Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays

Genetics

Volumn 163, Issue 1, 2003, Pages 79-89

  Winzeler, Elizabeth A ^a,d   Castillo Davis, Cristian I ^b   Oshiro, Guy ^a   Liang, David ^a   Richards, Daniel R ^c   Zhou, Yingyao ^a   Hartl, Daniel L ^b  

^a GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

^b HARVARD UNIVERSITY   (United States)

^c STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; DNA MICROARRAY; DNA POLYMORPHISM; FERMENTATION; FUNGAL GENETICS; FUNGAL STRAIN; GENE DELETION; GENE FUNCTION; GENE SEQUENCE; GENETIC IDENTIFICATION; GENETIC VARIABILITY; GENOME ANALYSIS; MICROBIAL POPULATION DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; YEAST;

CHROMOSOME MAPPING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; POLYMORPHISM, GENETIC; SACCHAROMYCES CEREVISIAE; TELOMERE; VARIATION (GENETICS);

FUNGI; MYXOGASTRIA;

EID: 0037277240     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (43)

1. BECHET, J., M. GREENSON and J. M. WIAME, 1970 Mutations affecting the repressibility of arginine biosynthetic enzymes in Saccharomyces cerevisiae. Eur. J. Biochem. 12: 31-39.
2. BEGUN, D. J., and C. F. AQUADRO, 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
3. BOREVITZ, J. O., D. LIANG, D. PLOUFFE, H. CHANG, T. ZHU et al., 2003 Large scale identification of single feature polymorphisms in complex genomes. Genome Res. (in press).
4. BROUN, P., M. W. GANAL and S. D. TANKSLEY, 1992 Telomeric arrays display high levels of heritable polymorphism among closely related plant varieties. Proc. Natl. Acad. Sci. USA 89: 1354-1357.
5. C. ELEGANS SEQUENCING CONSORTIUM, 1998 Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
6. CAVALIERI, D., J. P. TOWNSEND and D. L. HARTL, 2000 Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc. Natl. Acad. Sci. USA 97: 12369-12374.
7. CHEE, M., R. YANG, E. HUBBELL, A. BERNO, X. C. HUANG et al., 1996 Accessing genetic information with high-density DNA arrays. Science 274: 610-614.
8. CHU, S., J. DERISI, M. EISEN, J. MULHOLLAND, D. BOTSTEIN et al., 1998 The transcriptional program of sporulation in budding yeast. Science 282: 699-705.
9. CONWAY, D. J., C. ROPER, A. M. ODUOLA, D. E. ARNOT, P. G. KREMSNER et al., 1999 High recombination rate in natural populations of Plasmodium falciparum. Proc. Natl. Acad. Sci. USA 96: 4506-4511.
10. ESPOSITO, R. E., 1993 Humble beginnings, pp. 417-433 in The Early Days of Yeast Genetics, edited by P. L. M. HALL. Cold Spring Harbor Laboratory Press, Plainview, NY.
11. FELSENSTEIN, S. P., 1993 Phylogeny Inference Package. Department of Genetics, University of Washington, Seattle.
12. FREITAS-JUNIOR, L. H., E. BOTTIUS, L. A. PIRRIT, K. W. DEITSCH, C. SCHEIDIG et al., 2000 Frequent ectopic recombination of virulence factor genes in telomeric chromosome clusters of P. falciparum. Nature 407: 1018-1022.
13. GIAEVER, G., A. M. CHU, L. NI, C. CONNELLY, L. RILES et al., 2002 Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391.
14. GINGERAS, T. R., G. CHANDOUR, E. WANG, A. BERNO, P. M. SMALL et al., 1998 Simultaneous genotyping and species identification using hybridization pattern recognition analysis of generic Mycobacterium DNA arrays. Genome Res. 8: 435-448.
15. GLANTZ, S. A., 1997 Primer of Biostatistics. McGraw-Hill, New York.
16. GRENSON, M., M. MOUSSET, J. M. WIAME and J. BECHET, 1966 Multiplicity of the amino acid permeases in Saccharomyces cerevisiae. I. Evidence for a specific arginine-transporting system. Biochim. Biophys. Acta 127: 325-338.
17. GRUNENFELDER, B., and E. WINZELER, 2002 Treasures and limitations contained in genome-wide data sets. Nat. Rev. Genet. 3 (9): 653-661.
18. HARTWELL, L. H., 1967 Macromolecule synthesis in temperature-sensitive mutants of yeast. J. Bacteriol. 93: 1662-1670.
19. KANE, S. M., and R. ROTH, 1974 Carbohydrate metabolism during ascospore development in yeast. J. Bacteriol. 118: 8-14.
