Research
De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
- † Equal contributors
1 The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands
2 Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
3 Wageningen University Centre for Biosystems Genomics, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
4 Plant Research International, Business Unit of Bioscience, cluster Applied Bioinformatics, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
5 Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
6 DSM Biotechnology Center, PO Box 1, 2600MA Delft, The Netherlands
7 Amyris, Inc, 5885 Hollis Street, Suite 100, Emeryville CA 94608, USA
8 Institute for Molecular Biosciences, Max-von-Laue-Str. 9, Goethe University Frankfurt, D-60438 Frankfurt, Germany
9 Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
10 Netherlands Bioinformatics Center, 260 NBIC, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
11 Platform for Green Synthetic Biology, Julianalaan 67, 2628 BC Delft, The Netherlands
12 KeyGene N.V, Agro Business Park 90, 6708 PW Wageningen, The Netherlands
13 Center for Systems Biology, Soochow University, Suzhou 215006, China
Microbial Cell Factories 2012, 11:36 doi:10.1186/1475-2859-11-36
Published: 26 March 2012Additional files
Additional file 2:
Table S1. Repetitive transposon sequences were hard to assemble from whole genome shotgun data. Evidence of transposons was obtained in two ways. First, depth-of-coverage of CEN.PK113-7D and S288C reads on Ty retrotransposons sequences in the S288C genome was analysed. The number of retrotransposons was estimated from these ratios. Second, evidence for transposons in the assembly was obtained by counting the presence of contig breaks (CB) on transposon loci in S288C and the presence of assembled (AS) transposons (Figure S1). An assembled transposon locus with a gapped alignment (GA) around the transposon sequence in S288C indicates the transposon is absent from the CEN.PK genome.
Format: DOC Size: 30KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 3:
Figure S1. Analysis of transposon composition by alignment of the CEN.PK113-7D and S288c genomes. When an S288c transposon is not present in CEN.PK113-7D it results in a gapped alignment (GA) of about 6 Kbp. Transposons that are present can cause contig breaks (CB) in the assembly. Only YCLWTy5-1 was fully assembled (AS).
Format: PDF Size: 12KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 4:
Figure S2. Chromosome separation gel with RDL1 and PHO12 probed.
Format: PDF Size: 116KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 5:
Table S8. Primer used in this study.
Format: DOC Size: 33KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 6:
Table S2. SNVs in genes in CEN.PK113-7D compared to S288C.
Format: XLSX Size: 1.4MB Download file
Additional file 7:
Table S4. Mutations in the galactose uptake and ergosterol biosynthesis pathways compared to the SNVs found previously in CEN.PK113-7D [35].
Format: XLSX Size: 14KB Download file
Additional file 8:
Table S5. Mutations found in genes in the cAMP signaling pathway.
Format: DOC Size: 31KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 9:
Figure S4. Differences between CEN.PK113-7D and S288C in the MAPK signaling pathway.
Format: PDF Size: 20KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 10:
Table S3. Indels in genes in CEN.PK113-7D compared to S288C.
Format: XLSX Size: 63KB Download file
Additional file 11:
Figure S5. Multiple sequence alignment of Snf11p and Swi1p.
Format: PDF Size: 37KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional file 12:
Table S7. S. cerevisiae with an assembled genome deposited in GenBank. The classification assigned in the 'group' column was used to generate Figure 8.
Format: DOC Size: 47KB Download file
This file can be viewed with: Microsoft Word Viewer
Additional file 13:
Table S6. List of deleted genes, which is defined as not having a homologous hit in the CEN.PK113-7D genome for at least 95% and having a CEN.PK113-7D/S288c log2 ratio of less then -0.6. The PMR2 locus has a blue background color.
Format: XLSX Size: 16KB Download file
Additional file 14:
Figure S3. Chromosome separation gel with contig151 probed.
Format: PDF Size: 63KB Download file
This file can be viewed with: Adobe Acrobat Reader
