Saccharomyces cerevisiae: Gene Annotation and Genome Variability, State of the Art Through Comparative Genomics

Methods in Molecular Biology

Volumn 759, Issue , 2011, Pages 31-40

  Louis, Ed ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

comparative genomics; Gene annotation; genetic variation; next generation sequencing; novel genes

Indexed keywords

BREWING; COMPARATIVE GENOMICS; EUKARYOTE; FUNCTIONAL GENOMICS; GENE SEQUENCE; GENETIC VARIATION; HIGH THROUGHPUT SEQUENCING; NONHUMAN; OPEN READING FRAME; PREDICTION; SACCHAROMYCES CEREVISIAE; SYNTENY; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; DNA MICROARRAY; FUNGAL GENOME; GENETIC VARIABILITY; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR GENETICS; PULSED FIELD GEL ELECTROPHORESIS; SEQUENCE ANALYSIS;

MICROSATELLITE DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; ELECTROPHORESIS, GEL, PULSED-FIELD; GENETIC VARIATION; GENOME, FUNGAL; GENOMICS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE ANNOTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SEQUENCE ANALYSIS;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 80054760706     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-61779-173-4_2     Document Type: Chapter

References (41)

1. Fisk, D. G., Ball, C. A., Dolinski, K., et al. (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23, 857–865.
2. Christie, K. R., Hong, E. L., and Cherry, J. M. (2009) Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns. Trends Microbiol. 17, 286–294.
3. Hong, E. L., Balakrishnan, R., Dong, Q., et al. (2008) Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 36, D577–581.
4. Kellis, M., Patterson, N., Endrizzi, M., Birren, B., and Lander, E. S. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241–254.
5. Liti, G., and Louis, E. J. (2005) Yeast evolution and comparative genomics. Annu. Rev. Microbiol. 59, 135–153.
6. Cliften, P., Sudarsanam, P., Desikan, A., et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71–76.
7. Cliften, P. F., Hillier, L. W., Fulton, L., et al. (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res. 11, 1175–1186.
8. Wolfe, K. H., and Shields, D. C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708–713.
9. Byrne, K. P., and Wolfe, K. H. (2005) The yeast gene order browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 15, 1456–1461.
10. Byrne, K. P., and Wolfe, K. H. (2006) Visualizing syntenic relationships among the hemiascomycetes with the yeast gene order browser. Nucleic Acids Res. 34, D452–455.
11. Fischer, G., James, S. A., Roberts, I. N., Oliver, S. G., and Louis, E. J. (2000) Chro- mosomal evolution in Saccharomyces. Nature 405, 451–454.
12. Souciet, J., Aigle, M., Artiguenave, F., et al. (2000) Genomic exploration of the hemiascomycetous yeasts: 1. A set of yeast species for molecular evolution studies. FEBS Lett. 487, 3–12.
13. Fischer, G., Neuveglise, C., Durrens, P., Gail-lardin, C., and Dujon, B. (2001) Evolution of gene order in the genomes of two related yeast species. Genome Res. 11, 2009–2019.
14. Liti, G., Carter, D. M., Moses, A. M., et al. (2009) Population genomics of domestic and wild yeasts. Nature 458, 337–341.
15. Novo, M., Bigey, F., Beyne, E., et al. (2009) Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc. Natl. Acad. Sci. USA 106, 16333–16338.
16. Wei, W., McCusker, J. H., Hyman, R. W., et al. (2007) Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc. Natl. Acad. Sci. USA 104, 12825–12830.
17. Liti, G., Peruffo, A., James, S. A., Roberts, I. N., and Louis, E. J. (2005) Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex. Yeast 22, 177–192.
18. Buhler, C., Borde, V., and Lichten, M. (2007) Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae. PLoS Biol. 5, e324.
19. Klingberg, T. D., Lesnik, U., Arneborg, N., Raspor, P., and Jespersen, L. (2008) Comparison of Saccharomyces cerevisiae strains of clinical and nonclinical origin by molecular typing and determination of putative virulence traits. FEMS Yeast Res. 8, 631–640.
