Multiple independent losses of crossover interference during yeast evolutionary history

Abstract

Meiotic recombination is essential for the accurate chromosome segregation and the generation of genetic diversity through crossover and gene conversion events. Although this process has been studied extensively in a few selected model species, understanding how its properties vary across species remains limited. For instance, the ancestral ZMM pathway that generates interference-dependent crossovers has undergone multiple losses throughout evolution, suggesting variations in the regulation of crossover formation. In this context, we first characterized the meiotic recombination landscape and properties of the Kluyveromyces lactis budding yeast. We then conducted a comprehensive analysis of 29,151 recombination events (19, 212 COs and 9, 939 NCOs) spanning 577 meioses in the five budding yeast species Saccharomyces cerevisiae, Saccharomyces paradoxus, Lachancea kluyveri, Lachancea waltii and K. lactis. Eventually, we found that the Saccharomyces yeasts displayed higher recombination rates compared to the non-Saccharomyces yeasts. In addition, bona fide crossover interference and associated crossover homeostasis were detected in the Saccharomyces species only, adding L. kluyveri and K. lactis to the list of budding yeast species that lost crossover interference. Finally, recombination hotspots, although highly conserved within the Saccharomyces yeasts are not conserved beyond the Saccharomyces genus. Overall, these results highlight great variability in the recombination landscape and properties through budding yeasts evolution.

Fig 1. Kluyveromyces lactis recombination map.

Density of CO along the six chromosomes represented by scaffolds S1-6 using a 5 kb window. Horizontal dashed red lines represent the CO hotspot significance threshold (see Materials and methods). Under the density plot, CO coldspots and hotspots are shown in blue and red, respectively. For each chromosome the black dash represents the centromere position. The MAT locus on chromosome 3 and the rDNA locus on chromosome 4 are highlighted in black.

Fig 2. Summary description of detected events.

A. Barplot depicting frequencies of crossovers (CO) and noncrossovers (NCO) per chromosome per meiosis for S. cerevisiae (n = 72), S. paradoxus (n = 59), K. lactis (n = 205), L. waltii (n = 192) and L. kluyveri (n = 59) [n-total number of tetrads analyzed for each species]. Bars represent standard deviation. B. Scatter plot of mean crossover and noncrossover counts per chromosome versus chromosome size for S. cerevisiae, S. paradoxus, K. lactis, L. waltii and L. kluyveri (R, Pearson’s correlation). Best fit line obtained through linear regression. C. Cartoons representing CO events as defined in Anderson et al. 2011 [81]. i and ii. Simple CO with or without GC, with their midpoints not within 5 kb of another CO or NCO; iii. CO with a GC tract on a chromatid not involved in the CO; iv. CO with two GCs on a chromatid involved in the CO and on a chromatid not involved in the CO; v. CO with complex (discontinuous) GC. D. Pie chart representing the fraction of simple (Type 0 and 1) and complex (Type 2, 3, 4 and 8) crossovers across the five species. The complex COs were increased in non-Saccharomyces yeasts (K. lactis, L. waltii and L. kluyveri) compared to Saccharomyces yeasts (S. cerevisiae and S. paradoxus) (Wilcoxon test, p<0.01). The events have been classified as described in Anderson et al. 2011 [81].

Fig 3. Loss of crossover homeostasis in non-Saccharomyces yeasts (K. lactis, L. waltii and L. kluyveri) compared to Saccharomyces yeasts (S. cerevisiae and S. paradoxus).

Scatter plot depicting the relationship between the CO:NCO ratio and total interhomolog (CO+NCO) events per meiosis (R, Pearson’s correlation). Best fit line obtained through linear regression. Average CO:NCO ratios (not corrected/corrected) were 2.3/1.8, 2.0/1.8, 1.8/1.5, 2.5/2.2 and 2.6/2.5 respectively for S. cerevisiae, S. paradoxus, K. lactis, L. waltii and L. kluyveri. The corrected NCO frequency was estimated as described in Mancera et al. 2008 [50].

Fig 4. Altered crossover interference across the yeast species.

A. Interference (1 –CoC) for crossovers in S. cerevisiae, S. paradoxus, L. waltii, K. lactis and L. kluyveri respectively. The CoC was determined for each inter-interval distance for every possible interval pair across the genome and the average is plotted. B. Interference calculated as 1-CoC for a bin size and inter-interval distance of 25 kb is shown for COs only, NCOs only, or all events (CO+NCO) across the species.

Fig 5. Probability of observing no non-exchange chromosomes (E₀s) in the five species.

The probability of observing no E0 is plotted against the average CO number distributed randomly among the chromosomes (Poisson distribution). Numbers in red and blue indicate the observed and expected percentages of meiosis with non-exchange chromosomes, respectively.

Fig 6. Elevated evolutionary rates in ZMM genes.

A-C. Distribution of dN/dS ratios for all the genes across S. cerevisiae, L. kluyveri and K. lactis species respectively. ZMM genes are indicated in the distribution. Inset: Violin plot comparing the dN/dS ratios of meiosis genes with the rest of genes that have orthologs in all the three species. Hollow circles on the violin plot represent ZMM genes.