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Saccharomyces cerevisiae CEN.PK113-7D

ABSTRACT: Anaerobically evolved fungi that harbor Class II dihydroorotate dehydrogenase enzymes that function independently of the respiratory chain

PROVIDER: PRJNA745202 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15616355_1.fastq.gz	Fastqsanger.gz
	SRR15616355_2.fastq.gz	Fastqsanger.gz
	SRR15616356_1.fastq.gz	Fastqsanger.gz
	SRR15616356_2.fastq.gz	Fastqsanger.gz
	SRR15616357_1.fastq.gz	Fastqsanger.gz

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Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D.

Project description:The haploid Saccharomyces cerevisiae strain CEN.PK113-7D is a popular model system for metabolic engineering and systems biology research. Current genome assemblies are based on short-read sequencing data scaffolded based on homology to strain S288C. However, these assemblies contain large sequence gaps, particularly in subtelomeric regions, and the assumption of perfect homology to S288C for scaffolding introduces bias. In this study, we obtained a near-complete genome assembly of CEN.PK113-7D using only Oxford Nanopore Technology's MinION sequencing platform. Fifteen of the 16 chromosomes, the mitochondrial genome and the 2-μm plasmid are assembled in single contigs and all but one chromosome starts or ends in a telomere repeat. This improved genome assembly contains 770 Kbp of added sequence containing 248 gene annotations in comparison to the previous assembly of CEN.PK113-7D. Many of these genes encode functions determining fitness in specific growth conditions and are therefore highly relevant for various industrial applications. Furthermore, we discovered a translocation between chromosomes III and VIII that caused misidentification of a MAL locus in the previous CEN.PK113-7D assembly. This study demonstrates the power of long-read sequencing by providing a high-quality reference assembly and annotation of CEN.PK113-7D and places a caveat on assumed genome stability of microorganisms.

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Transcription profiling of yeast protrotophic laboratory strain CEN.PK113-7D grown under glutamine or ammonia limited conditions

Project description:The protrotophic laboratory strain CEN.PK113-7D (MAT a) was grown in laboratory fermentors with a working volume of 1 litre at dilution rate (D) of 0.20 per hour (in duplicate for each nitrogen (glutamine and ammonium) limited condition). After cultivation for few hundred generations in ammonium, samples from 2 continuous cultures were taken for array analysis. After cultivation for few hundred generations in glutamine, one evolved strain was picked and cultivated in 2 biological replicate chemostats until steady state was reached, and samples for array analysis were collected. All collected cell samples were cooled below 2 degree C within ten seconds by mixing 40% sample and 60% crushed ice.

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Project description:Expression data of Saccharomyces cerevisiae CEN.PK.113-7D grew in Batch and Chemostat condition using for comparison of RNA-seq and Microarray data

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