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The molecular mechanisms allowing organisms to adapt to new telomeric sequences remain poorly understood. Here, the authors engineer multiple yeast lines with human-like telomeric repeats to unveil their molecular and fitness response to reprogrammed telomeres, highlighting several adaptive measures.

Proteomic data from natural isolates of Saccharomyces cerevisiae provide insight into how these cells tolerate aneuploidy (an imbalance in the number of chromosomes), and reveal differences between lab-engineered aneuploids and diverse natural yeasts.

Jia-Xing Yue, Gianni Liti and colleagues use long-read sequencing to generate complete genome assemblies of 7 Saccharomyces cerevisiae and 5 Saccharomyces paradoxus strains. They use these data to define boundaries between chromosomal core and subtelomeric regions and to compare the evolutionary dynamics between these domesticated and wild yeast species.

GC-biased gene conversion has many implications for evolutionary genetics, but its prevalence is unknown. Here, direct sequencing of tetrads in four species shows large differences in gene-conversion rate but no evidence of overall GC bias.

Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising telomere-to-telomere assemblies of 142 strains representing phylogenetic and ecological diversity of the species characterizes its genome structural landscape.

Whole-genome sequencing of 1,011 natural isolates of the yeast Saccharomyces cerevisiae reveals its evolutionary history, including a single out-of-China origin and multiple domestication events, and provides a framework for genotype–phenotype studies in this model organism.

This study assesses the capacity for sexual and asexual reproduction and the chronological life span across 1,011 genome-sequenced budding yeast isolates and shows the remarkable impact of domestication on budding yeast evolution.

Genome-editing approaches have been used to fuse 16 yeast chromosomes to produce yeast strains with only 1 or 2 chromosomes. Surprisingly, this fusion has little effect on cell fitness.

By sequencing over seventy isolates of the domesticated baker's yeast Saccharomyces cerevisiae and its closest relative, S. paradoxus, this study describes variation in gene content, SNPs, indels, copy numbers and transposable elements, providing insights into the evolution of different lineages, phenotypic variation, domestication and population structure of Saccharomyces.

Domesticated industrial yeast strains are sterile, which hampers to breed strains with novel properties. Here, the authors employ the genetics paradigm return-to-growth to induce genome wide recombination in two sterile polyploid industrial yeasts and identify clones with superior biotechnological traits.

Analysis of 1,673 sequenced Saccharomyces cerevisiae isolates identifies 3,852 sequence blocks introgressed from Saccharomyces paradoxus, most of which are recent and clade-specific. By contrast, divergent Chinese strains of S. cerevisiae show little evidence of introgression but do share ancient polymorphisms with S. paradoxus due to incomplete lineage sorting.

A yeast clonal descendant of an ancient hybridization event is identified and sheds light on the early evolution of the Saccharomyces cerevisiae Alpechin lineage and its abundant Saccharomyces paradoxus introgressions.

Heritability of complex traits can be finely dissected using yeast crosses. Here, Kaspar Märtens and colleagues show that quantitative traits in yeast can be predicted from genotype and phenotype data with an average coefficient of determination of 0.91, providing the most accurate predictions of complex traits to date.

Hybrids are often considered evolutionary dead ends because they do not generate viable offspring. Here, the authors show that sterile yeast hybrids generate genetic diversity through meiotic-like recombination by aborting meiosis and return to asexual growth.

Dissecting the architecture of complex trait is challenging. Here, Hallin, Märtens et al. devises Phased Outbred Lines (POLs) in order to accurately decompose growth trait variation in diploid yeast across different environments.

The correct assembly of genomes from sequencing data remains a challenge due to difficulties in correctly assigning the location of repeated DNA elements. Here the authors describe GRAAL, an algorithm that utilizes genome-wide chromosome contact data within a probabilistic framework to produce accurate genome assemblies.

PGGB is a modular framework for efficiently building unbiased pangenome graphs, supporting diverse downstream analyses.

Combining experimental evolution with next-generation sequencing, the evolve and resequence (E&R) approach is a powerful method for dissecting the genomic changes underlying the adaptation of populations of laboratory organisms or molecules. This Review describes the E&R results from diverse systems and discusses the extent to which various features, including population genetics, experimental setups and reproduction modes, account for the distinct observed outcomes.

This protocol describes LRSDAY, a one-stop computational pipeline to analyze long-read sequencing data from yeast