20. Lucena, B. T., Silva-Filho, E. A., Coim-bra, M. R., Morais, J. O., Simoes, D. A., and Morais, M. A., Jr. (2007) Chromosome instability in industrial strains of Saccharomyces cerevisiae batch cultivated under laboratory conditions. Genet. Mol. Res. 6, 1072–1084.
21. Schuller, D., Pereira, L., Alves, H., Cambon, B., Dequin, S., and Casal, M. (2007) Genetic characterization of commercial Saccharomyces cerevisiae isolates recovered from vineyard environments. Yeast 24, 625–636.
22. Valero, E., Cambon, B., Schuller, D., Casal, M., and Dequin, S. (2007) Biodiversity of Saccharomyces yeast strains from grape berries of wine-producing areas using starter commercial yeasts. FEMS Yeast Res. 7, 317–329.
23. Althoff, D. M., Gitzendanner, M. A., and Segraves, K. A. (2007) The utility of amplified fragment length polymorphisms in phylogenetics: a comparison of homology within and between genomes. Syst. Biol. 56, 477–484.
24. Lopandic, K., Gangl, H., Wallner, E., et al. (2007) Genetically different wine yeasts isolated from Austrian vine-growing regions influence wine aroma differently and contain putative hybrids between Saccharomyces cerevisiae and Saccharomyces kudriavzevii. FEMS Yeast Res. 7, 953–965.
25. MacKenzie, D. A., Defernez, M., Dunn, W. B., et al. (2008) Relatedness of medically important strains of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics. Yeast 25, 501–512.
26. Goddard, M. R., Anfang, N., Tang, R., Gardner, R. C., and Jun, C. (2009) A distinct population of Saccharomyces cerevisiae in New Zealand: evidence for local dispersal by insects and human-aided global dispersal in oak barrels. Environ. Microbiol. 12, 63–73.
27. Legras, J. L., Merdinoglu, D., Cornuet, J. M., and Karst, F. (2007) Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol. Ecol. 16, 2091–2102.
28. Richards, K. D., Goddard, M. R., and Gardner, R. C. (2009) A database of microsatellite genotypes for Saccharomyces cerevisiae. Antonie Van Leeuwenhoek 96, 355–359.
29. Bourgon, R., Mancera, E., Brozzi, A., Steinmetz, L. M., and Huber, W. (2009) Array-based genotyping in S. cerevisiae using semi-supervised clustering. Bioinformatics 25, 1056–1062.
30. Dunn, B., Levine, R. P., and Sherlock, G. (2005) Microarray karyotyping of commer- cial wine yeast strains reveals shared, as well as unique, genomic signatures. BMC Genom. 6, 53.
31. Dunn, B., and Sherlock, G. (2008) Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus. Genome Res. 18, 1610–1623.
32. Gresham, D., Ruderfer, D. M., Pratt, S. C., et al. (2006) Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311, 1932– 1936.
33. Primig, M., Williams, R. M., Winzeler, E. A., et al. (2000) The core meiotic transcriptome in budding yeasts. Nat. Genet. 26, 415–423.
34. Schacherer, J., Ruderfer, D. M., Gresham, D., Dolinski, K., Botstein, D., and Kruglyak, L. (2007) Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS One 2, e322.
35. Schacherer, J., Shapiro, J. A., Ruderfer, D. M., and Kruglyak, L. (2009) Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature 458, 342–345.
36. Aa, E., Townsend, J. P., Adams, R. I., Nielsen, K. M., and Taylor, J. W. (2006) Population structure and gene evolution in Saccharomyces cerevisiae. FEMS Yeast Res. 6, 702–715.
37. Fay, J. C., and Benavides, J. A. (2005) Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet. 1, 66–71.
38. Fay, J. C., and Benavides, J. A. (2005) Hypervariable noncoding sequences in Saccharomyces cerevisiae. Genetics 170, 1575–1587.
39. Liti, G., Barton, D. B., and Louis, E. J. (2006) Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics 174, 839–850.
40. Louis, E. J. (1998) Whole chromosome analysis. In Brown, A. J. P. and Tuite, M. F. (eds.), Methods in Microbiology 26: Yeast Gene Analysis, pp. 15–31. San Diego: Academic.
41. James, S. A., O’Kelly, M. J., Carter, D. M., Davey, R. P., van Oudenaarden, A., and Roberts, I. N. (2009) Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Res. 19, 626–635.