Journal Article

Contrasting evolutionary genome dynamics between domesticated and wild yeasts

Lagomarsino, Marco Cosentino, Yue, Jia-Xing, Persson, Karl, Bergström, Anders, Li, Jing, Liti, Gianni, Durbin, Richard, Oliver, Karen, Warringer, Jonas, Fischer, Gilles, Hallin, Johan, Coupland, Paul, Aigrain, Louise

2017

Overview

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. Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus . These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae . Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 45 / 45/22 / 45/23 / 45/29 / 45/77 / 631/208/212/2302 / 631/208/325 / 631/208/514/1948 / Agriculture / analysis / Animal Genetics and Genomics / Assemblies / Automation / Baking yeast / Bioinformatics / Biological Evolution / Biomedicine / Cancer Research / candida-albicans / chromosomal rearrangements / Chromosome Inversion / Chromosome translocations / Chromosomes / Chromosomes, Fungal / Cores / Dynamics / Evolution / Evolution, Molecular / Gene expression / Gene Function / Gene sequencing / Genetic aspects / Genetic diversity / genetic reference panel / Genetics / Genetics & Heredity / Genetics and Genomics / Genetik och genomik / Genome, Fungal / Genome, Mitochondrial - genetics / Genomes / Genomics / Genomics - methods / Genotypes / High resolution / high-throughput / Human Genetics / human subtelomeres / Identification and classification / Inversions / Life Sciences / Medical research / Molecular biology / natural variation / phylogenetic / Phylogenetics / Population / Quality / Saccharomyces / Saccharomyces - genetics / Saccharomyces cerevisiae / Saccharomyces cerevisiae - genetics / Saccharomyces paradoxus / sensu-stricto complex / sequencing data / Subpopulations / Telomere - genetics / Yeast