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A Mg2+-dependent high-yield method for extracting high-molecular-weight genomic DNA from a single planarian specimen
Ao Li1, Bingrui Sun2, Ying Zhang2
1School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255049, PR China. aoli@sdut.edu.cn.
BMC Genomics
|May 26, 2025
Summary
A new protocol effectively isolates high-molecular-weight genomic DNA (HMW gDNA) from Dugesia japonica using a Mg2+-dependent lysis buffer. This method yields high-quality DNA suitable for long-read sequencing, overcoming previous extraction challenges.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- High-molecular-weight genomic DNA (HMW gDNA) isolation is critical for complete genome assembly.
- Standard protocols face challenges in extracting HMW gDNA from Dugesia japonica due to polysaccharides and nucleases.
Purpose of the Study:
- To develop a robust protocol for high-yield HMW gDNA extraction from single Dugesia japonica individuals.
- To overcome limitations of standard protocols in HMW gDNA isolation from this species.
Main Methods:
- Utilized a Mg2+-dependent lysis buffer to inhibit DNase activity, replacing metal cation chelation.
- Optimized Mg2+ concentration to 20 mM for local D. japonica specimens.
Main Results:
- Achieved high yields of HMW gDNA (10-15 µg per worm) with excellent quality.
- Extracted HMW gDNA demonstrated compatibility with PacBio HiFi and Oxford Nanopore sequencing platforms.
- The protocol showed species- and region-specific effectiveness, with limitations for certain D. japonica populations and Schmidtea mediterranea.
Conclusions:
- The developed protocol provides a simple, high-yield method for isolating HMW gDNA from D. japonica.
- Offers an alternative solution for organisms with persistent gDNA degradation issues using existing methods.
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