Dujon B: Yeast evolutionary genomics. Nat Rev Genet. 2010, 11 (7): 512-524. 10.1038/nrg2811.
Article
CAS
PubMed
Google Scholar
Nieduszynski CA, Liti G: From sequence to function: insights from natural variation in budding yeasts. Biochim Biophys Acta. 2011, 1810 (10): 959-966. 10.1016/j.bbagen.2011.02.004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Scannell DR, Zill OA, Rokas A, Payen C, Dunham MJ, Eisen MB, Rine J, Johnston M, Hittinger CT: The awesome power of yeast evolutionary genetics: new genome sequences and strain resources for the saccharomyces sensu stricto genus. G3. 2011, 1: 11-25. doi:10.1534/g3.111.000273.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M: Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science. 2003, 301 (5629): 71-76. 10.1126/science.1084337.
Article
CAS
PubMed
Google Scholar
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 2003, 423 (6937): 241-254. 10.1038/nature01644.
Article
CAS
PubMed
Google Scholar
Dujon B: Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet. 2006, 22 (7): 375-387. 10.1016/j.tig.2006.05.007.
Article
CAS
PubMed
Google Scholar
Fischer G, James SA, Roberts IN, Oliver SG, Louis EJ: Chromosomal evolution in Saccharomyces. Nature. 2000, 405 (6785): 451-454. 10.1038/35013058.
Article
CAS
PubMed
Google Scholar
Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J: Transcriptional regulatory code of a eukaryotic genome. Nature. 2004, 431 (7004): 99-104. 10.1038/nature02800.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nieduszynski CA, Knox Y, Donaldson AD: Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 2006, 20 (14): 1874-1879. 10.1101/gad.385306.
Article
PubMed Central
CAS
PubMed
Google Scholar
Müller CA, Nieduszynski CA: Conservation of replication timing reveals global and local regulation of replication origin activity. Genome Res. 2012, 22 (10): 1953-1962. 10.1101/gr.139477.112.
Article
PubMed Central
PubMed
Google Scholar
Wang SA, Bai FY: Saccharomyces arboricolus sp. nov., a yeast species from tree bark. Int J Syst Evol Microbiol. 2008, 58 (Pt 2): 510-514.
Article
CAS
PubMed
Google Scholar
Naumov GI, Naumova ES, Masneuf-Pomarede I: Genetic identification of new biological species Saccharomyces arboricolus Wang et Bai. Antonie Van Leeuwenhoek. 2010, 98 (1): 1-7. 10.1007/s10482-010-9441-5.
Article
PubMed
Google Scholar
Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M: Life with 6000 genes. Science. 1996, 274 (5287): 546-563-547. 10.1126/science.274.5287.546.
Article
CAS
PubMed
Google Scholar
Ronaghi M: Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001, 11 (1): 3-11. 10.1101/gr.11.1.3.
Article
CAS
PubMed
Google Scholar
Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V: Population genomics of domestic and wild yeasts. Nature. 2009, 458 (7236): 337-341. 10.1038/nature07743.
Article
PubMed Central
CAS
PubMed
Google Scholar
Siow CC, Nieduszynska SR, Muller CA, Nieduszynski CA: OriDB, the DNA replication origin database updated and extended. Nucleic Acids Res. 2012, 40 (1): D682-D686. 10.1093/nar/gkr1091.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cherry JM, Hong EL, Amundsen C, Balakrishnan R, Binkley G, Chan ET, Christie KR, Costanzo MC, Dwight SS, Engel SR: Saccharomyces Genome Database: the genomics resource of budding yeast. Nucleic Acids Res. 2012, 40 (1): D700-D705. 10.1093/nar/gkr1029.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bon E, Neuveglise C, Casaregola S, Artiguenave F, Wincker P, Aigle M, Durrens P: Genomic exploration of the hemiascomycetous yeasts: 5. Saccharomyces bayanus var. uvarum. FEBS Lett. 2000, 487 (1): 37-41. 10.1016/S0014-5793(00)02276-6.
Article
CAS
PubMed
Google Scholar
Fischer G, Neuveglise C, Durrens P, Gaillardin C, Dujon B: Evolution of gene order in the genomes of two related yeast species. Genome Res. 2001, 11 (12): 2009-2019. 10.1101/gr.212701.
Article
CAS
PubMed
Google Scholar
Slater GS, Birney E: Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005, 6: 31-10.1186/1471-2105-6-31.
Article
PubMed Central
PubMed
Google Scholar
Byrne KP, Wolfe KH: The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 2005, 15 (10): 1456-1461. 10.1101/gr.3672305.
Article
PubMed Central
CAS
PubMed
Google Scholar
Besemer J, Lomsadze A, Borodovsky M: GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001, 29 (12): 2607-2618. 10.1093/nar/29.12.2607.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brown CA, Murray AW, Verstrepen KJ: Rapid expansion and functional divergence of subtelomeric gene families in yeasts. Curr Biol. 2010, 20 (10): 895-903. 10.1016/j.cub.2010.04.027.
Article
PubMed Central
CAS
PubMed
Google Scholar
Zill OA, Scannell D, Teytelman L, Rine J: Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol. 2010, 8 (11): e1000550-10.1371/journal.pbio.1000550.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25 (5): 955-964.
Article
PubMed Central
CAS
PubMed
Google Scholar
Liti G, Peruffo A, James SA, Roberts IN, Louis EJ: Inferences of evolutionary relationships from a population survey of LTR-retrotransposons and telomeric-associated sequences in the Saccharomyces sensu stricto complex. Yeast. 2005, 22 (3): 177-192. 10.1002/yea.1200.
