Computational protocol: Phylogenetic Identification of Korean Gymnopus spp. and the First Report of 3 Species: G. iocephalus, G. polygrammus, and G. subnudus

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Protocol publication

[…] Genomic DNA samples were extracted from dry specimens with the AccuPrep Genomic DNA Extraction Kit (Bioneer, Daejeon, Korea). PCR amplification of the internal transcribed spacer (ITS) region was performed according to the previously described method []. To analyze each species, closely related sequences of Gymnopus spp. and reference sequences from other studies were retrieved from GenBank []. The determined sequences were proofread and aligned using MAFFT 7.130 [] and modified manually in the MacClade 4.08 software []. Datasets were tested by MrModeltest 2.3 using the Akaike information criterion (AIC) criteria with default options []. The GTR + I + G model was chosen for the AIC criteria as a result of the test. Bayesian analysis was performed with MrBayes 3.2.1 []. A phylogenetic tree was constructed by a method described elsewhere []. […]

Pipeline specifications

Software tools MAFFT, MacClade, MrModelTest, MrBayes
Application Phylogenetics