The Reference Genome Sequence of Saccharomyces Cerevisiae: then and Now

Overview

Journal G3 (Bethesda)

Publisher Oxford University Press

Specialties Genetics
Molecular Biology

Date 2013 Dec 31

PMID 24374639

Citations 228

Authors

Stacia R Engel

Fred S Dietrich

Dianna G Fisk

Gail Binkley

Rama Balakrishnan

Maria C Costanzo

Selina S Dwight

Benjamin C Hitz

Kalpana Karra

Robert S Nash

Shuai Weng

Edith D Wong

Paul Lloyd

Marek S Skrzypek

Stuart R Miyasato

Matt Simison

J Michael Cherry

Affiliations

Soon will be listed here.

Abstract

The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called "S288C 2010," was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science.

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References

Carlson M, Botstein D . Organization of the SUC gene family in Saccharomyces. Mol Cell Biol. 1983; 3(3):351-9. PMC: 368543. DOI: 10.1128/mcb.3.3.351-359.1983. View

Foury F, Roganti T, Lecrenier N, Purnelle B . The complete sequence of the mitochondrial genome of Saccharomyces cerevisiae. FEBS Lett. 1999; 440(3):325-31. DOI: 10.1016/s0014-5793(98)01467-7. View

POMPER S, BURKHOLDER P . Studies on the Biochemical Genetics of Yeast. Proc Natl Acad Sci U S A. 1949; 35(8):456-64. PMC: 1063057. DOI: 10.1073/pnas.35.8.456. View

Kim J, Vanguri S, Boeke J, Gabriel A, Voytas D . Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 1998; 8(5):464-78. DOI: 10.1101/gr.8.5.464. View

Murakami Y, Naitou M, Hagiwara H, Shibata T, Ozawa M, Sasanuma S . Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae. Nat Genet. 1995; 10(3):261-8. DOI: 10.1038/ng0795-261. View

Riles L, Dutchik J, Baktha A, McCauley B, Thayer E, Leckie M . Physical maps of the six smallest chromosomes of Saccharomyces cerevisiae at a resolution of 2.6 kilobase pairs. Genetics. 1993; 134(1):81-150. PMC: 1205446. DOI: 10.1093/genetics/134.1.81. View

Yang C, Theis J, Newlon C . Conservation of ARS elements and chromosomal DNA replication origins on chromosomes III of Saccharomyces cerevisiae and S. carlsbergensis. Genetics. 1999; 152(3):933-41. PMC: 1460674. DOI: 10.1093/genetics/152.3.933. View

MORTIMER R, JOHNSTON J . Genealogy of principal strains of the yeast genetic stock center. Genetics. 1986; 113(1):35-43. PMC: 1202798. DOI: 10.1093/genetics/113.1.35. View

Omura F, Hatanaka H, Nakao Y . Characterization of a novel tyrosine permease of lager brewing yeast shared by Saccharomyces cerevisiae strain RM11-1a. FEMS Yeast Res. 2007; 7(8):1350-61. DOI: 10.1111/j.1567-1364.2007.00310.x. View

10.

Feldmann H, Aigle M, ALJINOVIC G, Andre B, Baclet M, Barthe C . Complete DNA sequence of yeast chromosome II. EMBO J. 1994; 13(24):5795-809. PMC: 395553. DOI: 10.1002/j.1460-2075.1994.tb06923.x. View

11.

SZYBALSKI W . My road to Øjvind Winge, the father of yeast genetics. Genetics. 2001; 158(1):1-6. PMC: 1461622. DOI: 10.1093/genetics/158.1.1. View

12.

Jacq C, Alt-Morbe J, Andre B, Arnold W, Bahr A, Ballesta J . The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. Nature. 1997; 387(6632 Suppl):75-8. View

13.

Hawthorne D, MORTIMER R . Chromosome Mapping in Saccharomyces: Centromere-Linked Genes. Genetics. 1960; 45(8):1085-110. PMC: 1210110. DOI: 10.1093/genetics/45.8.1085. View

14.

LINK A, Olson M . Physical map of the Saccharomyces cerevisiae genome at 110-kilobase resolution. Genetics. 1991; 127(4):681-98. PMC: 1204396. DOI: 10.1093/genetics/127.4.681. View

15.

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

16.

Deshpande A, Newlon C . The ARS consensus sequence is required for chromosomal origin function in Saccharomyces cerevisiae. Mol Cell Biol. 1992; 12(10):4305-13. PMC: 360354. DOI: 10.1128/mcb.12.10.4305-4313.1992. View

17.

Johnston M, Hillier L, Riles L, Albermann K, Andre B, Ansorge W . The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature. 1997; 387(6632 Suppl):87-90. PMC: 6615710. View

18.

Engel S, Cherry J . The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database. Database (Oxford). 2013; 2013:bat012. PMC: 3595989. DOI: 10.1093/database/bat012. View

19.

Winston F, DOLLARD C . Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast. 1995; 11(1):53-5. DOI: 10.1002/yea.320110107. View

20.

Sliwa P, Korona R . Loss of dispensable genes is not adaptive in yeast. Proc Natl Acad Sci U S A. 2005; 102(49):17670-4. PMC: 1295593. DOI: 10.1073/pnas.0505517102. View