Question: How do I extract genomic DNA from plants?
Answer: For extracting plant HMW DNA, protocols written for generating large-insert BAC libraries or optical mapping can be a useful starting point. Typically, these protocols involve preparing a purified nuclei suspension from plant tissue and embedding the nuclei in agarose. These gel plug techniques yield high-quality HMW DNA fragments (several hundred kb to 1 Mb or larger) but can be more difficult to perform and take several days. For example, customers have successfully used the BioNano Plant kit, which uses agarose plugs, to generate mean fragment lengths >50 kb by Fragment Analyzer (https://bionanogenomics.com/wp-content/uploads/2017/01/30068-Bionano-Prep-Plant-Tissue-DNA-Isolation-Protocol.pdf).
An alternative is the CTAB extraction method. It is generally easier and can yield average DNA molecule sizes ranging from 20-70 kb. Our collaborators Allen Van Deyze and Kevan Stoffel at UC Davis have optimized the CTAB protocol for extraction of HMW gDNA from chili pepper leaves. Their protocol is available at https://pepchip.genomecenter.ucdavis.edu/download_center/CTAB_Extraction_for_Pepper.doc. The average DNA molecule size using this protocol was ~200 kb on a pulsed-field gel, and 53 kb as reported by the Supernova assembly algorithm.
Products: Genome, Exome