Fig. 3. Dosage compensation across isolates.

a, Comparison of relative mRNA and protein expression between natural isolate AHS and a disomic lab strain, both disomic for chromosome 9. Gene-by-gene log₂ mRNA or protein ratios are shown, sorted by chromosomal location. Genes located on aneuploid chromosomes are coloured. The solid grey line marks 0, and dashed coloured lines indicate the medians of the aneuploid mRNA or protein expression distributions, respectively. Box plots show the distributions of log₂ mRNA or protein ratios for all genes encoded on euploid or duplicated chromosomes (AHS: n = 1,513/48 euploid/aneuploid; disome 9: n = 1,322/45 euploid/aneuploid). In box plots, the centre marks the median, hinges mark the 25th and 75th percentiles and whiskers show all values that, at maximum, fall within 1.5 times the interquartile range; the median of the distributions is shown below the boxes. Only log₂ ratios between −2 and 2 are shown to improve readability. b, Quantification of relative dosage compensation at the mRNA level (top) and at the protein level (bottom) for natural isolates and disomic lab strains. The medians of the log₂ mRNA and log₂ protein distributions in Extended Data Fig. 4a,b are plotted against the relative chromosome copy number change. Linear regressions for mRNA (orange) and protein (purple) levels in natural isolates and disomic lab strains are shown. Linear models and R₂ values are shown for natural isolates. The dotted black line indicates the expected relative expression levels under no dosage compensation (y = x). c, Scatter plot comparing the isolate-wise extent of attenuation at the mRNA and protein level. Isolates AHS, CFV and ABV are highlighted. Distributions of mRNA-level (orange) and protein-level (purple) buffering across all aneuploid isolates are shown. The pie chart shows the number of isolates that are buffered more strongly at the protein or at the mRNA level. Isolates with complex aneuploidies of different relative copy number changes, as well as isolates that probably reverted to the euploid state, were excluded.