1. Genetics and Genomics
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Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds

  1. Abhishek Dutta
  2. Fabien Dutreux
  3. Joseph Schacherer  Is a corresponding author
  1. Université de Strasbourg, CNRS, GMGM UMR 7156, France
  2. Institut Universitaire de France (IUF), France
Research Article
Cite this article as: eLife 2021;10:e70339 doi: 10.7554/eLife.70339
5 figures, 2 tables and 8 additional files

Figures

Figure 1 with 5 supplements
Overall distribution of loss of heterozygosity (LOH) in the 169 mutation accumulation (MA) lines.

(A) LOH event tract size distribution across all 169 MA lines, the average tract sizes of the interstitial LOH (I-LOH) events (7.4 kb) and terminal LOH (T-LOH) events (55.3 kb), respectively. The global average LOH event size was 14.1 kb. (B) Violin plot of the LOH event counts in the MA lines population, I-LOH events were found to be significantly greater than T-LOH events (Wilcoxon test, p<2×10−16). (C) Distribution of MA lines based on the proportion of genome under LOH (%), dashed line indicates average proportion of genome under LOH across the 169 MA lines, 15.9% (±1.86).

Figure 1—figure supplement 1
Distribution of the heterozygous single nucleotide polymorphism (SNP) densities as a fraction of total heterozygous SNPs in 5 kb windows across the ancestral diploids as described in Table 1.
Figure 1—figure supplement 2
Chromosome-wide distribution of loss of heterozygosity (LOH) events across all mutation accumulation (MA) lines.

(A) All LOH events, (B) terminal LOH (T-LOH), events, and (C) interstitial LOH (I-LOH) events.

Figure 1—figure supplement 3
A terminal LOH (T-LOH) events are significantly larger than interstitial LOH (I-LOH) in the 169 mutation accumulation (MA) lines all backgrounds except H4 (Wilcoxon test, *p < 0.05; **p < 0.01; ***p<0.001; ****p < 0.0001; ns – not significant).
Figure 1—figure supplement 4
Boxplot depicting the fraction genome under loss of heterozygosity (LOH) in the nearly homozygous lines is significantly greater than the rest of the mutation accumulation (MA) lines (Wilcoxon test, p=6.1×10−10).
Figure 1—figure supplement 5
Chromosome-wide loss of heterozygosity (LOH) plots across representative lines from H1, H3, H4, and H9.

Orange and blue colors represent single nucleotide polymorphisms (SNPs) fixed toward either of the parents as described in Table 1 and Supplementary file 1. All the 14 nearly homozygous (NH) lines have been depicted. Dotted vertical lines represent position of the centromere.

Figure 2 with 3 supplements
Genetic background-dependent variation in the loss of heterozygosity (LOH) repertoire.

(A) The frequency of total LOH events across the nine genetic backgrounds are highly variable (Kruskal-Wallis test, p<2×10−16). (B) Variability in interstitial and terminal LOH events counts across all backgrounds H1–H9 (Kruskal-Wallis test, p<10−16), interstitial events were always in excess, except for in H6 (Wilcoxon test, *p < 0.05; **p < 0.01; ***p<0.001; ****p < 0.0001; ns – not significant). (C) Frequency of terminal LOH events increases with increasing heterozygosity in the nine genetic backgrounds (Pearson’s correlation; r = 0.69, p<2×10−16), interstitial and total events do not bear any correlation with the background heterozygosity (Pearson’s correlation; p>0.05). (D) Proportion of genome under LOH is significantly variable across the nine backgrounds (H1–H9) (Kruskal-Wallis test, p<2×10−16).

Figure 2—figure supplement 1
The frequency of interstitial LOH (I-LOH) events increases with increasing chromosome size for all backgrounds except for H1 and H9; no such correlation was observed for terminal LOH (T-LOH) events.
Figure 2—figure supplement 2
Overall fraction of interstitial and terminal loss of heterozygosity (LOH) tracts across the nine genetic backgrounds.
Figure 2—figure supplement 3
Fraction of the genome fixed toward either of the parental genomes across the nine genetic backgrounds.

Biased fixation was only observed in H4 and H5 backgrounds (binomial test, p<0.05).

Figure 3 with 1 supplement
Loss of heterozygosity (LOH) accumulation is associated with spore fertility.

(A) Total LOH events accumulated in mutation accumulation (MA) lines derived from ancestral diploids with high spore fertility, that is, meiotic spore viability greater than or equal to 75% and the fraction of four-spore viable tetrads greater than 50% (H1, H2, H3, H6, H7) is significantly lower than in MA lines derived from ancestral diploids with low spore fertility, that is, meiotic spore viability lesser than 75% and the fraction of four-spore viable tetrads less than 50% (H4, H5, H8, H9) (Wilcoxon test, p<2×10−16). (B) The size (in bp) of the LOH events accumulated in MA lines derived from ancestral diploids with high spore fertility is significantly larger than in MA lines derived from ancestral diploids with low spore fertility (Wilcoxon test, p<2×10−16). The average LOH event size in the high spore fertility and low spore fertility MA lines are 45.8 and 7.4 kb, respectively. (C) Spore viabilities in both the high and low spore fertility groups compared respective to their ancestral diploids. There is a significant improvement in the spore viabilities of the MA lines derived from the low spore fertility ancestors (Mann-Whitney U test, p=0.04), whereas the viabilities do not change in the MA lines derived from the high spore fertility ancestral diploids (Mann-Whitney U test, p=0.34). The spore viabilities of the individual MA lines and the ancestral diploids detailed in Supplementary file 4.

