They probably have different cell wall composition, varying from chitin, cellulose, glucans etc in different sub divisions, classes or orders
In my experience, it's not so much that different groups need different methods, it's that melanized/pigmented tissue from members of the Ascomycota (and, to a lesser extent Basidiomycota) need special extraction methods, especially when extracting from spores. Additionally, because macroscopic fruiting bodies or spore-bearing structures are historically more systematically important in the Basidiomycota, DNA samples may often be extracted from fruiting bodies rather than cultures, which require different methods. I've personally found that quick-and-easy extraction methods like microwave/colony PCR/PrepMan Ultra work on a wide variety of fungal cultures, including oomycetes (members of a different kingdom) and most members of Kingdom Fungi (especially when amplifying rDNA sequences is the goal of the extraction). Melanized fungi will do better with a "plant tissue kit" that deals better with the PCR inhibiting chemicals in the sample.
Hi Adekunle, Some fungi had a secondary metabolite (pigment, glycoprotein, polysaccharide....) most time affect the quality of the DNA, also you should use the DNA extraction protocol that served your goal of molecular test purpose.
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