Computational protocol: Taxonomy and Phylogeny of Peronospora Species (Oomycota) Parasitic to Stellaria and Pseudostellaria in Korea, with the Introduction of Peronospora casparyi sp. nov.

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Protocol publication

[…] Sequences of the ITS rDNA and the cox2 mtDNA were edited with the DNASTAR software package ver. 5.05 (DNAStar Inc., Madison, WI, USA). Alignments of each locus were performed using the QINS-i algorithm [] in MAFFT 7 [], in addition to the reference sequences of Peronospora parasitic to Stellaria species, available in GenBank. Maximum likelihood (ML) and minimum evolution (ME) methods were used to infer the phylogenetic trees. For ML analysis, 1,000 rounds of random addition of sequences as well as 10,000 fast bootstrap replicates were performed with RAxML 7.0.3 [] using the GTRCAT model. ME analysis was done using MEGA 7.0 [] with the default settings of the program, except for replacement with the Tamura-Nei model, and the robustness of the ME tree was evaluated with 10,000 bootstrap replicates. […]

Pipeline specifications

Software tools MAFFT, RAxML, MEGA
Application Phylogenetics
Organisms Beta vulgaris, Spinacia oleracea, Nicotiana tabacum, Aspergillus fumigatus