Also,

You can use the CTAB method. It´s a very well known, standardized, protocol and it gives always very good DNA yields. The hands-on time for this procedure takes one working day but it is worth it. You can use either spore you collected from the agar plate, or the mycelia (you can use a scalpel), but without removing agar. Just add 1 mL of distilled water with 0.9% NaCL, scap the spores/mycelia, centrifuge, remove the supernatant and wash 2 more times, and then start with the protocol. There are various studies referring to it.

For higher throughput extraction, liquid cultures are usually better in my opinion. In my case, I have used a method based on LN grinding, CTAB and chloroform: isoamyl alcohol extraction (no phenol!!) with a couple of fungi, one of them producing quite a lot of melanin, with success. If you want to take a look-see chapter 5 of my thesis below. Of course, there are many more protocols that work.

You literally have to scrap the surface of the colonies and avoid pieces of agar. It really depends on how much DNA you need and for what. I've done most of my fungal DNA extractions from agar plates. For barcoding/PCR is more than enough, at least using kits (I've used mostly MoBIO Powersoil).

For alternate media, you can pretty much use any solid media recipe without the agar as liquid media. I would suggest PDB, ME, YM or YEPD as possible candidates, but it depends on what your fungus likes (see paper below for recipes).

Article Fodinomyces uranophilus gen. nov. sp. nov. and Coniochaeta f...

Thesis Geomicrobiological aspects of the (bio)leaching of weathered...

Also,

You can use the CTAB method. It´s a very well known, standardized, protocol and it gives always very good DNA yields. The hands-on time for this procedure takes one working day but it is worth it. You can use either spore you collected from the agar plate, or the mycelia (you can use a scalpel), but without removing agar. Just add 1 mL of distilled water with 0.9% NaCL, scap the spores/mycelia, centrifuge, remove the supernatant and wash 2 more times, and then start with the protocol. There are various studies referring to it.

Overview

High throughput of many fungal isolates can be achieved by growing axenic cultures in either (a) 1.5mL microfuge tubes, half full with liquid media (500uL), with a hole punched through the top for aeration; or if greater volumes are required, (b) peteri plates containing 10mL liquid media.In both cases, media is decanted and several water washes done to removemedia carbohydrates.

Procedure

This procedure does not require phenol extraction. The B-mercaptoethanol can be omitted from the extraction buffer for safety, but yields will be slightly lower. The DNA is pure enough for restriction digests, PCR and genomic library construction.

Note

Modified from Moller, Bahnweg, Sandermann and Geiger, 1992, Nucleic Acids Res. 20: 6115-16.

Hi

You can use CTAB (Cetyl Trimethyl Ammonium Bromide) method.

This is a good method for extracting fungal DNA.

Good luck!