Examples of how SVs can impact the genomic landscapes of TEs in hybrids.

An ancestral heterozygous genome is shown as an example, with two subgenomes (black and gray) harboring TEs (green boxes) in distinct copy numbers and at different insertion loci. Examples of various types of SVs are shown in derived genomes: polyploidy (gain of haploid sets of chromosomes), aneuploidy (gain or loss of whole chromosomes), loss of heterozygosity (LOH, inter-homolog conversion of chromosome segments), and de novo transposition. The corresponding changes in TE copy numbers are shown at the right.

Long-read phasing and assembly yield subgenome-level representations of the genomes of hybrid yeast MA lines.

(A) Design of the MA crosses. Haploid derivatives of wild isolates used as parental strains for the MA crosses are shown on the Y-axis. Strains in bold are shared by multiple crosses. MA crosses are shown on the X-axis (left to right, from the least to the most divergent), with the number of lines randomly sampled for long-read sequencing shown in parentheses. The phylogenetic tree displays the evolutionary relatedness between wild populations of S. paradoxus and the sister species S. cerevisiae, based on genome-wide nucleotide variants (scale bar: substitutions per site) (Hénault et al., 2022). (B) Summary of the classification of long reads in two parental subgenomes. For each MA line library, the percent of sequenced bases classified as the MATa and MATα parental subgenomes are shown on the X and Y axes, respectively. Dotted lines indicate global classification rates. Full lines indicate expected subgenome classification ratios of 1:1 for diploid (circles) or tetraploid (squares) lines, and 2:1 or 1:2 for triploid (triangles) lines. The ploidy level of each line was previously measured by DNA staining and flow cytometry (Charron et al., 2019; Marsit et al., 2021). (C) Summary statistics of the de novo subgenome-level assemblies of the MA lines. Assembly size ratio refers to the ratio of subgenome assembly size to the corresponding parental assembly size.

SV types have unequal contributions to changes in the genomic distribution of Ty elements after evolution by MA.

(A) Number of Ty loci affected by each SV type. (B) Number of Ty loci affected by SVs per line for each cross. Dots represent individual MA lines and bars show the average per line. Polyploidy refers to increased ploidy level to triploidy or tetraploidy from the expected diploid initial state. LOH refers to the conversion of large chromosome segments (interstitial or terminal) from one parental genotype to the other. Aneuploidy refers to gains or losses of whole chromosomes. Truncation refers to partial deletion of a full-length Ty copy. De novo refers to the presence of a new full-length Ty copy not found in the corresponding parental background or any other MA line. Deletion refers to the local deletion of a full-length Ty copy. Excision refers to the replacement of a full-length Ty copy with a matching solo LTR, consistent with intra-element LTR-LTR recombination. (C) Average gain and loss of Ty CN per line for each cross, for SV classes that can have bidirectional effects on Ty CN. (D) Distributions of net Ty CN change for individual MA lines. Symbols indicate FDR-corrected P-values for Wilcoxon signed-rank tests for deviations from zero (*: p≤0.05, **: p≤0.01). (E) Net Ty copy number change for individual MA line subgenomes as a function of subgenome size change.

De novo retrotransposition events are rare in the MA lines.

Genome maps show the full-length Ty annotations from the subgenome assemblies of the MA lines with de novo insertions. Gray boxes represent chromosomes, which are numbered at the figure top. Empty triangles represent the parental annotations present at a CN greater or equal to one. Full triangles correspond to the confident de novo retrotransposition events. Triangle orientation indicates whether the annotation is on the plus (right pointing) or minus (left pointing) chromosome strand. The cross corresponding to each MA line is labeled at the right, with the total count of de novo retrotransposition events shown between parentheses. The average retrotransposition rates estimated from the de novo insertions (per line per generation per element) are the following: CC1, 1.0✕10-5; CC2, 4.9✕10-6; CC3, 7.6✕10-6; BB1, 1.5✕10-5; BC2, 1.7✕10-5; BA1, 6.5✕10-6; BA2, 2.2✕10-5; BSc1, 3.6✕10-5.

Ty1 transposition rate decreases as a function of chromosomal Ty1 CN in S. paradoxus.

Transposition rates were measured in eight haploid S. paradoxus backgrounds. Black bars indicate 95% confidence intervals. Empty symbols represent upper bound transposition rate estimates obtained by artificially inflating the mutant count by one when zero was observed. Marker shapes indicate the sequence variant of the tester Ty1 element, either SpB (circles) or SpC (squares). The S. paradoxus backgrounds and estimated Ty1 CNs are, from left to right: UWOPS-79-140 (SpB, 1.2); MSH-604 (SpB, 2.2); LL2012_021 (SpB, 4.6); LL2012_014 (SpB, 10.6); YPS744 (SpA, 14.4); LL2012_011 (SpC, 20.7); LL2011_012 (SpC, 26.3); LL2011_009 (SpC, 32.4).

Natural sequence variants of the tester Ty1 element show distinct transposition rates.

Transposition rates of the SpB (X-axis) and SpC (Y-axis) Ty1 variants are shown for haploid backgrounds (A) and diploid backgrounds (B). Black bars indicate 95% confidence intervals. Empty symbols represent upper bound transposition rate estimates obtained by artificially inflating the mutant count by one when zero was observed. The diagonal line indicates a 1:1 relation between transposition rates for the SpB and SpC Ty1 variants. The replicates of haploid backgrounds correspond to distinct strains from each population (see Figure 5), while the replicates for diploid backgrounds correspond to distinct mtDNA inheritance (see Figure 7).

Uniparental mtDNA inheritance affects the transposition rate of Ty1 in heterozygous backgrounds.

Transposition rates in diploid backgrounds as a function of whether the mtDNA is inherited from the MATa parent (X-axis) or the MATα (Y-axis) are shown. Black bars indicate 95% confidence intervals. Empty symbols represent upper bound transposition rate estimates obtained by artificially inflating the mutant count by one when zero was observed. Marker shapes indicate the sequence variant of the tester Ty1 element, either SpB (circles) or SpC (squares). The diagonal line indicates a 1:1 relation between transposition rates for reciprocal mtDNA inheritance. Colored arrows at the bottom left indicate the mtDNA haplotype that would correspond to a higher transposition rate on that side of the diagonal for each hybrid background.