Computational protocol: Five New Wood Decay Fungi (Polyporales and Hymenochaetales) in Korea

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Protocol publication

[…] Genomic DNA was extracted using a modified cetyltrimethylammonium bromide extraction protocol and the ITS locus was amplified using the primers ITS1F and ITS4b []. PCRs were conducted using a C1000 thermal cycler (Bio-Rad, Hercules, CA, USA) using the AccuPower PCR Premix (Bioneer Co., Daejeon, Korea) in a final volume of 20 µL containing 10 pmol of each primer and 1 µL of DNA using the conditions described by Park et al. []. PCR products were purified using the Expin PCR Purification Kit (GeneAll Biotechnology, Seoul, Korea) according to the manufacturer's instructions. DNA sequencing was performed by Macrogen (Seoul, Korea), using an ABI3700 automated DNA sequencer.Amplicons were aligned, proofread, and edited using MEGA 5 []. Representative sequences were deposited in GenBank (accession numbers presented in ). Reference sequences were downloaded from GenBank and multiple alignments were performed using the default settings of MAFFT v7 []. Neighbor joining (NJ) trees were constructed with MEGA 5 (Kimura 2-parameter model) with 1,000 bootstrap replicates []. […]

Pipeline specifications

Software tools MEGA, MAFFT
Application Phylogenetics
Chemicals Carbon