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Cui LY, Liu BY, Li HM, Zhu YX, Zhou YH, Su C, Tian YP, Xu HT, Liu D, Li XP, Ma Y, Jiang GS, Liu H, Yang SH, Lan TM, Xu YC. A simple and effective method to enrich endogenous DNA from mammalian faeces. Mol Ecol Resour 2024; 24:e13939. [PMID: 38372463 DOI: 10.1111/1755-0998.13939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
Utilization of faeces has long been a popular approach for genetic and ecological studies of wildlife. However, the success of molecular marker genotyping and genome resequencing is often unpredictable due to insufficient enrichment of endogenous DNA in the total faecal DNA that is dominated by bacterial DNA. Here, we report a simple and cheap method named PEERS to predominantly lyse animal cells over bacteria by using sodium dodecyl sulphate so as to discharge endogenous DNA into liquid phase before bacterial DNA. By brief centrifugation, total DNA with enriched endogenous fraction can be extracted from the supernatant using routine methods. Our assessments showed that the endogenous DNA extracted by PEERS was significantly enriched for various types of faeces from different species, preservation time and conditions. It significantly improves the genotyping correctness and efficiency of genome resequencing with the total additional cost of $ 0.1 and a short incubation step to treat a faecal sample. We also provide methods to assess the enrichment efficiency of mitochondrial and nuclear DNA and models to predict the usability of faecal DNA for genotyping of short tandem repeat, single-nucleotide polymorphism and whole-genome resequencing.
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Affiliation(s)
- Liang Yu Cui
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Bo Yang Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Hai Meng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yi Xin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Heng Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Chang Su
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Yin Ping Tian
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Hai Tao Xu
- Heilongjiang Siberian Tiger Park, Harbin, China
| | - Dan Liu
- Heilongjiang Siberian Tiger Park, Harbin, China
| | - Xiao Ping Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Yue Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Guang Shun Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Feline Research Center, Harbin, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Shu Hui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Tian Ming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Yan Chun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
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