The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology
Open accessAbstract
Saccharomyces cerevisiae CEN.PK 113-7D is widely used for metabolic engineering and systems biology research in industry and academia. We sequenced, assembled, annotated and analyzed its genome. Single-nucleotide variations (SNV), insertions/deletions (indels) and differences in genome organization compared to the reference strain S. cerevisiae S288C were analyzed. In addition to a few large deletions and duplications, nearly 3000 indels were identified in the CEN.PK113-7D genome relative to S288C. These differences were overrepresented in genes whose functions are related to transcriptional regulation and chromatin remodelling. Some of these variations were caused by unstable tandem repeats, suggesting an innate evolvability of the corresponding genes. Besides a previously characterized mutation in adenylate cyclase, the CEN.PK113-7D genome sequence revealed a significant enrichment of non-synonymous mutations in genes encoding for components of the cAMP signalling pathway. Some phenotypic characteristics of the CEN.PK113-7D strains were explained by the presence of additional specific metabolic genes relative to S288C. In particular, the presence of the BIO1 and BIO6 genes correlated with a biotin prototrophy of CEN.PK113-7D. Furthermore, the copy number, chromosomal location and sequences of the MAL loci were resolved. The assembled sequence reveals that CEN.PK113-7D has a mosaic genome that combines characteristics of laboratory strains and wild-industrial strains.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Intragenic tandem repeats generate functional variability
Verstrepen, K. J., Jansen, A., Lewitter, F., & Fink, G. R. (2005) · Nature Genetics · doi:10.1038/ng1618 · Cited by 616
van Dijken, J. P., Bauer, J., Brambilla, L., Duboc, P., Francois, J. M., Gancedo, C., Giuseppin, M. L. F., Heijnen, J. J., Hoare, M., Lange, H. C., et al. (2000) · Enzyme and Microbial Technology · doi:10.1016/s0141-0229(00)00162-9 · Cited by 598
Self-citationCNV-seq, a new method to detect copy number variation using high-throughput sequencing
Xie, C., & Tammi, M. T. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-80 · Cited by 582
Wisselink, H. W., Toirkens, M. J., Wu, Q., Pronk, J. T., & van Maris, A. J. A. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.02268-08 · Cited by 247
Self-citationvan Maris, A. J. A., Geertman, J.-M. A., Vermeulen, A., Groothuizen, M. K., Winkler, A. A., Piper, M. D. W., van Dijken, J. P., & Pronk, J. T. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.1.159-166.2004 · Cited by 227
Self-citationWisselink, H. W., Toirkens, M. J., del Rosario Franco Berriel, M., Winkler, A. A., van Dijken, J. P., Pronk, J. T., & van Maris, A. J. A. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00177-07 · Cited by 209
Self-citationHunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency
Wenger, J. W., Piotrowski, J., Nagarajan, S., Chiotti, K., Sherlock, G., & Rosenzweig, F. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002202 · Cited by 154
Oud, B., Maris, A. J. A., Daran, J.-M., & Pronk, J. T. (2012) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2011.00776.x · Cited by 82 · cited 1×
“Finally, laboratory evolution is rapidly gaining popularity as a tool to analyse genome function and to select for yeast strains with industrially relevant properties [7-11].”
BackgroundSelf-citation
Cited by
Mans, R., van Rossum, H. M., Wijsman, M., Backx, A., Kuijpers, N. G. A., van den Broek, M., Daran-Lapujade, P., Pronk, J. T., van Maris, A. J. A., & Daran, J.-M. G. (2015) · FEMS Yeast Research · doi:10.1093/femsyr/fov004 · Cited by 485
Self-citationNookaew, I., Papini, M., Pornputtapong, N., Scalcinati, G., Fagerberg, L., Uhlén, M., & Nielsen, J. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks804 · Cited by 309
Self-citationSieuwerts, S., Bron, P. A., & Smid, E. J. (2018) · LWT · doi:10.1016/j.lwt.2017.12.022 · Cited by 173
“PK113-7D (Nijkamp et al., 2012) was grown in YPD broth ((10 g l−1 yeast extract (Difco, Franklin lakes, NJ), 10 g l−1 peptone (Difco), 20 g l−1 glucose (Scharlau)) at 30 °C. Cultures were maintained as frozen stocks at −80 °C cell cultures containing 22% glycerol (Scharlau, Sentmenat, Spain).”
MethodElsemman, I. E., Rodriguez Prado, A., Grigaitis, P., Garcia Albornoz, M., Harman, V., Holman, S. W., van Heerden, J., Bruggeman, F. J., Bisschops, M. M. M., Sonnenschein, N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28467-6 · Cited by 120
Self-citationBruder, S., Reifenrath, M., Thomik, T., Boles, E., & Herzog, K. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0526-3 · Cited by 78
Metadata
- Authors
- Nijkamp, J. F., van den Broek, M., Datema, E., de Kok, S., Bosman, L., Luttik, M. A., Daran-Lapujade, P., Vongsangnak, W., Nielsen, J., Heijne, W. H., Klaassen, P., Paddon, C. J., Platt, D., Kötter, P., van Ham, R. C., Reinders, M. J., Pronk, J. T., de Ridder, D., & Daran, J.-M.
- Venue
- Microbial Cell Factories
- Published
- 2012-03-26
- Volume
- 11
- Issue
- 1
- Pages
- 36-36
- ISSN
- 1475-2859 (ISSN-L)
- OpenAlex
- W2096336948
- Cited by
- 285
- References
- 11
- FWCI
- 8.83
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. https://app.cochat.ai/papers/10.1186/1475-2859-11-36
- The paper
- Nijkamp, J. F., van den Broek, M., Datema, E., de Kok, S., Bosman, L., Luttik, M. A., Daran-Lapujade, P., Vongsangnak, W., Nielsen, J., Heijne, W. H., Klaassen, P., Paddon, C. J., Platt, D., Kötter, P., van Ham, R. C., Reinders, M. J., Pronk, J. T., de Ridder, D., & Daran, J.-M. (2012). De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microbial Cell Factories. https://doi.org/10.1186/1475-2859-11-36
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
