Phytophthora: taxonomic and phylogenetic revision of the genus-SUPP

Abstract

Supplementary files:<br />Supplementary File S1. Methods for isolation, maintenance, sporulation, and storage of Phytophthora species.<br />Supplementary File S2. IDphy2 Molecular Protocols for Sanger Sequencing with seven genes. <br />Supplementary File S3. ITS rDNA, COI, MOTUs, 3G HTS and 2G HTS local databases.<br />Supplementary Fig. S1. Order Peronosporales. Maximum likelihood tree inferred with IQ-TREE v. 2 from a three-locus (ITS, COI and β-tub) alignment (Supplementary Table S1). Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches.<br />Supplementary Fig. S2. Phytophthora and related obligate biotrophic taxa. Maximum likelihood tree inferred with IQ-TREE v. 2 from a five-locus (COI, β-tub, EF1α, L10 and HSP90) alignment (Supplementary Table S1). Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches.<br />Supplementary Fig. S3. Seven-locus Phytophthora phylogeny featuring 213 described species. Bayesian tree inferred with MrBayes v. 3.2.7. Posterior probabilities ≥ 0.90 are shown. Sequence accessions are listed in Table 2.<br />Supplementary Fig. S4. ITS-only maximum likelihood tree. Tree inferred using IQ-TREE v. 2 from a 217 taxon alignment with 1 178 nucleotide positions and 404 binary gap positions. Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches.<br /> Supplementary Fig. S5. COI-only maximum likelihood tree. Tree inferred using IQ-TREE v. 2 from a 190 taxon alignment with 744 nucleotide positions. Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches.<br /> Supplementary Fig. S6. YPT1-only maximum likelihood tree. Tree inferred using IQ-TREE v. 2 from a 180 taxon alignment with 850 nucleotide positions and 322 binary gap positions. Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches.<br /> Supplementary Fig. S7. β-tub-only maximum likelihood tree. Tree inferred using IQ-TREE v. 2 from a 213 taxon alignment with 1 053 nucleotide positions. Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches. <br />Supplementary Fig. S8. EF1α-only maximum likelihood tree. Tree inferred using IQ-TREE v. 2 from a 192 taxon alignment with 879 nucleotide positions. Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches. <br />Supplementary Fig. S9. L10-only maximum likelihood tree. Tree inferred using IQ-TREE v. 2 from a 186 taxon alignment with 465 nucleotide positions. Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches. <br />Supplementary Fig. S10. HSP90-only maximum likelihood tree. Tree inferred using IQ-TREE v. 2 from a 190 alignment with 933 nucleotide positions. Ultrafast bootstrap support values ≥ 50 % are shown above and posterior probabilities ≥ 0.90 from a Bayesian analysis are below branches.<br /> Supplementary Table S1. Taxa added for Figs. 1, 2.Bourret, Tyler; Abad, Gloria; Burgess, Treena (2023), “Supporting data for taxonomic and phylogenetic revision of the genus Phytophthora based on the types”, Mendeley Data, V1, doi: 10.17632/yg2rmfzstw.1