Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds

Abstract

The dynamics and diversity of the appearance of genetic variants play an essential role in the evolution of the genome and the shaping of biodiversity. Recent population-wide genome sequencing surveys have highlighted the importance of loss-of-heterozygosity (LOH) events and have shown that they are a neglected part of the genetic diversity landscape. To assess the extent, variability, and spectrum, we explored the accumulation of LOH events in 169 heterozygous diploid Saccharomyces cerevisiae mutation accumulation lines across nine genetic backgrounds. In total, we detected a large set of 22,828 LOH events across distinct genetic backgrounds with a heterozygous level ranging from 0.1 to 1%. LOH events are very frequent with a rate consistently much higher than the mutation rate, showing their importance for genome evolution. We observed that the interstitial LOH (I-LOH) events, resulting in internal short LOH tracts, were much frequent (n = 19,660) than the terminal LOH (T-LOH) events, i.e., tracts extending to the end of the chromosome (n = 3,168). However, the spectrum, the rate, and the fraction of the genome under LOH vary across genetic backgrounds. Interestingly, we observed that the more the ancestors were heterozygous, the more they accumulated T-LOH events. In addition, frequent short I-LOH tracts are a signature of the lines derived from hybrids with low spore fertility. Finally, we found lines showing almost complete homozygotization during vegetative progression. Overall, our results highlight that the variable dynamics of the LOH accumulation across distinct genetic backgrounds might lead to rapid differential genome evolution during vegetative growth.

A modified fluctuation assay reveals a natural mutator phenotype that drives mutation spectrum variation within Saccharomyces cerevisiae

“…These drawbacks have motivated the development of newer methods that take advantage of high-throughput sequencing, such as mutation accumulation (MA) assays in which a laboratory population is serially bottlenecked for many generations, eliminating most effects of natural selection and allowing mutations to be directly counted by sequencing at the end of the experiment. MA studies have been used to estimate mutation rates in a wide variety of organisms (Lynch et al 2008;Sharp et al 2018;Zhu et al 2014;Farlow et al 2015;Wang et al 2019;Keightley et al 2009), including a recent study of 9 heterozygous S.cerevisiae strains (Dutta, Dutreux, and Schacherer 2021). However, higher throughput MA experiments require DNA repair genes to be knocked out to induce higher mutation rates that can be accurately measured with fewer generations of labor-intensive propagation, as in (Liu and Zhang 2021).…”

Overdominant Mutations Restrict Adaptive Loss of Heterozygosity at Linked Loci

“…Given that LOH conversion tracts frequently extend the full length of a chromosome arm ( Barbera and Petes 2006 ; Lee et al 2009 ; Dutta et al 2021 ), the linked effects we observe will hold true for all chromosomes in asexually evolving diploid populations, particularly in the early stages of adaptation when overdominant beneficial mutations will be most frequent ( Manna et al 2011 ; Sellis et al 2011 ). The strength of the linked effects, however, will vary depending on local rates of mitotic recombination and the length of repair tracts as well as the distribution of mutational effects on fitness—and the degree of dominance of those mutations—along a chromosome.…”

“…WHI2, SFL1 , and PDR5 are all centromere proximal to STE4 , and since conversion tracts produced by mitotic recombination frequently extend from a medial breakpoint to the telomere ( Sui et al 2020 ; Dutta et al 2021 ), adaptive LOH of any of these three loci is likely to extend through the STE4 locus. We examined evolved autodiploid genotypes for evidence of LOH events occurring after a STE4 mutation arises on the right arm of Chromosome XV and we find none.…”

“…Recessive beneficial mutations can be converted to beneficial homozygous mutations through loss-of-heterozygosity (LOH) events during asexual propagation of diploid yeast populations ( Gerstein et al 2014 ). For highly heterozygous populations, such as interspecific hybrids, LOH becomes the dominant mechanism of adaptation ( Smukowski Heil et al 2017 ; James et al 2019 ) due to a high rate of LOH relative to point mutation ( Barbera and Petes 2006 ; Lee et al 2009 ; Dutta et al 2021 ) and to a reservoir of beneficial mutations that are masked in the heterozygous state.…”

“…The rate of LOH increases with distance from the centromere ( Peter et al 2018 ) and several hotspots for LOH have been identified, most strikingly at the rDNA locus on Chromosome XII ( Fisher et al 2018 ; Marad et al 2018 ). LOH can occur by gene conversion, which produces small (∼3 kb) interstitial conversion tracts, or by break-induced replication, which leads to LOH conversion tracts that extend through the telomere ( Symington et al 2014 ; Sui et al 2020 ; Dutta et al 2021 ). The latter occur at a lower rate but are more frequently observed in experimental evolution ( Smukowski Heil et al 2017 ; Marad et al 2018 ; James et al 2019 ).…”