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Whole genome sequencing of Saccharomyces cerevisiae: from genotype to phenotype for improved metabolic engineering applications

José Manuel Otero125, Wanwipa Vongsangnak128, Mohammad A Asadollahi126, Roberto Olivares-Hernandes12, Jérôme Maury27, Laurent Farinelli3, Loïc Barlocher3, Magne Østerås3, Michel Schalk4, Anthony Clark4 and Jens Nielsen12*

Author Affiliations

1 Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden

2 Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark DK-2800, Kgs. Lyngby, Denmark

3 Fasteris SA, Geneva, Switzerland

4 Firmenich SA, Corporate Research & Development Division, Geneva, Switzerland

5 Vaccine & Biologics Process Development, Vaccine Research & Development, Merck Research Labs, West Point, PA, USA

6 Biotechnology Group, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan 81746-73441, Iran

7 Fluxome Sciencies A/S, Research & Development, DK-3660 Stenlose, Denmark

8 Center for Systems Biology, Soochow University, Suzhou 215006, China

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BMC Genomics 2010, 11:723  doi:10.1186/1471-2164-11-723

Published: 22 December 2010

Additional files

Additional file 1:

Additional Files. Figure S1. Title: Gene Ontology terms for SNP characterization. Description: Gene Ontology (GO) function and component terms for the nonsynonymous SNPs identified in CEN.PK113-7D compared to S288c. Figure S2. Title: SNP enrichment in S. cerevisiae metabolism. Description: The metabolic map, produced using the Saccharomyces Genome Database (SGD) Expression Viewer (SRI International Pathway Tools version 12.0, based upon S. cerevisiae S288c, version 12.0) was created using the SNP data produced for CEN.PK113-7D compared to S288c. Figure S3. Title: Methodology for SNP characterization at amino acid level. Description: The flow-diagram describes the bioinformatics approach taken to estimate the likelihood of occurrence of a nonsynonymous SNP in CEN.PK113-7D or S288c. Figure S4. Title: Conservation distance. Description: The Conservation Distance, previously described in Additional file 1, Figure S3, is plotted for all 210 nonsynonymous SNPs. Figure S5. Title: SNP analysis of ERG8 at nucleotide positions 49 and 247. Description: The gene ERG8 of the ergosterol synthesis pathway contains a total of 4 nonsynonymous SNPs, two of which, located at nucleotide positions 49 and 247, are analyzed. Figure S6. Title: Amino acid characterization of SNPs detected between S288c and CEN.PK113-7D. Description: Amino Acid Characterization-CEN.PK113-7D vs S288c Profiles. Figure S7. Title: Gene Ontology terms for S288c v. CEN.PK113-7D (Glucose). Description: Gene Ontology (GO) process, function, and component terms for differentially expressed genes of S288c vs. CEN.PK113-7D cultivated on glucose. Figure S8. Title: Gene Ontology terms for S288c vs. CEN.PK113-7D (Galactose). Description: Gene ontology (GO) process, function, and component terms for differentially expressed genes of S288c vs. CEN.PK113-7D cultivated on galactose. Figure S9. Title: Metabolic pathway expression mapping for S288c Glucose vs. CEN.PK113-7D Glucose. Description: The metabolic map produced using the Saccharomyces Genome Database (SGD) Expression Viewer (SRI International Pathway Tools version 12.0, based upon S. cerevisiae S288c, version 12.0) was created using statistically significant log2-fold expression values for S288c glucose vs. CEN.PK113-7D glucose. Figure S10. Title: Metabolic pathway expression mapping for S288c Galactose vs. CEN.PK113-7D Galactose. Description: The metabolic map produced using the Saccharomyces Genome Database (SGD) Expression Viewer (SRI International Pathway Tools version 12.0, based upon S. cerevisiae S288c, version 12.0) was created using statistically significant log2-fold expression values for S288c galactose vs. CEN.PK113-7D galactose. Table S1. Title: Transcriptome-S288c v CEN.PK113-7D Glucose. Description: List of significant genes (padj< 0.01). Table S2. Title: Transcriptome-S288c v CEN.PK113-7D Galactose. Description: List of significant genes (padj < 0.01). Table S3. Title: Description of S. cerevisiae strains. Table S4. Title: EDENA determination for de novo assembly of S288c and CEN.PK113-7D sequences

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