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Saccharomyces cerevisiae assembly and gene annotation

Assembly

Saccharomyces cerevisiae is a unicellular fungus. It is commonly known as baker's, brewer's or budding yeast. It is used in the production of a number of human foodstuffs, including alcoholic beverages and in the baking industry, and is widely used as a model species in the study of eukaryotic biology. In 1996, the genome of S. cerevisiae was the first eukaryotic genome to be completely deciphered.

The data on this site is a direct import of the Saccharomyces Genome Database (SGD) dataset for the Saccharomyces cerevisiae S288C genome. The assembly provided is R64-1-1, supplemented with additional cross-references and annotations. The protein-coding and non-coding gene model annotation was imported from SGD in April 2018. This gene set is based on Liachko et al. 2013 , and contains 7036 protein-coding genes. Additionally, 91 transposable element genes (TE genes) that were previously annotated as protein-coding genes have now been correctly captured as TE genes. We have also included the variation data from the Saccharomyces Genome Resequencing Project (SGRP) and functional genomics data from Yeast Genome 2.0 Array and Yeast Genome S98 Array.

References

  • A large-scale full-length cDNA analysis to explore the budding yeast transcriptome.

    Miura F., Kawaguchi N., Sese J., Toyoda A., Hattori M., Morishita S., Ito T.

    Proc. Natl. Acad. Sci. U.S.A. 103(47): 17846-51 (2006)

    PubMed:17101987

  • Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.

    Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A

    Proc. Natl. Acad. Sci. U.S.A. (2009)

    PubMed:19208812

  • Genetic and physical maps of Saccharomyces cerevisiae.

    Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D

    Nature 1997 387(6632 Suppl):67-73.

    PubMed:9169866

  • Life with 6000 genes.

    Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG

    Proc. Natl. Acad. Sci. U.S.A. (1996)

    Science:8849441

  • Population genomics of domestic and wild yeasts.

    Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ.

    Nature. 2009 Mar 19;458(7236):337-41. Epub 2009 Feb 11.

    PubMed:19212322

  • High-resolution mapping of complex traits with a four-parent advanced intercross yeast population.

    Cubillos FA, Parts L, Salinas F, Bergström A, Scovacricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J, Louis EJ, Durbin R, Liti G

    Genetics. November 1, 2013 vol. 195 no. 3 1141-1155.

    PubMed:24037264

  • The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now

    Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM

    G3 (Bethesda) 20 Mar 2014, 4(3):389-398.

    PubMed:24374639

  • High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast.

    Liachko I, Youngblood RA, Keich U, Dunham MJ

    Genome Research 12 Dec 2012, 23(4):698-704.

    PubMed:23241746

Gene annotation

This species and other fungi are also available from our sister site, Ensembl Fungi

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyR64-1-1 (Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database), INSDC Assembly GCA_000146045.2, Sep 2011
Base Pairs12,157,105
Golden Path Length12,157,105
Annotation providerSGD
Annotation methodImport
Genebuild startedJan 2017
Genebuild releasedOct 2018
Genebuild last updated/patchedOct 2018
Database version100.4

Gene counts

Coding genes6,600
Non coding genes424
Small non coding genes424
Pseudogenes12
Gene transcripts7,127

Other

Short Variants263,537

About this species

HASH(0x290349a8)