Article
CAS
PubMed
Google Scholar
Naumov GI, James SA, Naumova ES, Louis EJ, Roberts IN: Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae. Int J Syst Evol Microbiol. 2000, 50 (Pt 5): 1931-1942.
Article
CAS
PubMed
Google Scholar
Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A: The generic genome browser: a building block for a model organism system database. Genome Res. 2002, 12 (10): 1599-1610. 10.1101/gr.403602.
Article
PubMed Central
CAS
PubMed
Google Scholar
McKay SJ, Vergara IA, Stajich JE: Using the Generic Synteny Browser (GBrowse_syn). Current protocols in bioinformatics. 2010, 31: 9.12.1-9.12.25.
Google Scholar
Warringer J, Zorgo E, Cubillos FA, Zia A, Gjuvsland A, Simpson JT, Forsmark A, Durbin R, Omholt SW, Louis EJ: Trait variation in yeast is defined by population history. PLoS Genet. 2011, 7 (6): e1002111-10.1371/journal.pgen.1002111.
Article
PubMed Central
CAS
PubMed
Google Scholar
Song SH, Vieille C: Recent advances in the biological production of mannitol. Appl Microbiol Biotechnol. 2009, 84 (1): 55-62. 10.1007/s00253-009-2086-5.
Article
CAS
PubMed
Google Scholar
Hall C, Dietrich FS: The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. Genetics. 2007, 177 (4): 2293-2307. 10.1534/genetics.107.074963.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hittinger CT, Goncalves P, Sampaio JP, Dover J, Johnston M, Rokas A: Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature. 2010, 464 (7285): 54-58. 10.1038/nature08791.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rokas A, Williams BL, King N, Carroll SB: Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 2003, 425 (6960): 798-804. 10.1038/nature02053.
Article
CAS
PubMed
Google Scholar
Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, Missawa SK, Galzerani F, Costa GG, Vidal RO, Noronha MF: Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res. 2009, 19 (12): 2258-2270. 10.1101/gr.091777.109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Liti G, Barton DB, Louis EJ: Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics. 2006, 174 (2): 839-850. 10.1534/genetics.106.062166.
Article
PubMed Central
CAS
PubMed
Google Scholar
Novo M, Bigey F, Beyne E, Galeote V, Gavory F, Mallet S, Cambon B, Legras JL, Wincker P, Casaregola S: Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci USA. 2009, 106 (38): 16333-16338. 10.1073/pnas.0904673106.
Article
PubMed Central
CAS
PubMed
Google Scholar
Johnson LJ, Koufopanou V, Goddard MR, Hetherington R, Schafer SM, Burt A: Population genetics of the wild yeast Saccharomyces paradoxus. Genetics. 2004, 166 (1): 43-52. 10.1534/genetics.166.1.43.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kuehne HA, Murphy HA, Francis CA, Sniegowski PD: Allopatric divergence, secondary contact, and genetic isolation in wild yeast populations. Curr biol. 2007, 17 (5): 407-411. 10.1016/j.cub.2006.12.047.
Article
CAS
PubMed
Google Scholar
Sampaio JP, Goncalves P: Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and are sympatric with S. cerevisiae and S. paradoxus. Appl Environ Microbiol. 2008, 74 (7): 2144-2152. 10.1128/AEM.02396-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Langkjaer RB, Nielsen ML, Daugaard PR, Liu W, Piskur J: Yeast chromosomes have been significantly reshaped during their evolutionary history. J Mol Biol. 2000, 304 (3): 271-288. 10.1006/jmbi.2000.4209.
Article
CAS
PubMed
Google Scholar
Libkind D, Hittinger CT, Valerio E, Goncalves C, Dover J, Johnston M, Goncalves P, Sampaio JP: Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci USA. 2011, 108 (35): 14539-14544. 10.1073/pnas.1105430108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Quince C, Lanzen A, Davenport RJ, Turnbaugh PJ: Removing noise from pyrosequenced amplicons. BMC Bioinformatics. 2011, 12: 38-10.1186/1471-2105-12-38.
Article
PubMed Central
PubMed
Google Scholar
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT: Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods. 2009, 6 (9): 639-641. 10.1038/nmeth.1361.
Article
CAS
PubMed
Google Scholar
Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M: Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res. 2008, 18 (12): 1979-1990. 10.1101/gr.081612.108.
Article
PubMed Central
CAS
PubMed
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002, 30 (14): 3059-3066. 10.1093/nar/gkf436.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997, 13 (5): 555-556.
CAS
PubMed
Google Scholar
Darling AC, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004, 14 (7): 1394-1403. 10.1101/gr.2289704.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes. Genome Biol. 2004, 5 (2): R12-10.1186/gb-2004-5-2-r12.
Article
PubMed Central
PubMed
Google Scholar
Warringer J, Anevski D, Liu B, Blomberg A: Chemogenetic fingerprinting by analysis of cellular growth dynamics. BMC Chem Biol. 2008, 8: 3-10.1186/1472-6769-8-3.
Article
PubMed Central
PubMed
Google Scholar
Homer N, Merriman B, Nelson SF: BFAST: an alignment tool for large scale genome resequencing. PLoS One. 2009, 4 (11): e7767-10.1371/journal.pone.0007767.
Article
PubMed Central
PubMed
Google Scholar
Benson G: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999, 27 (2): 573-580. 10.1093/nar/27.2.573.
Article
PubMed Central
CAS
PubMed
Google Scholar