High-molecular-weight DNA extraction for broadleaved and conifer tree species

Aggerwal G, Edhigalla P, Walia P (2022) A comprehensive review of high-quality plant DNA isolation. The Pharma Innovation Journal 11(6):171–176 Search in Google Scholar

Baid G, Cook DE, Shafin K, Yun T, Llinaris-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert J-P, Vasawani A, McLean CY, Nattestad M, Chang P-C, Carroll A (2023) DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nature Publishing Group. Nat Biotechnol 41(2): 232-238. https://doi.org/10.1038/s41587-022-01435-7 Search in Google Scholar

Carey SJ, Becklund LE, Fabre PP, Schenk JJ (2023) Optimizing the lysis step in CTAB DNA extractions of silica-dried and herbarium leaf tissues. Wiley-Blackwell. Appl Plant Sci 11(3):e11522. https://doi.org/10.1002/aps3.11522 Search in Google Scholar

Couch JA, Fritz PJ (1990) Isolation of DNA from plants high in polyphenolics. Springer; Kluwer Academic Publishers. Plant Mol Biol Rep 8(1):8–12. https://doi.org/10.1007/BF02668875 Search in Google Scholar

Fleck S, Tomlin C, Da Coelho FS, Richter M, Danielsen E, Backenstose N, Krabbenhoft T, Lindqvist C, Albert V (2022) High quality long-read genomes produced from single MinION flow cells clarify polyploid and demographic histories of critically endangered ash species (Fraxinus: Oleaceae)). https://doi.org/10.21203/rs.3.rs-2350866/v1 Search in Google Scholar

Formato M, Scharenberg F, Pacifico S, Zidorn C (2022) Seasonal variations in phenolic natural products in Fagus sylvatica (European beech) leaves. Phytochemistry 203):113385. https://doi.org/10.1016/j.phytochem.2022.113385 Search in Google Scholar

Gaytán Á, Moreira X, Castagneyrol B, van Halder I, Frenne P de, Meeussen C, Timmermans BGH, Hoopen JPJG ten, Rasmussen PU, Bos N, Jaatinen R, Pulkkinen P, Söderlund S, Covelo F, Gotthard K, Tack AJM (2022) The co-existence of multiple oak leaf flushes contributes to the large within-tree variation in chemistry, insect attack and pathogen infection. New Phytol 235(4):1615–1628. https://doi.org/10.1111/nph.18209 Search in Google Scholar

Grohme MA, Schloissnig S, Rozanski A, Pippel M, Young GR, Winkler S, Brandl H, Henry I, Dahl A, Powell S, Hiller M, Myers E, Rink JC (2018) The genome of Schmidtea mediterranea and the evolution of core cellular mechanisms. Nature Publishing Group. Nature 554(7690):56–61. https://doi.org/10.1038/nature25473 Search in Google Scholar

Healey A, Furtado A, Cooper T, Henry RJ (2014) Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species. Plant Methods. Plant Methods 10):21. https://doi.org/10.1186/1746-4811-10-21 Search in Google Scholar

Huang J, Hartmann H, Ogaya R, Schöning I, Reichelt M, Gershenzon J, Peñuelas J (2023) Hormone and carbohydrate regulation of defense secondary metabolites in a Mediterranean forest during drought. Environmental and Experimental Botany 209):105298. https://doi.org/10.1016/j.envexpbot.2023.105298 Search in Google Scholar

Inglis PW, Pappas MdCR, Resende LV, Grattapaglia D (2018) Fast and inexpensive protocols for consistent extraction of high quality DNA and RNA from challenging plant and fungal samples for high-throughput SNP genotyping and sequencing applications. PLoS One 13(10):e0206085. https://doi.org/10.1371/journal.pone.0206085 Search in Google Scholar

Japelaghi RH, Haddad R, Garoosi G-A (2011) Rapid and efficient isolation of high quality nucleic acids from plant tissues rich in polyphenols and polysaccha-rides. Springer; Humana Press Inc. Mol Biotechnol 49(2):129–137. https://doi.org/10.1007/s12033-011-9384-8 Search in Google Scholar

Jebb D, Huang Z, Pippel M, Hughes GM, Lavrichenko K, Devanna P, Winkler S, Jermiin LS, Skirmuntt EC, Katzourakis A, Burkitt-Gray L, Ray DA, Sullivan KAM, Roscito JG, Kirilenko BM, Dávalos LM, Corthals AP, Power ML, Jones G, Ransome RD, Dechmann DKN, Locatelli AG, Puechmaille SJ, Fedrigo O, Jarvis ED, Hiller M, Vernes SC, Myers EW, Teeling EC (2020) Six reference-quality genomes reveal evolution of bat adaptations. Nature Publishing Group. Nature 583(7817):578–584. https://doi.org/10.1038/s41586-020-2486-3 Search in Google Scholar

Jones MM, Nagalingum NS, Handley VM (2023) Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos. Appl Plant Sci. Appl Plant Sci 11(3):e11525. https://doi.org/10.1002/aps3.11525 Search in Google Scholar

Jouve L, Jacques D, Douglas GC, Hoffmann L, Hausman J-F (2007) Biochemical characterization of early and late bud flushing in common ash (Fraxinus excelsior L.). Plant Science 172(5):962–969. https://doi.org/10.1016/j.plantsci.2007.02.008 Search in Google Scholar

