Fig 2. Chromosome XII amplification compensates for rDNA contraction in RM.

(A) Aneuploidies identified in the MALs. Blue tones indicate chromosome copy number. The chromosomes are sorted by their size with larger chromosomes on the top. (B) Upper left, the short read sequencing revealed segmental CNV on chromosome XII of NA/WE-RM-4. The red arrows indicate the breakpoint of each segmental CNV. Upper right dot plot, the x-axis represents NA and WE reference genomes, y-axis represents the assembled contigs of NA/WE-RM-4 obtained from long read sequencing. Lower left, zoom-in dot plot of the chromosome XII inversion. The bar below represents chromosome XII, with black circle and red rectangle indicating centromere and rDNA repeats respectively. Lower right, CNV-associated inversion structure: the extra copy of chromosome XII right arm together with the centromere was inverted and replaced the left arm. (C) rDNA copy number per chromosome XII (upper panel) and rDNA copy number per sample (lower panel) normalized by the ancestors for all MALs binned based on the evolved condition and the copy number of chromosome XII. Boxplot: center lines = median; boxes = interquartile range (IQR); whiskers = 1.5×IQR; points = outliers beyond 1.5×IQR. (D) Cell doubling time (upper panel) and yield (lower panel) of RM-evolved MALs phenotyped with (left) or without (right) RM. The blue and red boxplots represent MALs with and without chromosome XII gain respectively. The p value was calculated to compare the cell doubling time and yield between the initial and last timepoint populations by Mann–Whitney U test.