A taxogenomic view of the genus Torulaspora: an expansion from ten to twenty-two species

Data S1. Different yeast isolation procedures used in this study.Fig. S1. Average nucleotide identity (ANI) matrix for the genus Torulaspora. The analysis used the same genomes as in Fig. 1. Inter-species ANI values are shown in white or black backgrounds and represent the averages of all possible genome comparisons between two species. Numerals in black backgrounds correspond to comparisons between novel species and their closest relatives. Pairwise averages of all relevant intraspecific ANI values are shown in coloured or grey backgrounds; these values are not available (NA) when only one genome per species was studied.Fig. S2. Phylogenetic tree based on a sequence alignment of the D1/ D2 region of the LSU rDNA of representatives of all Torulaspora species, including sequences retrieved from GenBank for which genome data are not available. The phylogeny tree was constructed with the maximum-likelihood method and the Tamura–Nei model of sequence evolution, with equal base frequence, and was rooted with Zygotorulaspora mrakii. The final dataset had a total of 588 positions. Names in black indicate sequences retrieved by us from genome assemblies (bold highlights type strains). Note that, in some cases, more than one sequence was retrieved from the genome. Names in blue represent sequences retrieved from GenBank; in these cases, the original species designations were maintained. Species names and delimitations based on taxogenomics are indicated on the right side. The scale bar represents the estimated number of substitutions per site. Percentage bootstrap values of 1000 replicates are given at each node.Fig. S3. Phylogenetic tree based on a sequence alignment of the complete ITS region of the rDNA of representatives of all Torulaspora species, including sequences retrieved from GenBank for which genome data are not available. The phylogenetic tree was constructed with the maximum-likelihood method and the Hasegawa-Kishino-Yano model of sequence evolution and was rooted with Zygotorulaspora mrakii. The final dataset had a total of 843 positions. Names in black indicate sequences retrieved by us from genome assemblies (bold highlights type strains). Note that, in some cases, more than one sequence was retrieved from the genome. Names in blue represent sequences retrieved from GenBank; in these cases, the original species designations were maintained. Species names and delimitations based on phylogenomics are indicated on the right side. The scale bar represents the estimated number of substitutions per site. Percentage bootstrap values of 1000 replicates are given at each node.Fig. S4. Phylogenetic tree based on a sequence alignment combining the D1/D2 and ITS regions of the rDNA of representatives of all Torulaspora species, including sequences retrieved from GenBank for which genome data are not available. The phylogenetic tree was constructed with the maximum-likelihood method and the TPM2u model of sequence evolution and was rooted with Zygotorulaspora mrakii. Alignment positions containing gaps and missing data were eliminated before the analysis. The final dataset had a total of 1411 positions. Names in black indicate sequences retrieved by us from genome assemblies (bold highlights type strains). Note that, in some cases, more than one sequence was retrieved from the genome. Names in blue represent sequences retrieved from GenBank; in these cases, the original species designations were maintained. Species names and delimitations based on phylogenomics are indicated on the right side. The scale bar represents the estimated number of substitutions per site. Percentage bootstrap values of 1000 replicates are given at each node.Fig. S5. Molecular validation of the synonyms of T. delbrueckii. (A) List of synonyms of T. delbrueckii and details on ITS and whole- genome sequences. (B) Phylogenetic tree based on a sequence alignment of the complete ITS region of all species in the genus Torulaspora (depicted in black) and the current synonyms of T. delbrueckii (depicted in blue). The highlighted box corresponds to the species T. delbrueckii. The phylogenetic tree constructed with the maximum-likelihood method and the TIM2 model of sequence evolution, chosen according to the BIC, and rooted with Zygotorulaspora mrakii. The final dataset had a total of 813 positions. Names in bold indicate the novel species. The scale bar represents the estimated number of substitutions per site. Percentage bootstrap values of 1000 replicates equal or higher that 95 % are depicted as black circles at tree nodes.Fig. S6. Expanded phenotype map for the genus Torulaspora. The results of physiological tests including carbon fermentation, carbon assimilation, nitrogen assimilation, temperature preference, and sensitivity to select compounds for members of the Torulaspora genus are arranged by phylogenetic relationship, indicated by the associated tree. The presence of a square indicates a tested trait while the absence of a square indicates a trait that was not tested for that isolate. A full square indicates a positive phenotype (e.g. fermentation of a substrate or growth at a specified temperature) while an empty square indicates a negative phenotype (e.g. failure to assimilate a substrate or lack of growth in the presence of certain compounds). Phenotypic results were obtained in this work or were taken from the literature as indicated in Table S3.Table S1. Strains and genomes analysed in this study and relevant information pertaining to them (strains are ordered as in the phylogeny of Fig. 1).Table S2. Sources of D1/D2 and ITS rDNA sequences used to construct Figs S2, S3, and S4.Table S3. Sources of the phenotypic information depicted in Fig. 2.Table S4. Signature amino acids of α-glucosidase-encoding genes (strains are ordered as in Fig. 2). Signature amino acids that correlate to substrate specificity for maltases and isomaltases, numbered as in Saccharomyces cerevisiae IMA1, are compared for isomaltase-, maltase- and maltase/isomaltase-like sequences. Relevant amino acid signatures for maltase and isomaltase activity are highlighted in yellow and blue, respectively, and mixed maltase–isomaltase affinity is colour-coded in green.Table S5. Standard physiological and biochemical profiles of the novel Torulaspora species described this study (results shown for each strain).Table S6. Standard physiological and biochemical profiles of all species in the genus Torulaspora (species are ordered as in the phylogeny of Fig. 1).