Kalendar R, Boronnikova S, Seppänen M (2021) Isolation and Purification of DNA from Complicated Biological Samples. Humana, New York, NY. Methods Mol Biol 2222):57–67. https://doi.org/10.1007/978-1-0716-0997-2_3 Search in Google Scholar

Kang M, Chanderbali A, Lee S, Soltis DE, Soltis PS, Kim S (2023) High-molecular-weight DNA extraction for long-read sequencing of plant genomes: An optimization of standard methods. Appl Plant Sci 11(3):e11528. https://doi.org/10.1002/aps3.11528 Search in Google Scholar

Kersten B, Rellstab C, Schroeder H, Brodbeck S, Fladung M, Krutovsky KV, Gugerli F (2022) The mitochondrial genome sequence of Abies alba Mill. reveals a high structural and combinatorial variation. BMC Genomics 23(1):776. https://doi.org/10.1186/s12864-022-08993-9 Search in Google Scholar

La Cerda GY de, Landis JB, Eifler E, Hernandez AI, Li F-W, Zhang J, Tribble CM, Karimi N, Chan P, Givnish T, Strickler SR, Specht CD (2023) Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales. Appl Plant Sci. Appl Plant Sci 11(3):e11524. https://doi.org/10.1002/aps3.11524 Search in Google Scholar

Li Z, Parris S, Saski CA (2020) A simple plant high-molecular-weight DNA extraction method suitable for single-molecule technologies. BioMed Central. Plant Methods 16(1):38. https://doi.org/10.1186/s13007-020-00579-4 Search in Google Scholar

Lin S, Wang H, Dai J, Ge Q (2024) Spring wood phenology responds more strongly to chilling temperatures than bud phenology in European conifers. Tree Physiol 44(1). https://doi.org/10.1093/treephys/tpad146 Search in Google Scholar

Loomis WD, Battaile J (1966) Plant phenolic compounds and the isolation of plant enzymes. Phytochemistry 5(3):423–438. https://doi.org/10.1016/S0031-9422(00)82157-3 Search in Google Scholar

Müller NA, Kersten B, Leite Montalvão AP, Mähler N, Bernhardsson C, Bräutigam K, Carracedo Lorenzo Z, Hoenicka H, Kumar V, Mader M, Pakull B, Robinson KM, Sabatti M, Vettori C, Ingvarsson PK, Cronk Q, Street NR, Fladung M (2020) A single gene underlies the dynamic evolution of poplar sex determination. Nature Publishing Group. Nat. Plants 6(6):630–637. https://doi.org/10.1038/s41477-020-0672-9 Search in Google Scholar

Nishii K, Möller M, Foster RG, Forrest LL, Kelso N, Barber S, Howard C, Hart ML (2023) A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants. BioMed Central. Plant Methods 19(1):41. https://doi.org/10.1186/s13007-023-01009-x Search in Google Scholar

Oxford Nanopore Technologies (2023) Input DNA/RNA QC. https://community.nanoporetech.com/docs/prepare/library_prep_protocols/input-dna-rnaqc/v/idi_s1006_v1_revb_18apr2016/assessing-input-dna Search in Google Scholar

PacBio (2022a) Extracting HMW DNA from plant nuclei using Nanobind kits: Procedure & checklist. https://www.pacb.com/wp-content/uploads/Procedure-checklist-Extracting-HMW-DNA-from-plant-nuclei-using-Nanobind-kits.pdf Search in Google Scholar

PacBio (2022b) Technical note Preparing DNA for PacBio HiFi sequencing—extraction and quality control. https://www.pacb.com/wp-content/uploads/Technical-Note-Preparing-DNA-for-PacBio-HiFi-Sequencing-Extraction-and-Quality-Control.pdf Search in Google Scholar

Porebski S, Bailey LG, Baum BR (1997) Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Springer; Springer-Verlag. Plant Mol Biol Rep 15(1):8–15. https://doi.org/10.1007/BF02772108 Search in Google Scholar

Pucker B, Irisarri I, Vries J de, Xu B (2022) Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions. Cambridge University Press. Quantitative Plant Biology 3):e5. https://doi.org/10.1017/qpb.2021.18 Search in Google Scholar

Rogers SO, Bendich AJ (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Springer; Martinus Nijhoff, The Hague/Kluwer Academic Publishers. Plant Mol Biol 5(2):69–76. https://doi.org/10.1007/BF00020088 Search in Google Scholar

Russo A, Mayjonade B, Frei D, Potente G, Kellenberger RT, Frachon L, Copetti D, Studer B, Frey JE, Grossniklaus U, Schlüter PM (2022) Low-Input High-Molecular-Weight DNA Extraction for Long-Read Sequencing From Plants of Diverse Families. Front Plant Sci 13):883897. https://doi.org/10.3389/fpls.2022.883897 Search in Google Scholar

Schenk JJ, Becklund LE, Carey SJ, Fabre PP (2023) What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol. Appl Plant Sci). https://doi.org/10.1002/aps3.11517 Search in Google Scholar

Witzell J, Martín JA (2008) Phenolic metabolites in the resistance of northern forest trees to pathogens — past experiences and future prospects. Can. J. For. Res. 38(11):2711–2727. https://doi.org/10.1139/X08-112 Search in Google Scholar

Zerpa-Catanho D, Zhang X, Song J, Hernandez AG, Ming R (2021) Ultra-long DNA molecule isolation from plant nuclei for ultra-long read genome sequencing. STAR Protocols 2(1):100343. https://doi.org/10.1016/j.xpro.2021.100343 Search in Google Scholar