Phylogenetic data of the publication: Taxonomy, biogeography and evolution of thirty-four taxa in Phytophthora Clade 7a including eleven new species from natural forests and updated descriptions for P. fragariae, P. rubi and the ‘P. ×alni hybrid complex’.

This repository provides additional data to accompany the paper: “Taxonomy, biogeography and evolution of thirty-four taxa in Phytophthora Clade 7a including eleven new species from natural forests and updated descriptions for P. fragariae, P. rubi and the ‘P. ×alni hybrid complex’ ”. Z.Á. Nagy, M. Horta Jung, I. Milenković, T. Kudláček, T. Bourret, K. Kageyama, A. Hieno, H. Masuya, S. Uematsu, N.M. Chi, P.Q. Thu, T.-T. Chang, C.-H. Fu, T. Corcobado, J. Janoušek, T. Májek, M. Mullett, M. Tomšovský, M. Ferreira, R. Singh, C. Maia, Z. Stanivuković, Z. Tomić, J. Bakonyi, J.F. Webber, C.M. Brasier, T. Jung. https://doi.org/10.3114/sim.2026.114.05 This article reports the finding and official description of 11 new Phytophthora species belonging to the Clade 07a. For phylogenetic analyses, the DNA sequences obtained in this study were complemented with publicly available sequences of isolates sourced from the GenBank Nucleotide Collection and GenBank Whole-Genome Shotgun contigs. The phylogenetic structure of Clade 7a and the relative phylogenetic positions of the 11 new species were studied using a mitochondrial 3-partition (cox1, nadh1, rps10), a nuclear 8-partition (LSU, ITS, βtub, hsp90, tigA, rpl10, tef-1α, enl) and a combined 11-partition (LSU, ITS, βtub, hsp90, tigA, rpl10, tef-1α, enl, cox1, nadh1, rps10) dataset of 122 type and other key isolates from the 11 new and 18 previously described species and three informally designated taxa within Clade 7a with P. cinnamomi from Clade 7c and P. sojae from Clade 7b as outgroup taxa. Briefly, the sequences of all loci used in the analyses were aligned using the MAFFT v. 7. Bayesian Inference (BI) analyses were performed using BEAST 2 or MrBayes 3 and Maximum-Likelihood (ML) analyses were carried out using RAxML-NG or IQ-TREE. This repository makes available the input files for the phylogenetic analysis (sequence alignments) and the output results (trees obtained from BI and ML analyses). For details of how these data were generated, users are referred to the published article and supplementary information. In addition, the file “Supplementary phylogenetic results” it is made available, providing a section with detailed description of phylogenetic analysis.