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本研究针对疫霉属（Phytophthora）开展了系统性分类与系统发育学研究。本研究整合了三套重叠的系统发育数据集（见表5、补充表S1）：针对图1（及补充图S1），构建了聚焦于霜霉目（Peronosporales）的三位点（ITS、COI、βTUB）序列比对；针对图2（及补充图S2），构建了聚焦于疫霉属与霜霉菌类的五位点（COI、βTUB、EF1α、L10、HSP90）序列比对；针对图3（及补充图S3），构建了聚焦于疫霉属的七位点（ITS、COI、YPT1、βTUB、EF1α、L10、HSP90）序列比对。此外，针对图3中涉及的7个位点，分别构建了单基因系统发育树（补充图S4至S10）。 序列比对输入文件以Phylip格式（.phy）提供。在IQ-TREE 2最大似然分析中，我们采用NEXUS格式文件（.nex）中的分区方案作为输入，配合序列比对文件一同使用。IQ-TREE 2的输出文件（.iqtree）包含分区方案、模型方案以及最大似然法构建的系统发育树。本研究使用PartitionFinder2来确定贝叶斯推断所需的最优分区方案与模型方案，其输出结果以文本文件（.txt）形式提供。MrBayes的输出结果以Newick格式的树文件（.tre）形式提供。 本研究的支撑数据来自以下文献：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. 疫霉属：该属的分类学与系统发育修订. 《真菌学研究（Studies in Mycology）》 106: 259–349. doi:10.3114/sim.2023.106.05