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Daniels BN, Nurge J, Sleeper O, Lee A, López C, Christie MR, Toonen RJ, White C, Davidson JM. Genomic DNA extraction optimization and validation for genome sequencing using the marine gastropod Kellet's whelk. PeerJ 2023; 11:e16510. [PMID: 38077446 PMCID: PMC10710129 DOI: 10.7717/peerj.16510] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
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.
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Affiliation(s)
- Benjamin N. Daniels
- Center for Coastal Marine Sciences, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
- Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
| | - Jenna Nurge
- Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
| | - Olivia Sleeper
- Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
| | - Andy Lee
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
| | - Cataixa López
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, United States of America
| | - Mark R. Christie
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States of America
| | - Robert J. Toonen
- Hawai‘i Institute of Marine Biology, University of Hawai‘i at Mānoa, Kāne‘ohe, HI, United States of America
| | - Crow White
- Center for Coastal Marine Sciences, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
| | - Jean M. Davidson
- Biological Sciences Department, California Polytechnic State University - San Luis Obispo, San Luis Obispo, CA, United States of America
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Malde K, Seliussen BB, Quintela M, Dahle G, Besnier F, Skaug HJ, Øien N, Solvang HK, Haug T, Skern-Mauritzen R, Kanda N, Pastene LA, Jonassen I, Glover KA. Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics 2017; 18:76. [PMID: 28086785 PMCID: PMC5237217 DOI: 10.1186/s12864-016-3416-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/12/2016] [Indexed: 11/24/2022] Open
Abstract
Background In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. An example of this can be seen in the minke whale species complex. Antarctic minke whales are genetically and morphologically distinct from the common minke found in the north Atlantic and Pacific oceans, and the two species are estimated to have been isolated from each other for 5 million years or more. Recent atypical migrations from the southern to the northern hemisphere have been documented and fertile hybrids and back-crossed individuals between both species have also been identified. However, it is not known whether this represents a contemporary event, potentially driven by ecosystem changes in the Antarctic, or a sporadic occurrence happening over an evolutionary time-scale. We successfully used whole genome resequencing to identify a panel of diagnostic SNPs which now enable us address this evolutionary question. Results A large number of SNPs displaying fixed or nearly fixed allele frequency differences among the minke whale species were identified from the sequence data. Five panels of putatively diagnostic markers were established on a genotyping platform for validation of allele frequencies; two panels (26 and 24 SNPs) separating the two species of minke whale, and three panels (22, 23, and 24 SNPs) differentiating the three subspecies of common minke whale. The panels were validated against a set of reference samples, demonstrating the ability to accurately identify back-crossed whales up to three generations. Conclusions This work has resulted in the development of a panel of novel diagnostic genetic markers to address inter-oceanic and global contact among the genetically isolated minke whale species and sub-species. These markers, including a globally relevant genetic reference data set for this species complex, are now openly available for researchers interested in identifying other potential whale hybrids in the world’s oceans. The approach used here, combining whole genome resequencing and high-throughput genotyping, represents a universal approach to develop similar tools for other species and population complexes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3416-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ketil Malde
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway.,Department of Informatics, University of Bergen, N-5020, Bergen, Norway
| | | | - María Quintela
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Geir Dahle
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Francois Besnier
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Hans J Skaug
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway.,Department of Mathematics, University of Bergen, N-5020, Bergen, Norway
| | - Nils Øien
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Hiroko K Solvang
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Tore Haug
- Institute of Marine Research, PO box 6404, N-9294, Tromsø, Norway
| | | | - Naohisa Kanda
- Institute of Cetacean Research, Toyomi-cho 4-5, Chuo-ku, Tokyo, 104-0055, Japan.,Japan NUS Co., Ltd, Nishi-Shinjuku Kimuraya Bldg 5F, 7-5-25, Nishi-Shinjuku, 160-0023, Japan
| | - Luis A Pastene
- Institute of Cetacean Research, Toyomi-cho 4-5, Chuo-ku, Tokyo, 104-0055, Japan
| | - Inge Jonassen
- Department of Informatics, University of Bergen, N-5020, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway. .,Department of Biology, University of Bergen, N-5020, Bergen, Norway.
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