OPTIMIZATION OF FISH ENVIRONMENTAL DNA SAMPLE PROCESSING AND PRESERVATION TECHNOLOGY BASED ON DROPLET DIGITAL PCR

WANG Yue; LIU Huan-Zhang; LI Sha; YU Dan

doi:10.7541/2022.2021.281

Volume 46 Issue 3

Mar. 2022

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ACTA HYDROBIOLOGICA SINICA > 2022 > 46(3): 332-341. > DOI: 10.7541/2022.2021.281

WANG Yue, LIU Huan-Zhang, LI Sha, YU Dan. OPTIMIZATION OF FISH ENVIRONMENTAL DNA SAMPLE PROCESSING AND PRESERVATION TECHNOLOGY BASED ON DROPLET DIGITAL PCR[J]. ACTA HYDROBIOLOGICA SINICA, 2022, 46(3): 332-341. DOI: 10.7541/2022.2021.281

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OPTIMIZATION OF FISH ENVIRONMENTAL DNA SAMPLE PROCESSING AND PRESERVATION TECHNOLOGY BASED ON DROPLET DIGITAL PCR

WANG Yue^1,2,,
LIU Huan-Zhang²,
LI Sha^3,4,
YU Dan^2, ,

1.
Dalian Ocean University, Dalian 116023, China
2.
The Key Laboratory of Aquatic Biodiversity and Conversation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
3.
Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang 443100, China
4.
Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Yichang 443100, China

Funds: Supported by National Key R & D Program of China (2018YFD0900806); Director’s Fund of the Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, China Three Gorges Corporation (0704174); National Natural Science Foundation of China (31872234, 31801982); Sino BON-Inland Water Fish Diversity Observation Network (SINO BON)

Received Date: October 20, 2021
Rev Recd Date: January 09, 2022
Available Online: March 07, 2022
Published Date: March 14, 2022

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Abstract

Abstract

In this study, the methods of fish environmental DNA (eDNA) capture, extraction and preservation were optimized by Droplet Digital PCR (ddPCR) quantitative technology using Carassius auratus in the laboratory, and the direct PCR technology without DNA extraction was preliminarily explored. The results showed that the mixed cellulose ester membrane produced the most ddPCR product, among the six kinds of filter membrane, and the polycarbonate membrane produced the lowest ddPCR product with only 1/17 of mixed cellulose ester membrane. The method which extracted the highest amount of DNA was the Qiagen DNeasy PowerWater kit, and the lowest was the high-salt method. The Qiagen DNeasy PowerWater kit yielded better results compared to the high-salt method, showing a 5.5-fold improvement in DNA yield. Different filter membranes and extraction methods have significant interactions on the total amount of final ddPCR product (P<0.001), filtration through the mixed cellulose ester membranes and Qiagen DNeasy PowerWater kit significantly outperformed other combinations of capture and extraction methods. Filter membranes stored at –20℃ or stored in Longmire's buffer solution recovered the most ddPCR product. The results of direct PCR amplification without DNA extraction showed that the high-fidelity enzyme of Vazyme can directly amplify the water samples and obtain the target DNA product. This study, compared the key steps in the eDNA operation process in detail, and the optimal protocol of fish eDNA sample processing and preservation was determined, which provided a reference for the establishment of eDNA standardized experimental process.
- Environmental DNA,
- Filter,
- Extraction method,
- Preservation condition

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References

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OPTIMIZATION OF FISH ENVIRONMENTAL DNA SAMPLE PROCESSING AND PRESERVATION TECHNOLOGY BASED ON DROPLET DIGITAL PCR

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