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Saccharomyces cerevisiae W303

ABSTRACT: Elucidation of ubiquitin-related functions by ubiquitin overexpression approach

PROVIDER: PRJDB17962 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR550211_1.fastq.gz	Fastqsanger.gz
	DRR550211_2.fastq.gz	Fastqsanger.gz
	DRR550212_1.fastq.gz	Fastqsanger.gz
	DRR550212_2.fastq.gz	Fastqsanger.gz

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Saccharomyces cerevisiae cells: W303-1A vs W303-1A delta MSN2, MSN4

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Whole-Genome Sequence and Variant Analysis of W303, a Widely-Used Strain of <i>Saccharomyces cerevisiae</i>.

Project description:The yeast Saccharomyces cerevisiae has emerged as a superior model organism. Selection of distinct laboratory strains of S. cerevisiae with unique phenotypic properties, such as superior mating or sporulation efficiencies, has facilitated advancements in research. W303 is one such laboratory strain that is closely related to the first completely sequenced yeast strain, S288C. In this work, we provide a high-quality, annotated genome sequence for W303 for utilization in comparative analyses and genome-wide studies. Approximately 9500 variations exist between S288C and W303, affecting the protein sequences of ∼700 genes. A listing of the polymorphisms and divergent genes is provided for researchers interested in identifying the genetic basis for phenotypic differences between W303 and S288C. Several divergent functional gene families were identified, including flocculation and sporulation genes, likely representing selection for desirable laboratory phenotypes. Interestingly, remnants of ancestor wine strains were found on several chromosomes. Finally, as a test of the utility of the high-quality reference genome, variant mapping revealed more accurate identification of accumulated mutations in passaged mismatch repair-defective strains.

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Genome-wide DNase-seq profiling of Saccharomyces cerevisiae (W303 strain)

Project description:Intact nuclei from an asynchronous population of W303 Saccharomyces cerevisiae in log-phase growth were subjected to a 16-minute DNase I digestion (0.1 U/μL) at 37 °C. DNA was then recovered, and single-end Illumina sequencing libraries were prepared using the Crawford DNase-seq method (Song and Crawford, 2010).

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The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt.

Project description:Saccharomyces cerevisiae strain W303 is a widely used model organism. However, little is known about its genetic origins, as it was created in the 1970s from crossing yeast strains of uncertain genealogy. To obtain insights into its ancestry and physiology, we sequenced the genome of its variant W303-K6001, a yeast model of ageing research. The combination of two next-generation sequencing (NGS) technologies (Illumina and Roche/454 sequencing) yielded an 11.8 Mb genome assembly at an N50 contig length of 262 kb. Although sequencing was substantially more precise and sensitive than whole-genome tiling arrays, both NGS platforms produced a number of false positives. At a 378× average coverage, only 74 per cent of called differences to the S288c reference genome were confirmed by both techniques. The consensus W303-K6001 genome differs in 8133 positions from S288c, predicting altered amino acid sequence in 799 proteins, including factors of ageing and stress resistance. The W303-K6001 (85.4%) genome is virtually identical (less than equal to 0.5 variations per kb) to S288c, and thus originates in the same ancestor. Non-S288c regions distribute unequally over the genome, with chromosome XVI the most (99.6%) and chromosome XI the least (54.5%) S288c-like. Several of these clusters are shared with ?1278B, another widely used S288c-related model, indicating that these strains share a second ancestor. Thus, the W303-K6001 genome pictures details of complex genetic relationships between the model strains that date back to the early days of experimental yeast genetics. Moreover, this study underlines the necessity of combining multiple NGS and genome-assembling techniques for achieving accurate variant calling in genomic studies.

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