Diploid yeast strains lacking single chromosomes (monosomics).

(a) Representative colonies of wild-type diploid (WT) and monosomic mutant strains (M1…M16) when grown together for 24 hours at 30 °C on agar-solidified YPD medium. (b) DNA whole genome sequencing coverage. (c) Examples of large colonies emerging among the small monosomic ones.

Contribution of positive epistasis to fitness of monosomics.

(a) Growth performance of heterozygous single-gene deletion strains tested in this study. Left: list of chromosomes with numbers of assayed deletion strains. Right: frequency distribution of rDR (doubling rate related to that of the control). (b) Growth performance of monosomics. Colored bars represent expected performance calculated as a sum of the single-gene effects per chromosome, rDRE=1+∑di, where di=rDRi−1 (deviation from the control). Gray bars show the observed performance of monosomic strains, rDRM. White arrows mark the expected departure from wild-type fitness (expected genetic load), gray the observed one. Black arrows show the extent and direction of epistasis. Three monosomics were not included in these assays (see the main text).

Absence of transcriptional compensation in monosomic strains.

(a) Halved RNA production on monosomic chromosomes. For every ORF, the obtained number of RNA-seq reads was divided by the number expected for it under expression being constant over an entire genome. (b) Expression under monosomy vs. single-deletion fitness (rDR). X-axis shows the length of a monosomic chromosome with centromeres marked as circles and gene deletions as bars; colors show the effect of monosomy on the level of a particular mRNA with a particular color showing a range of log2 fold change (FC) relative to the control. Y-axis: the difference in rDR between a single gene deletion strain and the control, d=rDR-1. The correlation between fitness effect (rDR-1) and shift in expression (log2FC) is reported as Spearman’s coefficient rs with associated and p-value (not corrected for the multiplicity of comparisons).

Parallel and divergent shifts in transcriptomes of monosomic strains.

Heat maps show monosomic mRNA frequencies divided by respective diploid (control) ones. (a) Gene Ontology categories selected to demonstrate similarities in transcriptional profiles of monosomic strains. (b) Regulons demonstrating differences in gene expression between monosomic strains. Expanded versions of all panels can be found in Supplementary Figure S1.

Yeast Slim GO Biological Process categories of the tested deletions and the predicted and observed relative doubling rate of the monosomic strains.

Parallel and divergent shifts in transcriptomes of monosomic strains.

Heat maps show monosomic mRNA frequencies divided by respective diploid (control) ones. (a) Gene Ontology categories selected to demonstrate similarities in transcriptional profiles of monosomic strains. (b) Regulons demonstrating differences in gene expression between monosomic strains. (This figure is an expanded version of Fig. 4 in the main text.)

DNA whole genome sequencing coverage after the postulated endoreduplication.

Two isolates descending from the parental diploid strains with marked chromosomes VII or XIII are shown. They were subjected to sequencing after being found to lack phenotypic markers and produce four viable spores.

Correlation of counts of individual mRNAs between wild-type and monosomic strains.

Counts are expressed as fractions of either wild-type BY or monosomic M1, M2 and M3 total transcriptomes. Gray circles represent mRNAs from the unaffected 15 chromosomes and group around the diagonal. Blue represent spike mRNAs. Red circles represent mRNAs from the monosomic chromosomes (I, II or III in the respective graphs). Note that the monosomic counts are, as expected, underrepresented in the respective monosomic strains (red circles are below the diagonal). Monosomic counts of spike are higher than that of BY (blue circles are above the diagonal). As reported in the main text, the total fraction of spike counts in BY is 4.04%. Analogous sums for M1, M2 and M3 are 6.08, 15.6 and 24.2%. This can be seen here as an increasing distance between the gray and blue circles.