MOESM3 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 3: Figure S2. The ploidy estimates for each chromosome in the CBS 1483 assembly based on Illumina short read data from this study. The red horizontal lines correspond to the median coverage of each chromosome

MOESM7 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 7: Figure S6. More complete version of the tree tracing of Fig. 5. Tree-tracing of the genome-scale similarity across the S. cerevisiae (sub-)genomes of various Saccharomyces strains, as determined using Alpaca. The frequency at which a genome from the reference data set of 157 S. cerevisiae strains from Gallone et al [62] was identified as most similar for a sub-region of the CBS 1483 genome is depicted. The reference dataset is represented as a population tree, upon which only lineages with similarity are indicated with a thickness proportional to the frequency at which they were found as most similar. In addition to the genomes of CBS 1513, CBS 1483, CBS 7539 and CBS 1171, the tree-tracing figures of S. pastorianus Group 1 strains CBS 1503 and CBS 1538, of S. pastorianus Group 2 strains CBS 2156, WS34/70 and Hei-A, and of S. cerevisiae strains CBS 1463, A81062, CBS 6308, CBS 1487, CEN.PK113-7D and S288C are shown

MOESM6 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 6: Figure S5. A more complete version of the similarity profiles of the S. cerevisiae (sub-)genomes of various Saccharomyces strains as shown in Fig. 4. Each S. cerevisiae chromosome of the CBS 1483 assembly was partitioned in non-overlapping sub-regions of 2 Kbp. The colors represent the most similar lineages based on k-mer similarity of 157 S. cerevisiae strains from Gallone et al [62]: Asia (blue), Beer1 (green), Beer2, (gold), Mixed (orange), West-Africa (purple), Wine (red). Mosaic strains are shown in black and ambiguous or low-similarity sub-regions in white. Similarity patterns are shown for the Group 2 S. pastorianus strains CBS 1483, CBS 2156, WS34/70 and Hei-A, for the Group 1 S. pastorianus strains CBS 1503, CBS 1513 and CBS 1538, for S. cerevisiae ale-brewing strains CBS 7539, CBS 1463, A81062, CBS 1171, CBS 6308 and CBS 1483, and for S. cerevisiae laboratory strains CEN.PK113-7D and S288C

MOESM8 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 8: Figure S7. The ploidy estimates for each chromosome of the S. pastorianus isolate of the Heineken A-yeast® lineage based on alignment of short-read data to the chromosome-level assembly of CBS 1483

MOESM4 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 4: Figure S3. Copy number predictions for ORFs in the genome assembly of CBS 1483. Each dot represents an ORF whose x-value represents the location in the corresponding chromosome and the y-value the estimated copy number based on coverage analysis of long-read-only alignments. Dots in yellow indicate ORFs whose coverage significantly deviates from the surrounding genomic region, indicating copy number variation of the ORF within different copies of the same chromosome

MOESM5 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 5: Figure S4. Similarity profiles of the S. eubayanus (sub-)genomes of Group 1 and 2 S. pastorianus strains, as determined using Alpaca. Each S. eubayanus chromosome of the CBS 1483 assembly was partitioned in non-overlapping sub-regions of 2 Kbp. The colors represent the most similar lineages based on k-mer similarity of 29 S. eubayanus strains from Peris et al [63]: admixed (purple), Patagonia-A (red), Patagonia-B (blue). Similarity patterns are shown for the Group 2 strains CBS 1483, CBS 2156 and WS34/70 and the Group 1 strains CBS 1503, CBS 1513 and CBS 1538

MOESM2 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 2: Figure S1. Read-length distribution obtained of the long-read libraries of CBS 1483 produced in this study. This plot shows the four different sequencing libraries obtained from whole genome sequencing of CBS 1483 using the MinION® platform. The Y-axes the frequency and the X-axes depict read-lengths (capped at 30 Kbp) using bins of 500 bp. The libraries were obtained with different sequencing chemistries due to the rapid development of Oxford Nanopore MinION sequencing

MOESM9 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 9: Table S1. Whole genome sequencing data generated in this study, under NCB Accession PRJNA522669

MOESM10 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 10: Table S2. Homozygous sub-regions of the S. cerevisiae sub-genome used for the SNP-based phylogenetic analysis

MOESM1 of Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Additional file 1. A Gene annotations of the long-read assembly of CBS 1483 as predicted by MAKER2. B Added sequence in the long-read assembly relative to the van den Broek et al. 2015 assembly. C Lost sequence in the long-read assembly relative to the van den Broek et al. 2015 assembly. D Gene ontology analysis of genes identified in the long-read assembly which were absent in the van den Broek et al. 2015 assembly. E Genes from brewing-relevant subtelomeric gene families in the long-read assembly of CBS 1483. F Heterozygous sequences in the long-read assembly of CBS 1483. G ORFs with copy number deviating from the copy number of surrounding sequences in the long-read assembly of CBS 1483. H Sequences of the repeats identified in FLO genes of S. cerevisiae S288C and S. eubayanus CBS 12357