eDNA extracted from water samples, after which DNA barcoding was performed according to sequence analysis to determine the presence of the target species in the water. The method was validated using water from the Zhouzhi Heihe River with known B. taibaiensis populations and found that B. taibaiensis eDNA can move at least 150 m downstream from its point of origin. This study is the first to establish an optimal method for obtaining the eDNA of Batrachuperus from water samples, which provides a theoretical basis for resource investigation and the protection of B. taibaiensis in future research. It is also an example of the eDNA extraction of other species that live in similar waters and are less genetically diverse between species.
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spelling pubmed-90997212022-05-14 Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding Ma, Hongying Zhang, Han Deng, Jie Zhao, Hu Kong, Fei Jiang, Wei Zhang, Hongxing Dong, Xianggui Wang, Qijun Animals (Basel) Article SIMPLE SUMMARY: The Taibai stream salamander (Batrachuperus taibaiensis) is a protected species endemic to the Zhouzhi Heihe River. Few traditional studies have been conducted on the distribution of B. taibaiensis, leading to irregular discoveries. Environmental DNA (eDNA) is an ideal species detection technique that can increase accuracy and decrease the cost of population surveys. Here, we have established an optimal method for obtaining the eDNA of B. taibaiensis from water samples, which provides a theoretical basis and reference for resource investigation and protection of B. taibaiensis. Moreover, this study highlights the detection of a rare species in a river for use in further research. ABSTRACT: The Taibai stream salamander (Batrachuperus taibaiensis) is a recently described species of the genus Batrachuperus that occurs in the Zhouzhi Heihe River and is endangered in its native range. Here, we have established a method for water environmental DNA (eDNA) analysis of Batrachuperus using a series of optimizations. We have designed a specific set of primers for the genus Batrachuperus to amplify a 160 bp fragment of Cytb. The sequences were obtained from nested PCR on eDNA extracted from water samples, after which DNA barcoding was performed according to sequence analysis to determine the presence of the target species in the water. The method was validated using water from the Zhouzhi Heihe River with known B. taibaiensis populations and found that B. taibaiensis eDNA can move at least 150 m downstream from its point of origin. This study is the first to establish an optimal method for obtaining the eDNA of Batrachuperus from water samples, which provides a theoretical basis for resource investigation and the protection of B. taibaiensis in future research. It is also an example of the eDNA extraction of other species that live in similar waters and are less genetically diverse between species. MDPI 2022-04-25 /pmc/articles/PMC9099721/ /pubmed/35565532 http://dx.doi.org/10.3390/ani12091105 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ma, Hongying
Zhang, Han
Deng, Jie
Zhao, Hu
Kong, Fei
Jiang, Wei
Zhang, Hongxing
Dong, Xianggui
Wang, Qijun
Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding
title Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding
title_full Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding
title_fullStr Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding
title_full_unstemmed Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding
title_short Detection the eDNA of Batrachuperus taibaiensis from the Zhouzhi Heihe River Using a Nested PCR Method and DNA Barcoding
title_sort detection the edna of batrachuperus taibaiensis from the zhouzhi heihe river using a nested pcr method and dna barcoding
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9099721/
https://www.ncbi.nlm.nih.gov/pubmed/35565532
http://dx.doi.org/10.3390/ani12091105
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