Phylogenetic data of the publication: “Worldwide forest surveys reveal forty-three new species in Phytophthora Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity”
Description
This repository provides additional data to accompany the paper: “Worldwide forest surveys reveal forty-three new species in Phytophthora Clade 2 with fundamental implications for the evolution and biogeography of the genus and global plant biosecurity”. T. Jung, I. Milenković, Y. Balci, J. Janoušek, T. Kudláček, Z.Á. Nagy, B. Baharuddin, J. Bakonyi, K.D. Broders, S.O. Cacciola, T.-T. Chang, N.M. Chi, T. Corcobado, A. Cravador, B. Đorđević, A. Durán, M. Ferreira, C.-H. Fu, L. Garcia, A. Hieno, H.-H. Ho, C. Hong, M. Junaid, K. Kageyama, T. Kuswinanti, C. Maia, T. Májek, H. Masuya, G. Magnano di San Lio, B. Mendieta-Araica, N. Nasri, L. Oliveira, A. Pane, A. Pérez-Sierra, A. Rosmana, E. Sanfuentes von Stowasser, B. Scanu, R. Singh, Z. Stanivuković, M. Tarigan, P.Q. Thu, Z. Tomić, M. Tomšovský, S. Uematsu, J.F. Webber, H.-C. Zeng, F.-C. Zheng, C.M. Brasier, M. Horta Jung. This article reports the finding and official description of 43 new Phytophthora species belonging to the Clade 02. 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 2 was studied using a 13-partition (LSU, ITS, βtub, hsp90, tigA, rpl10, tef-1α, enl, ras-ypt1, cox1, cox2, nadh1, rps10) dataset of 91 type and other key isolates from the 43 new and 36 previously described species and two informally designated taxa within Clade 2 with P. infestans from Clade 1c and P. pseudosyringae from Clade 3 as outgroup taxa. The relative phylogenetic positions of the 43 new species within their respective subclades were studied using six separate 13-partition (LSU, ITS, βtub, hsp90, tigA, rpl10, tef-1α, enl, ras-ypt1, cox1, cox2, nadh1, rps10) datasets for subclades 2a (120 isolates from 6 new and 11 known species and 5 informally designated taxa); 2b (104 isolates from 9 new and 9 known species and 3 informally designated taxa); 2c (106 isolates from 15 new and 9 known species); 2d (39 isolates from 6 new and 5 known species and 1 informally designated taxon); 2e (26 isolates from 3 new and 1 known species and 1 informally designated taxon); and 2f (13 isolates from 4 new species). In all analyses P. infestans from Clade 1c and P. pseudosyringae from Clade 3 were used 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 and Maximum-Likelihood (ML) analyses were carried out using RAxML-NG. 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.