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Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk
Benjamin N Daniels1,2, Jenna Nurge2, Olivia Sleeper2
1Center for Coastal Marine Sciences, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America.
Peerj
|December 11, 2023
Summary
We developed an affordable and effective DNA extraction protocol for marine invertebrates, specifically Kellet
Area of Science:
- Marine Biology
- Genomics
- Molecular Biology
Background:
- Genomic research on marine invertebrates is limited by challenges in DNA extraction.
- High polysaccharide and secondary metabolite content in marine invertebrates impedes DNA purification.
Purpose of the Study:
- To develop and test a robust DNA extraction protocol for marine invertebrates.
- To address the under-representation of invertebrates in genomic studies.
Main Methods:
- Compared four DNA extraction methods for Kellet's whelk (Kelletia kelletii).
- Validated the Salting Out protocol for DNA yield, quality, and scalability.
- Optimized the protocol for high-molecular-weight (HMW) DNA extraction.
Main Results:
- The Salting Out protocol was cost-effective, yielding high-quality DNA.
- The protocol was validated and scaled for over 3,000 samples.
- Extracted HMW DNA suitable for various sequencing platforms (ONT MinION, Illumina NovaSeq).
Conclusions:
- The Salting Out protocol provides a versatile solution for marine invertebrate genomics.
- This method supports diverse applications including RAD-seq, GT-seq, and whole-genome sequencing.
- Facilitates genomic research on understudied marine invertebrate species.
