Accurate tracking of the mutational landscape of diploid hybrid genomes

Abstract

Background Genome evolution promotes diversity within a population via mutations, recombination, and whole-genome duplication. However, quantifying precisely these factors in diploid hybrid genomes is challenging. Here we present an integrated experimental and computational workflow to accurately track the mutational landscape of yeast diploid hybrids (MuLoYDH) in terms of single-nucleotide variants, small insertions/deletions, copy-number variants and loss-of-heterozygosity. ResultsHaploid Saccharomyces parents were combined into diploid hybrids with fully phased genome and controlled levels of heterozygosity. The resulting hybrids represented the ancestral state and were evolved under different laboratory protocols. Variant simulations enabled to efficiently integrate competitive and standard mapping, depending on local levels of heterozygosity and read length. Experimental validations proved high accuracy and resolution of our computational approach. Finally, applying MuLoYDH to four different diploids revealed striking genetic background effects. Homozygous S. cerevisiae showed ∼4-fold higher mutation rate compared to S. paradoxus. In contrast, interspecies hybrids exhibited mutation rates similar to intraspecies hybrids despite 10-fold higher heterozygosity. MuLoYDH unveiled that a substantial fraction of the genome (∼200 bp per generation) was shaped by loss-of-heterozygosity and this process was strongly inhibited by high levels of heterozygosity. ConclusionsWe report a comprehensive framework for characterizing the mutational spectrum of yeast diploid hybrids with unprecedented resolution, which can be generalised to other genetic systems. Applying MuLoYDH to laboratory-evolved hybrids provided novel quantitative insights into the evolutionary processes that mould yeast genomes.

Heterogeneous mutation rates and spectra in yeast hybrids

“…In this study we demonstrate significant, though small differences in mutation rates between 11 types of hybrid crosses of yeast. Low mutation rates in S. paradoxus SpA reported previously (Tattini et al 2019) are closest to BA2 (4% parental divergence), which has the lowest mutation rate among all crosses. Including genetically diverse backgrounds is therefore essential for uncovering species diversity in mutation rates.…”

“…Crosses between closely related yeast strains are more likely to undergo homologous recombination (Tattini et al 2019; Marsit et al 2021), a process which can generate errors (Hicks et al 2010; Deem et al 2011) and potentially lead to higher mutation rates. Using data from (Marsit et al 2021) we found no difference in the number of de novo mutations around the breaks of LOH segments (+/-2 kbp) compared to the rest of chromosomes carrying LOH (binomial test, 2 out of 109 mutations, expected frequency = 0.012, P -value = 0.395) in all crosses with S. paradoxus SpB parent.…”

“…Alternatively, parental effects can dominate in shaping mutation rates in hybrids (Bashir et al 2014). MA experiments by Tattini et al (Tattini et al 2019) showed that an interspecific hybrid between one S. cerevisiae and S. paradoxus strain has mutation rates similar to S. cerevisiae diploid strain. However, to better understand the role of hybridization and genotype effects on mutation rate, different genetic backgrounds need to be considered.…”

Domestication reprogrammed the budding yeast life cycle

“…Third, loss of sporulation means loss of the capacity to form gametes and meiotic recombination. Recombination also occurs under yeast mitosis but at vastly lower rates 64,65 . Thus, domestication near abolished or impaired the yeast capacity to combine beneficial variants into one genotype, to cleanse otherwise healthy genomes from deleterious mutations 66,67 , to prevent their catastrophic accumulation through a ratchet mechanism 68 and to generate a sufficiently broad diversity of genotypes to fully exploit and adapt to multi-faceted wild niches 69 .…”

The budding yeast life cycle: More complex than anticipated?

“…For instance, after three and seven rounds of meiosis and inbreeding, 70% and 90% of the heterozygous SNPs were, respectively, lost (Dutta et al, 2017). In addition, rare sexual cycles are separated by active phases of clonal expansion during which mitotic recombination can occur thereby promoting extensive loss‐of‐heterozygosity (LOH) regions (Llorente, Smith, & Symington, 2008; Peter et al, 2018; Tattini et al, 2019). Under such a scenario where inbreeding prevails during sexual cycles and LOH frequently occurs during mitotic cycles, it is expected that heterozygosity should be extremely low, with the generation of heterozygous diploids being restricted to rare outcrossing events between spores from diverged lineages (Figure 1).…”