ArticleMolecular biology and evolution2019
Accurate Tracking of the Mutational Landscape of Diploid Hybrid Genomes.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 64 citations in OpenAlex.
- Upper bound on the mutational burden imposed by a CRISPR-Cas9 gene-drive element.G3 (Bethesda, Md.) · 2026Article
- The adaptive molecular landscape of reprogrammed telomeric sequences.Nature communications · 2026Article
- Improved genotype inference reveals cis- and trans-driven variation in the loss-of-heterozygosity rates in yeast.Genetics · 2026Article
- Experimental Test of Evolutionary Safety of a CRISPR-Cas9 Gene-Drive Element.bioRxiv : the preprint server for biology · 2025Article
- Hybrid adaptation is hampered by Haldane's sieve.Nature communications · 2024Article
- Ancient and recent origins of shared polymorphisms in yeast.Nature ecology & evolution · 2024Article
- Genome instability footprint under rapamycin and hydroxyurea treatments.PLoS genetics · 2023Article
- phyBWT2: phylogeny reconstruction via eBWT positional clustering.Algorithms for molecular biology : AMB · 2023Article
- Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae.Nature genetics · 2023Article
- Loss of Heterozygosity and Its Importance in Evolution.Journal of molecular evolution · 2023Review
- Telomeres are shorter in wild Saccharomyces cerevisiae isolates than in domesticated ones.Genetics · 2023Article
- JLOH: Inferring loss of heterozygosity blocks from sequencing data.Computational and structural biotechnology journal · 2023Article
- UGDR: a generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes.BMC bioinformatics · 2022Article
- Recent insights into the evolution of mutation rates in yeast.Current opinion in genetics & development · 2022Review
- Genomic Adaptations ofMicroorganisms · 2022Review
- Genome-scale patterns in the loss of heterozygosity incidence in Saccharomyces cerevisiae.Genetics · 2022Article
- Domestication reprogrammed the budding yeast life cycle.Nature ecology & evolution · 2022Article
- Article
- Heterogeneous Mutation Rates and Spectra in Yeast Hybrids.Genome biology and evolution · 2021Article
- Aborting meiosis allows recombination in sterile diploid yeast hybrids.Nature communications · 2021Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mutations, recombinations, and genome duplications may promote genetic diversity and trigger evolutionary processes. However, quantifying these events 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, aneuploidies, and loss-of-heterozygosity. Pairs of haploid Saccharomyces parents were combined to generate ancestor hybrids with phased genomes and varying levels of heterozygosity. These diploids were evolved under different laboratory protocols, in particular mutation accumulation experiments. Variant simulations enabled the efficient integration of competitive and standard mapping of short reads, depending on local levels of heterozygosity. Experimental validations proved the high accuracy and resolution of our computational approach. Finally, applying MuLoYDH to four different diploids revealed striking genetic background effects. Homozygous Saccharomyces cerevisiae showed a ∼4-fold higher mutation rate compared with its closely related species S. paradoxus. Intraspecies hybrids unveiled that a substantial fraction of the genome (∼250 bp per generation) was shaped by loss-of-heterozygosity, a process strongly inhibited in interspecies hybrids by high levels of sequence divergence between homologous chromosomes. In contrast, interspecies hybrids exhibited higher single-nucleotide mutation rates compared with intraspecies hybrids. MuLoYDH provided an unprecedented quantitative insight into the evolutionary processes that mold diploid yeast genomes and can be generalized to other genetic systems.
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