Figure 3—figure supplement 1
The total number of interstitial LOH (I-LOH) and terminal LOH (T-LOH) events are significantly greater in the mutation accumulation (MA) lines derived from ancestral diploids with low fertility (Wilcoxon test, *p < 0.05; **p < 0.01; ***p<0.001; ****p < 0.0001; ns – not significant).
Figure 4 with 3 supplements
Mutation rates are constant across the backgrounds and within the nearly homozygous (NH) lines (range 0.67–1.9 × 10−10 mutations/site/division; Kruskal-Wallis test, p>0.05).

The overall, mean single nucleotide mutation (SNM) rate in the 169 MA lines 1.1 × 10−10 per site per division is not different from previous estimates in various diploid Saccharomyces cerevisiae strains. NH lines represent the SNM rates in the NH lines. SNMs have been detailed in Supplementary files 5 and 6.

Figure 4—figure supplement 1
SNM spectrum across the nine hybrid backgrounds.

(A) The spectrum of single nucleotide mutations (SNMs) in the mutation accumulation (MA) lines is variable across all genetic backgrounds (Chi-square test, p<0.05; Supplementary file 56). (B) The transition to transversion ratio is similar across all genetic backgrounds, significantly increased only in H3 (Chi-square test, p<0.05; Supplementary file 56). (C) The GC > AT/AT > GC mutational bias was similar in all genetic backgrounds, significantly increased only in H1 (Chi-square test, p<0.05; Supplementary file 56).

Figure 4—figure supplement 2
The frequency of mutations was significantly impacted at C/G sites than A/T sites by the neighboring nucleotides (Chi-square test, p<0.05; Supplementary file 56).

Horizontal red lines indicate mean events.

Figure 4—figure supplement 3
The frequency of aneuploid chromosomes across the nine genetic backgrounds (H1–H9).

Two backgrounds carried ancestral trisomies, H3 (+1 chrIX) and H9 (+1 chrIX; +1 chrXVI).

Author response image 1

Tables

Table 1
Hybrid mutation accumulation (MA) lines.
HybridCross*Het positionsNo. of sequenced linesNo. of bottlenecksTotal no. of divisions
H1ABS × BKL9972201002446
H2ABP × BFQ1878912751842
H3BAP × BAN2087520751863
H4BTI × ABA4941220751772
H5ACD × AKQ5222320751777
H6ACK × CMQ55570201002392
H7ACG × BAK6945619751844
H8CGD × AKE11324119751769
H9BAM × CPG116475191002452
  1. * Standardized names from Peter et al., 2018.

Author response table 1
Mean event counts for 5 kb at chromosome ends vs rest of the genome.
Hybrid
Background
Mean density
at chr_ends
Mean density
rest_genome
H13.663.98
H27.066.81
H37.579.26
H415.0022.19
H520.0523.67
H620.2722.80
H731.5431.78
H836.2046.73
H946.5847.70

Additional files

Supplementary file 1

Haploid strains used to generate the nine hybrid diploids, standardized names as per Peter et al., 2018.

https://cdn.elifesciences.org/articles/70339/elife-70339-supp1-v2.xlsx
Supplementary file 2

Mean growth rate estimates at bottleneck 0 and at the end of the experiment for the nine genetic backgrounds.

These estimates were used to determine the number of divisions at every bottleneck (see Materials and methods).

https://cdn.elifesciences.org/articles/70339/elife-70339-supp2-v2.xlsx
Supplementary file 3

All loss of heterozygosity (LOH) tracts across the 169 mutation accumulation (MA) lines supported by at least two single nucleotide polymorphisms (SNPs).

Tracts were merged if consecutive tracts were disrupted by less than two SNPs. LOH tracts in nearly homozygous lines highlighted in yellow.

https://cdn.elifesciences.org/articles/70339/elife-70339-supp3-v2.xlsx
Supplementary file 4

Meiotic spore viability in the mutation accumulation (MA) lines, H9-8 and H9-11 excluded as they did not sporulate.

SV-percentage spore viability in the MA lines; statistical significance of differences in spore viability between ancestral diploid and the derived MA lines were determined using the p-values from Fisher’s exact test (GraphPad prism). N – number of tetrads analyzed for spore viability, ns – not significant; p>0.05.

https://cdn.elifesciences.org/articles/70339/elife-70339-supp4-v2.xlsx
Supplementary file 5

Mutations detected in the 169 mutation accumulation (MA) lines.

Multi-nucleotide mutations (MNMs) highlighted in purple.

https://cdn.elifesciences.org/articles/70339/elife-70339-supp5-v2.xlsx
Supplementary file 6

Chi-square test p-values for the single nucleotide mutation (SNM) spectrum variation.

Chi-square test was performed using the Microsoft excel function Chisq.test().

https://cdn.elifesciences.org/articles/70339/elife-70339-supp6-v2.xlsx
Supplementary file 7

List of strains used in this study.

https://cdn.elifesciences.org/articles/70339/elife-70339-supp7-v2.xlsx
Transparent reporting form
https://cdn.elifesciences.org/articles/70339/elife-70339-transrepform-v2.docx

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