Nature and distribution of large sequence polymorphisms in Saccharomyces cerevisiae

FEMS Yeast Research

Volumn 11, Issue 7, 2011, Pages 587-594

  Muller, Ludo A H ^a,b   Mccusker, John H ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Deletion; Introgression; Large sequence polymorphism; Saccharomyces cerevisiae; Tiling array

Indexed keywords

GENOMIC DNA;

ARTICLE; BACTERIAL STRAIN; DIPLOIDY; DNA SEQUENCE; FUNGAL STRAIN; GENE DELETION; GENE SEQUENCE; GENETIC POLYMORPHISM; GENOME; HAPLOID SPORE; HAPLOIDY; HOMOZYGOSITY; HYBRIDIZATION; NONHUMAN; POLYMERASE CHAIN REACTION; SACCHAROMYCES CEREVISIAE;

ADAPTATION, BIOLOGICAL; BASE SEQUENCE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA, FUNGAL; EVOLUTION, MOLECULAR; MICROARRAY ANALYSIS; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

SACCHAROMYCES CEREVISIAE; SACCHAROMYCES PARADOXUS;

EID: 80053941520     PISSN: 15671356     EISSN: 15671364     Source Type: Journal    
DOI: 10.1111/j.1567-1364.2011.00748.x     Document Type: Article

References (32)

1. Barnett JA, Payne RW & Yarrow D (2000) Yeasts: Characteristics and Identification, 3rd edn. Cambridge University Press, Cambridge.
2. Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, Weigel D, Berry CC, Winzeler E & Chory J (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13: 513-523.
3. Britten RJ, Rowen L, Williams J & Cameron RA (2003) Majority of divergence between closely related DNA samples is due to indels. P Natl Acad Sci U S A 100: 4661-4665.
4. Cherry JM, Adler C, Ball C, et al. (1998) SGD: Saccharomyces Genome Database. Nucleic Acids Res 26: 73-80.
5. Dujon B (2005) Hemiascomycetous yeasts at the forefront of comparative genomics. Curr Opin Genet Dev 15: 614-620.
6. Feuk L, Carson AR & Scherer SW (2006) Structural variation in the human genome. Nat Rev Genet 7: 85-97.
7. Gimble FS & Thorner J (1992) Homing of a DNA endonuclease gene by meiotic gene conversion in Saccharomyces cerevisiae. Nature 357: 301-306.
8. Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham M, Botstein D & Kruglyak L (2006) Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311: 1932-1936.
9. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41: 95-98.
10. Hiraishi H, Miyake T & Ono B (2008) Transcriptional regulation of Saccharomyces cerevisiae CYS3 encoding cystathionine gamma-lyase. Curr Genet 53: 225-234.
11. Kellis M, Patterson N, Endrizzi M, Birren B & Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
12. Leh-Louis V, Wirth B, Potier S, Souciet JL & Despons L (2004) Expansion and contraction of the DUP240 multigene family in Saccharomyces cerevisiae populations. Genetics 167: 1611-1619.
13. Liti G, Barton DBH & Louis EJ (2006) Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174: 839-850.
14. Louis EJ (1995) The chromosome ends of Saccharomyces cerevisiae. Yeast 11: 1553-1573.
15. Louis EJ, Naumova ES, Lee A, Naumov G & Haber JE (1994) The chromosome end in yeast: its mosaic nature and influence on recombinational dynamics. Genetics 136: 789-802.
16. Mangahas JL, Alexander MK, Sandell LL & Zakian VA (2001) Repair of chromosome ends after telomere loss in Saccharomyces. Mol Biol Cell 12: 4078-4089.
17. Miyake T, Hiraishi H, Sammoto H & Ono B (2003) Involvement of the VDE homing endonuclease and rapamycin in regulation of the Saccharomyces cerevisiae GSH11 gene encoding the high affinity glutathione transporter. J Biol Chem 278: 39632-39636.
18. Muller LAH & McCusker JH (2009) A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae. FEMS Yeast Res 9: 143-152.
19. Poirey R, Despons L, Leh V, Lafuente MJ, Potier S, Souciet JL & Jauniaux JC (2002) Functional analysis of the Saccharomyces cerevisiae DUP240 multigene family reveals membrane-associated proteins that are not essential for cell viability. Microbiology 148: 2111-2123.
20. Rachidi N, Barre P & Blondin B (1999) Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol Gen Genet 261: 841-850.
21. Roeder GS, Smith M & Lambie EJ (1984) Intrachromosomal movement of genetically marked Saccharomyces cerevisiae transposons by gene conversion. Mol Cell Biol 4: 703-711.
22. Rozen S & Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz S & Misener S, eds), pp. 365-386. Humana Press, Totowa, NJ.
23. Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D & Kruglyak L (2007) Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS ONE 2: e322.
24. Schacherer J, Shapiro JA, Ruderfer DM & Kruglyak L (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458: 342-345.
25. Sherman F (1991) Getting started with yeast. Methods in Enzymology (Guthrie C & Fink GR, eds), pp. 3-21. Academic Press, New York, NY.
26. Sniegowski PD, Dombrowski PG & Fingerman E (2002) Saccharomyces cerevisiae and Saccharomyces paradoxus coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics. FEMS Yeast Res 1: 299-306.
27. Thompson JD, Higgins DG & Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
28. Wei W, McCusker JH, Hyman RW et al. (2007) Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. P Natl Acad Sci U S A 104: 12825-12830.
29. Winzeler EA, Shoemaker DD, Astromoff A et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.
30. Winzeler EA, Castillo-Davis CI, Oshiro G, Liang D, Richards DR, Zhou Y & Hartl DL (2003) Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics 163: 79-89.
31. Zhang H, Skelton A, Gardner RC & Goddard MR (2010) Saccharomyces paradoxus and Saccharomyces cerevisiae reside on oak trees in New Zealand: evidence for migration from Europe and interspecies hybrids. FEMS Yeast Research 10: 941-947.
32. Zhou J-Q, Monson EM, Teng S-C, Schulz VP & Zakian VA (2000) The Pif1p helicase, a catalytic inhibitor of telomerase lengthening of yeast telomeres. Science 289: 771-774.