Supporting data for taxonomic and phylogenetic revision of the genus Phytophthora based on the types
This project is a systematic and phylogenetic study of the genus Phytophthora. Three overlapping phylogenetic data sets were assembled (Table 5, Table S1): for Fig. 1 (and Fig. S1), a three-locus (ITS, COI, βTUB) alignment focusing on the order Peronosporales, for Fig. 2 (and Fig. S2), a five-locus (COI, βTUB, EF1α, L10, HSP90) alignment focusing on Phytophthora and downy mildews, and for Fig. 3 (and Fig. S3), a seven-locus (ITS, COI, YPT1, βTUB, EF1α, L10, HSP90) alignment focusing on Phytophthora. Single-locus trees were also inferred for each of the seven loci appearing in Fig. 3 (Figs. S4-S10). Input alignments are included in Phylip (.phy) format. For the IQ-TREE 2 maximum likelihood analysis, partitioning schemata appearing in NEXUS-formatted files (.nex) were used as input along with alignments. IQ-TREE 2 output files (.iqtree) contain partitioning and model schemata and maximum likelihood output trees. PartitionFinder2 was employed to discern optimal partitioning and model schemata for Bayesian inference, and the output is included as text (.txt) files. MrBayes output is included as Newick-formatted tree files (.tre). Supporting data for Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola SO, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ. 2023. Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259–349. doi.org/10.3114/sim.2023.106.05
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Sequence accessions appearing in Table 5 and Table S1 were assembled and aligned to create the .phy alignments. The .phy files, along with the partitioning schemata listed in the .nex files were used as input for the IQ-TREE 2 and PartitionFinder2 analyses. The output of the PartitionFinder2 analysis was used as input for MrBayes.