Fig. 4: Dynamics of complex regions.
a, Crossbars within violin plots indicate individual mean telomere lengths, and the horizontal line shows the global mean telomere length across all ends (n = 100 independent strains in each boxplot). No correction for multiple testing was applied, but the false discovery rates were estimated by calculating the proportion of false positives with 1, 2 and 3 stars black for the rank product and gray for the rank sum test) corresponding to P < 0.05, 0.01 and 0.001, respectively. b, Crossbars indicate TEL03L mean lengths (n = 100 independent strains in each boxplot). Two-sided Wilcoxon mean comparison P values are indicated. c, Region A was transferred from a Torulaspora species to BLD_1a and AAB strains and interrupted by a Ty2 insertion in AAB. The most inner part of the telomeric repeats is close to the Torulaspora repeats (AAGGTTGA/TGGTGT50), while the distal portion consists of the Saccharomyces (TG1-3). d, Telomere repeats gradually transition from Torulaspora-type to S. cerevisiae-type. The colors correspond to the repeat types presented in c. e, S. cerevisiae and S. kudriavzevii chromosomes are represented in blue and in dark red, respectively. Both breakpoints on chromosomes VI and VII occur in regions that have low sequence divergence compared to the genome-wide average (red dashed line). f, The topology of the tree is the same as in Fig. 1. tRNA gene gains and losses are represented in dark blue and orange, respectively. Anticodon modifications are written in light blue. Strain names are colored in dark blue for gains, orange for losses and in mauve when different types of events co-occurred. g, Chromosomal repartition of all types of transposable elements across the 100 de novo assembled genomes (top). For isolates harboring several types of elements in a single region, the complete Ty is preferentially represented, followed by the truncated Ty. Chromosomal repartition of complete Ty elements (bottom). Only one element is plotted per isolate. For isolates with several families in a given insertion site, the family found in the reference genome was preferentially represented.
