Fig. 2
Continuous improvement of PDV production and generation of SVs. a Fold changes of PDV production in the top 10 SCRaMbLEd strains. b Phenotypic analysis of SCRaMbLEants and fold changes of PDV production after each round of SCRaMbLE. Initial strain, yWJS1; first cycle SCRaMbLEant, yWJS067; second cycle, yWJS168; third cycle, yWJS184; forth cycle, yWJS249; fifth cycle, yWJS321. c Boxplots showing WGS read cover depth, which indicated recurrent chromosomal aneuploidies by SCRaMbLEing the ring_synV in haploid yeast strain. The strains yWJS044 (aneuploid chromosomes: I, III, ring_synV and VI), yWJS047, and yWJS067 were generated by SCRaMbLEing initial strain yWJS1. The strains yWJS184 (aneuploid chromosome: XIII) and yWJS321 (aneuploid chromosomes: XII and XIII) were generated by SCRaMbLEing yWJS067. The coverage depth stands for the chromosome CN that were determined from WGS result. The aneuploid chromosomes were marked in red, and ring_synV was marked in purple. The centre line in each box denotes the median of read coverage depth, the upper bound of box denotes the upper quartile and the lower bound denotes the lower quartile, the upper whisker denotes the maximum read coverage depth and the lower whisker denotes the minimum read coverage depth. d CNV heatmap of ring_synV. Read depth-based CN estimations (loxPsym divided segments) are indicated by color (scale provided to the right). Values are averages from three experiments, and error bars denote s.d. Strain information was listed in Supplementary Data 3
