Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing

The overall goal of this protocol is to isolate high molecular weight genomic DNA from powdery mildew haploid conidia for long-read genome sequencing. This method can answer key questions in the plant pathogenic fungal biology field, such as the structure and composition of hard to study genomes. The main advantage of this technique is that it allows for the extraction of high-quality genomic DNA from a pathogen that is difficult to work with.

To begin the experiment, quickly remove steel balls from conidia cryovials with a magnet. Add 700 microliters of 65 degree Celsius lysis buffer and vortex the solution for five to 10 seconds. After five to 10 seconds, a slurry is formed.

Add 300 microliters of 65 degree pre-warmed 5%volume by volume sarkosyl and gently invert it five times. Incubate the tubes for 30 minutes at 65 degrees Celsius. Using a wide bore pipette tip, transfer the entire solution to a new two milliliter microcentrifuge tube.

Add one volume of chloroform isoamyl alcohol to the lysis solution, and gently invert the tube to mix five times. Incubate the mixture for 10 minutes at room temperature. Gently invert the tube to mix five times at the halfway point, and again at the end of the incubation.

Next, centrifuge and room temperature for 15 minutes. Using a wide bore pipette tip, carefully transfer the aqueous layer to a new two milliliter microcentrifuge tube, and avoid including material from the interface. Add 750 microliter volume of room temperature 100%isopropanol and gently invert the tube six times.

Then centrifuge the mixture at room temperature for 15 minutes. Carefully remove the supernatant and discard it. Add 450 microliters pre-chilled 70%ethanol.

Centrifuge the mixture for five minutes at room temperature. Carefully remove the supernatant and discard it. Centrifuge at 1000 times g for three seconds.

Carefully remove the supernatant with a fine pipette tip and discard the supernatant. Air dry the pellet for 15 minutes at room temperature. Resuspend the pellet in 300 microliters of TE.Incubate the DNA overnight at four degrees Celsius.

The next morning, gently flick to resuspend any DNA that has not gone into solution. To remove RNA contamination, add 10 microliters RNase. Gently invert the tube three times and centrifuge the DNA at 1000 times g for three seconds.

Then incubate the DNA at 37 degrees Celsius for two hours. Add 300 microliters phenol chloroform isoamyl alcohol and gently invert to mix five times and incubate the DNA for 10 minutes at room temperature. Gently invert the tube to mix the DNA five times at the halfway mark and again at the end of the incubation.

Next centrifuge the tube for 15 minutes at room temperature. Using a wide bore pipette tip transfer the supernatant to a new 1.5 milliliter microcentrifuge tube. Add three microliters of 3 molar sodium acetate pH 5.2 then gently invert the tube five times.

Add 750 microliters of pre-chilled 100%ethanol and gently invert the tube five times. Incubate the mixture overnight at 20 degrees Celsius. The following morning, centrifuge the tube for 30 minutes at four degrees Celsius.

Carefully remove and discard the supernatant. Add 450 microliters of pre-chilled 70%ethanol. Then centrifuge the tube for five minutes at four degrees Celsius.

After pelleting the DNA, carefully remove the supernatant. Spin the tube again at 1000 times g for three seconds to bring down residual supernatant. Remove residual supernatant with fine tipped pipette.

Air dry the pellet for 30 to 60 minutes at room temperature. After air drying, resuspend the pellet in 27.5 microliters of TE.The next day, gently flip to resuspend any residual material that did not go into solution. Aliquot 2.5 microliters into 22.5 microliters TE for quality control tests.

Store the DNA samples at four degrees Celsius until submission for sequencing. For long term storage, store samples at 80 degrees Celsius and minimize freeze thaw cycles to prevent shearing. Using the protocol, purified genomic DNA was used to run gel electrophoresis which obtained DNA that passed quality control with a strong single band above 20kbp and minimal smearing, DNA that gave a marginal result with a single band running above 20kbp, and a failed result that displays smearing below 20kbp and includes fragments at 100bp.

Pulsed-field gel electrophoresis, or PFGE, was performed to distinguish between an acceptable DNA sample with a majority of DNA greater than 48.5kbp and a marginal DNA sample with the majority of DNA between 20 and 48.5kbp. Following this procedure, other methods like single molecule long-read sequencing can be performed to answer additional questions about the powdery mildew genome.