Exploring_genome_architecture_and_stability_in_the_absence_of_any_single_non_essential_gene

While identification and analysis of genes required for maintaining genomic stability have traditionally relied on gene-reporter assays and individual gene-deletions, the development of affordable whole-genome sequencing technologies provides ways to do this more globally and at scale. Here, we describe tools to extract information on copy-number variation of tandem and interspersed repetitive DNA elements, chromosomes and mitochondrial DNA from whole-genome sequencing data. With these, we have surveyed the Saccharomyces cerevisiae gene knockout collection to characterize genomic instability caused by absence of any single one of ~4500 non-essential genes. Analysis of this dataset reveals genes affecting maintenance of various genomic elements, connections between maintenance of the nuclear and mitochondrial genomes, and how many strains have adapted to life in the absence of a non-essential gene.