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）开展系统性分类与系统发育学研究。共组装了3组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）的数据集为3个基因座（ITS、COI、βTUB）的序列比对，聚焦霜霉目（Peronosporales）；针对图2（及补充图S2）的数据集为5个基因座（COI、βTUB、EF1α、L10、HSP90）的序列比对，聚焦疫霉属与霜霉菌；针对图3（及补充图S3）的数据集为7个基因座（ITS、COI、YPT1、βTUB、EF1α、L10、HSP90）的序列比对，聚焦疫霉属。此外，本研究还针对图3所用的7个基因座分别构建了单基因座系统发育树（补充图S4至S10）。输入的序列比对文件采用Phylip格式（.phy）存储。在IQ-TREE 2的最大似然分析中，采用NEXUS格式（.nex）的分区方案文件配合序列比对文件作为输入。IQ-TREE 2的输出文件（.iqtree）包含分区信息、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以确定贝叶斯推断所需的最优分区与模型方案，其输出结果以文本文件（.txt）格式提供。MrBayes的输出结果为Newick格式的系统发育树文件（.tre）。本数据集支撑的文献为：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学修订》（Phytophthora: taxonomic and phylogenetic revision of the genus）. *Studies in Mycology* 106: 259–349. doi.org/10.3114/sim.2023.106.05