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Xie P, Ke Y, Kuo L. Modified CTAB protocols for high-molecular-weight DNA extractions from ferns. Appl Plant Sci 2023; 11:e11526. [PMID: 37342164 PMCID: PMC10278929 DOI: 10.1002/aps3.11526] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 06/22/2023]
Abstract
Premise Efficient protocols for extracting high-molecular-weight (HMW) DNA from ferns facilitate the long-read sequencing of their large and complex genomes. Here, we perform two cetyltrimethylammonium bromide (CTAB)-based protocols to extract HMW DNA and evaluate their applicability in diverse fern taxa for the first time. Methods and Results We describe two modified CTAB protocols, with key adjustments to minimize mechanical disruption during lysis to prevent DNA shearing. One of these protocols uses a small amount of fresh tissue but yields a considerable quantity of HMW DNA with high efficiency. The other accommodates a large amount of input tissue, adopts an initial step of nuclei isolation, and thus ensures a high yield in a short period of time. Both methods were proven to be robust and effective in obtaining HMW DNA from diverse fern lineages, including 33 species in 19 families. The DNA extractions mostly had high DNA integrity, with mean sizes larger than 50 kbp, as well as high purity (A260/A230 and A260/A280 > 1.8). Conclusions This study provides HMW DNA extraction protocols for ferns in the hope of facilitating further attempts to sequence their genomes, which will bridge our genomic understanding of land plant diversity.
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Affiliation(s)
- Pei‐Jun Xie
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Ya‐Ting Ke
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
| | - Li‐Yaung Kuo
- Institute of Molecular and Cellular BiologyNational Tsing Hua UniversityHsinchu CityTaiwan
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Dahn HA, Mountcastle J, Balacco J, Winkler S, Bista I, Schmitt AD, Pettersson OV, Formenti G, Oliver K, Smith M, Tan W, Kraus A, Mac S, Komoroske LM, Lama T, Crawford AJ, Murphy RW, Brown S, Scott AF, Morin PA, Jarvis ED, Fedrigo O. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience 2022; 11:6659719. [PMID: 35946988 PMCID: PMC9364683 DOI: 10.1093/gigascience/giac068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/26/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. RESULTS We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. CONCLUSION We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.
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Affiliation(s)
| | | | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Iliana Bista
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, Cambridgeshire CB2 3EH, UK
| | | | | | | | - Karen Oliver
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michelle Smith
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Anne Kraus
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Stephen Mac
- Arima Genomics, Inc., San Diego, CA 92121, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Tanya Lama
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Samara Brown
- The Rockefeller University, New York, NY 10065, USA
| | - Alan F Scott
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA 92037, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Olivier Fedrigo
- Correspondence address. Olivier Fedrigo, Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA. E-mail:
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