Phylogenomics and functional annotation of 530 non-Saccharomyces yeasts from winemaking environments reveals their fermentome and flavorome

The supplementary tables are deposited at the Figshare repository: https://doi.org/10.6084/m9.figshare.28278929. <br />Table S1. Quality control of the 661 genomes considered in the present study. Dark Grey - genomes excluded from further analysis. Red – particular parameters used to exclude the genomes (see methods for details). Light Grey - genomes further excluded due to lack of quality in the subsequent analysis (provided as a separate Excel file). <br />Table S2. Taxonomic information of the 134 yeast species considered in this work, in particular regarding discrepancies found in different taxonomic databases, and the aggregation of different synonyms under the same accepted name. <br />Table S3. Comparison of number of Protein Coding Sequences (CDS) after genome annotation with our pipeline, in comparison with annotations available in NCBI and in literature. Numbers in red indicate the highest number of genes identified in the total number of annotations compared. Red background additionally indicates novel annotation done in this work for that particular strain. <br />Table S4. Functional annotation of the 530 non-Saccharomyces proteomes considered in this study (see methods for details). <br />Table S5. Number of genes (average of all the strains of each species (first row) ± standard deviation (second row)) annotated into each KEGG Pathway, organized by taxonomic level. <br />Table S6. Heatmap analysis of the KEGG Pathway modules completeness in the 530 non-Saccharomyces genomes. <br />Table S7. Heatmap analysis of the KEGG Pathway modules completeness in the different yeast families (numbers on the third row), orders (second row), and phyla (first row). * - families with only one species represented. <br />Table S8. Information about the 93 genes identified as the “Fermentome of S. cerevisiae”, according with Walker et al. 2014, and their presence in the genome of 530 non-Saccharomyces yeasts. Blue cells - gene present; Grey cells - absence of the gene. <br />Table S9. BLAST results of S. cerevisiae proteins in the non-Saccharomyces genomes. ok - homologous protein detected (Blast e-value > e-6). absent - protein not detected (Blast e-value < e-6). <br />Table S10. 41 genes defined as the Fermentome of non-Saccharomyces yeasts within the present work. Genes highlighted in orange represent the ones present in more than 95% of fermentative strains, and in less than 5% of non-fermentative strains (script Fermentome). The remaining ones, highlighted in yellow, were detected in more than 90% of fermentative strains, and in less than 10% of non-fermentative strains. <br />Table S11. Presence of the 96 genes in the 530 non-Saccharomyces genomes, selected from the literature as being relevant for aroma and flavour production in wine. ok - gene identified in the genome; Empty grey cell - gene not identified. Identification of fermentative yeast species: red - no; orange - variable; green - yes.