Fine-tuning a method for DNA-extraction of myxomycetes

In this paper we describe in detail the procedure for a genomic DNA extraction method from spores of myxomycetes that was inspired by the direct PCR technique. We include results of small-scale tests that were set up for the optimization of this extraction method. These tests were performed to select the grinding breads, assess the result of different estimated spore quantities, compare the extraction medium, evaluate the temperature to weaken the cell walls of amoeboflagellates, and to ascertain whether the storage method of the extract is appropriate. The results are presented as agarose gel images of either crude genomic DNA extracts or PCR products of partial SSU and are discussed in detail. From the tests the following combination was withheld: extraction solution TE pH: 8, grinding with 1 mm Zirconia/Silica beads during 60 sec at 30 Hz, cell weakening at 90°C and storage at -20°C. The specimens that were used for the tests are listed in this paper along with collection data and the GenBank accession numbers for the submitted SSU sequences. This simple approach can serve as a fast, cheap, and cleaner alternative to other extraction protocols, or it can be used as a preparation phase for such established methods.