Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet’s whelk

Author:

Daniels Benjamin N.12,Nurge Jenna2,Sleeper Olivia2,Lee Andy3,López Cataixa4,Christie Mark R.35,Toonen Robert J.4,White Crow1,Davidson Jean M.2

Affiliation:

1. Center for Coastal Marine Sciences, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America

2. Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America

3. Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America

4. Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, United States of America

5. Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States of America

Abstract

Next-generation sequencing technologies, such as Nanopore MinION, Illumina Hiseq and Novaseq, and PacBio Sequel II, hold immense potential for advancing genomic research on non-model organisms, including the vast majority of marine species. However, application of these technologies to marine invertebrate species is often impeded by challenges in extracting and purifying their genomic DNA due to high polysaccharide content and other secondary metabolites. In this study, we help resolve this issue by developing and testing DNA extraction protocols for Kellet’s whelk (Kelletia kelletii), a subtidal gastropod with ecological and commercial importance, by comparing four DNA extraction methods commonly used in marine invertebrate studies. In our comparison of extraction methods, the Salting Out protocol was the least expensive, produced the highest DNA yields, produced consistent high DNA quality, and had low toxicity. We validated the protocol using an independent set of tissue samples, then applied it to extract high-molecular-weight (HMW) DNA from over three thousand Kellet’s whelk tissue samples. The protocol demonstrated scalability and, with added clean-up, suitability for RAD-seq, GT-seq, as well as whole genome sequencing using both long read (ONT MinION) and short read (Illumina NovaSeq) sequencing platforms. Our findings offer a robust and versatile DNA extraction and clean-up protocol for supporting genomic research on non-model marine organisms, to help mediate the under-representation of invertebrates in genomic studies.

Funder

The National Science Foundation

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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