20. LI, C., and W. H. WONG, 2001 Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc. Natl. Acad. Sci. USA 98: 31-36.
21. LIU, H., C. A. STYLES and G. R. FINK, 1993 Elements of the yeast pheromone response pathway required for filamentous growth of diploids. Science 262: 1741-1744.
22. LOCKHART, D. J., and E. A. WINZELER, 2000 Genomics, gene expression and DNA arrays. Nature 405: 827-836.
23. LOUIS, E. J., E. S. NAUMOVA, A. LEE, G. NAUMOV and J. E. HABER, 1994 The chromosome end in yeast: its mosaic nature and influence on recombinational dynamics. Genetics 136: 789-802.
24. MCCUSKER, J. H., and J. E. HABER, 1988 Cycloheximide-resistant temperature-sensitive lethal mutations of Saccharomyces cerevisiae. Genetics 119: 303-315.
25. MCCUSKER, J. H., K. V. CLEMONS, D. A. STEVENS and R. W. DAVIS, 1994 Saccharomyces cerevisiae virulence phenotype as determined with CD-1 mice is associated with the ability to grow at 42 degrees C and form pseudohyphae. Infect. Immun. 62: 5447-5455.
26. MEWES, H. W., K. HEUMANN, A. KAPS, K. MAYER, F. PFEIFFER et al., 1999 MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 27: 44-48.
27. MORTIMER, R. K., and J. R. JOHNSTON, 1986 Genealogy of principal strains of the yeast genetic stock center. Genetics 113: 35-43.
28. MORTIMER, R. K., P. ROMANO, G. SUZZI and M. POLSINELLI, 1994 Genome renewal: a new phenomenon revealed from a genetic study of 43 strains of Saccharomyces cerevisiae derived from natural fermentation of grape musts. Yeast 10: 1543-1552.
29. NACHMAN, M. W., V. L. BAUER, S. L. CROWELL and C. F. AQUADRO, 1998 DNA variability and recombination rates at X-linked loci in humans. Genetics 150: 1133-1141.
30. OSHIRO, G., L. M. WODICKA, M. P. WASHBURN, J. R. YATES, III, D. J. LOCKHART et al., 2002 Highly parallel identification of new genes in Saccharomyces cerevisiae. Genome Res. 12: 1210-1220.
31. PRIMIG, M., R. M. WILLIAMS, E. A. WINZELER, G. G. TEVZADZE, A. R. CONWAY et al., 2000 The core meiotic transcriptome in budding yeasts. Nat. Genet. 26: 415-423.
32. RAGHURAMAN, M. K., E. A. WINZELER, D. COLLINGWOOD, S. HUNT, L. WODICKA et al., 2001 Replication dynamics of the yeast genome. Science 294: 115-121.
33. ROBERTS, D. J., A. G. CRAIG, A. R. BERENDT, R. PINCHES, G. NASH et al., 1992 Rapid switching to multiple antigenic and adhesive phenotypes in malaria. Nature 357: 689-692.
34. STEINMETZ, L. M., H. SINHA, D. R. RICHARDS, J. I. SPIEGELMAN, P. J. OEFNER et al., 2002 Dissecting the architecture of a quantitative trait locus in yeast. Nature 416: 326-330.
35. TAVAZOIE, S., J. D. HUGHES, M. J. CAMPBELL, R. J. CHO and G. M. CHURCH, 1999 Systematic determination of genetic network architecture. Nat. Genet. 22: 281-285.
36. THOMAS, B. J., and R. ROTHSTEIN, 1989 Elevated recombination rates in transcriptionally active DNA. Cell 56: 619-630.
37. TROESCH, A., H. NGUYEN, C. G. MIYADA, S. DESVARENNE, T. R. GINGERAS et al., 1999 Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J. Clin. Microbiol. 37: 49-55.
38. VALGEIRSDOTTIR, K., K. L. TRAVERSE and M. L. PARDUE, 1990 HeT DNA: a family of mosaic repeated sequences specific for heterochromatin in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 87: 7998-8002.
39. WINZELER, E. A., D. R. RICHARDS, A. R. CONWAY, A. L. GOLDSTEIN, S. KALMAN et al., 1998 Direct allelic variation scanning of the yeast genome. Science 281: 1194-1197.
40. WINZELER, E., D. SHOEMAKER, A. ASTROMOFF, H. LIANG, K. ANDERSON et al., 1999 Functional characterization of the Saccharomyces cerevisiae genome by precise deletion and parallel analysis. Science 285: 901-906.
41. WODICKA, L., H. DONG, M. MITTMANN, M.-H. HO and D. J. LOCKHART, 1997 Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15: 1359-1367.
42. WYRICK, J. J., J. G. APARICIO, T. CHEN, J. D. BARNETT, E. G. JENNINGS et al., 2001 Genome-wide distribution of ORC and MCM proteins in S. cerevisiae: high-resolution mapping of replication origins. Science 294: 2357-2360.
43. YEAST GENOME DIRECTORY, 1997 The yeast genome directory. Nature 387: 5.