Supplemental Tables.

Table A in S1 File. Table of raw reads for triplicate samples of growth in minimal medium (min) in wort on Day 2 (Day 2) and in wort on Day 4 (Day 4). The Geneid correspond to the S. eubayanus or S. cerevisiae geneids from the reference genomes. Where gene names are known these have been added to column 2. Columns 3 and 4 show the copy number for each gene in CBS1538 and W34/70 respectively. Table B in S1 File. Differential gene expression for comparison of transcript reads in wort on Day 2 vs growth in minimal medium. The log2-fold change and p-adjusted values for each gene is shown. Table C in S1 File. Differential gene expression for comparison of transcript reads in wort on Day 4 vs growth in minimal medium. The log2-fold change and p-adjusted values for each gene is shown. Table D in S1 File. Differential gene expression for comparison of transcript reads in wort on Day 2 vs Day 4. The log2-fold change and p-adjusted values for each gene is shown. Table E in S1 File. List of genes up-regulated and down-regulated in the comparisons of all three conditions, Day 2 vs min, Day 4 vs min and Day 2 vs Day 4. Table F in S1 File. Consolidated transcriptome of CBS1538 and W34/70. A combined transcriptome of S. pastorianus genes was generated by summing the reads for S. cerevisiae and S. eubayanus orthologues using the consolidate function in Excel. Unmatched genes were retained in the combined transcriptome with reads mapped respectively to the S. cerevisiae or S. eubayanus reference genomes. The raw reads for triplicate samples of growth in minimal medium (min) in wort on Day 2 (Day 2) and in wort on Day 4 (Day 4) are shown. The copy number for each gene was extracted from the reads coverage of the de novo genome sequencing of the S. pastorianus strains CBS1538 and W34/70 respectively and mapped to a combined genome of S. cerevisiae and S. eubayanus derived from S. cerevisiae S288C, assembly R64 and S. eubayanus (SEU3.0) and were summed for the matched orthologues to give a total gene copy number for each gene id (Columns D and E). Genes with zero reads were removed from the dataset. Table G in S1 File. Differential gene expression data from the consolidated transcriptome analysis. Differential gene expression for comparison of transcript reads in CBS1538 vs W34/70 in minimal medium and in wort on Day 2 and Day 4. The log2-fold change and p-adjusted values for each gene is shown. Table H in S1 File. List of genes up-regulated and down-regulated in CBS1538 and W34/70 from the consolidated transcriptome dataset under the three physiological conditions examined in this study and their intersects.
(XLSX)