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Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima.

Gore-Lloyd D, Sumann I, Brachmann AO, Schneeberger K, Ortiz-Merino RA, Moreno-Beltrán M, Schläfli M, Kirner P, Santos Kron A, Rueda-Mejia MP, Somerville V, Wolfe KH, Piel J, Ahrens CH, Henk D, Freimoser FM.

Mol Microbiol. 2019 May 12. doi: 10.1111/mmi.14272. [Epub ahead of print]


Coverage-Versus-Length Plots, a Simple Quality Control Step for de Novo Yeast Genome Sequence Assemblies.

Douglass AP, O'Brien CE, Offei B, Coughlan AY, Ortiz-Merino RA, Butler G, Byrne KP, Wolfe KH.

G3 (Bethesda). 2019 Mar 7;9(3):879-887. doi: 10.1534/g3.118.200745.


The reported point centromeres of Scheffersomyces stipitis are retrotransposon long terminal repeats.

Coughlan AY, Wolfe KH.

Yeast. 2019 May;36(5):275-283. doi: 10.1002/yea.3375. Epub 2019 Jan 29.


Zygosaccharomyces pseudobailii, another yeast interspecies hybrid that regained fertility by damaging one of its MAT loci.

Braun-Galleani S, Ortiz-Merino RA, Wu Q, Xu Y, Wolfe KH.

FEMS Yeast Res. 2018 Nov 1;18(7). doi: 10.1093/femsyr/foy079.


Population genomics shows no distinction between pathogenic Candida krusei and environmental Pichia kudriavzevii: One species, four names.

Douglass AP, Offei B, Braun-Galleani S, Coughlan AY, Martos AAR, Ortiz-Merino RA, Byrne KP, Wolfe KH.

PLoS Pathog. 2018 Jul 19;14(7):e1007138. doi: 10.1371/journal.ppat.1007138. eCollection 2018 Jul.


Genome Sequence of Torulaspora microellipsoides CLIB 830T.

Galeote V, Bigey F, Devillers H, Ortiz-Merino RA, Dequin S, Wolfe KH, Neuvéglise C.

Genome Announc. 2018 Jun 28;6(26). pii: e00615-18. doi: 10.1128/genomeA.00615-18.


Draft Genome Sequence of a Highly Heterozygous Yeast Strain from the Metschnikowia pulcherrima Subclade, UCD127.

Venkatesh A, Murray AL, Boyle AB, Quinn Farrington L, Maher TJ, Ó'Gaora P, Wolfe KH, O'Brien CE, Butler G.

Genome Announc. 2018 Jun 21;6(25). pii: e00550-18. doi: 10.1128/genomeA.00550-18.


Draft Genome Sequence of the Yeast Nadsonia starkeyi-henricii UCD142, Isolated from Forest Soil in Ireland.

O'Boyle S, Bergin SA, Hussey ÉE, McLaughlin AD, Riddell LR, Byrne KP, Wolfe KH, O'Brien CE, Butler G.

Genome Announc. 2018 Jun 21;6(25). pii: e00549-18. doi: 10.1128/genomeA.00549-18.


Draft Genome Sequences of Two Natural Isolates of the Yeast Barnettozyma californica from Ireland, UCD09 and UCD89.

Mullen AA, Lynch CD, Hill SM, Holohan CP, Ó Cróinín T, Wolfe KH, O'Brien CE, Butler G.

Genome Announc. 2018 Jun 21;6(25). pii: e00548-18. doi: 10.1128/genomeA.00548-18.


TPP riboswitch-dependent regulation of an ancient thiamin transporter in Candida.

Donovan PD, Holland LM, Lombardi L, Coughlan AY, Higgins DG, Wolfe KH, Butler G.

PLoS Genet. 2018 May 31;14(5):e1007429. doi: 10.1371/journal.pgen.1007429. eCollection 2018 May.


Evolutionary instability of CUG-Leu in the genetic code of budding yeasts.

Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH.

Nat Commun. 2018 May 14;9(1):1887. doi: 10.1038/s41467-018-04374-7.


Ploidy Variation in Kluyveromyces marxianus Separates Dairy and Non-dairy Isolates.

Ortiz-Merino RA, Varela JA, Coughlan AY, Hoshida H, da Silveira WB, Wilde C, Kuijpers NGA, Geertman JM, Wolfe KH, Morrissey JP.

Front Genet. 2018 Mar 21;9:94. doi: 10.3389/fgene.2018.00094. eCollection 2018.


Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii.

Ortiz-Merino RA, Kuanyshev N, Byrne KP, Varela JA, Morrissey JP, Porro D, Wolfe KH, Branduardi P.

Appl Environ Microbiol. 2018 Feb 14;84(5). pii: e02294-17. doi: 10.1128/AEM.02294-17. Print 2018 Mar 1.


Flip/flop mating-type switching in the methylotrophic yeast Ogataea polymorpha is regulated by an Efg1-Rme1-Ste12 pathway.

Hanson SJ, Byrne KP, Wolfe KH.

PLoS Genet. 2017 Nov 27;13(11):e1007092. doi: 10.1371/journal.pgen.1007092. eCollection 2017 Nov.


Evolution of Mating in the Saccharomycotina.

Wolfe KH, Butler G.

Annu Rev Microbiol. 2017 Sep 8;71:197-214. doi: 10.1146/annurev-micro-090816-093403. Epub 2017 Jun 28. Review.


Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch.

Ortiz-Merino RA, Kuanyshev N, Braun-Galleani S, Byrne KP, Porro D, Branduardi P, Wolfe KH.

PLoS Biol. 2017 May 16;15(5):e2002128. doi: 10.1371/journal.pbio.2002128. eCollection 2017 May.


An Evolutionary Perspective on Yeast Mating-Type Switching.

Hanson SJ, Wolfe KH.

Genetics. 2017 May;206(1):9-32. doi: 10.1534/genetics.117.202036. Review.


Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.

Schröder MS, Martinez de San Vicente K, Prandini TH, Hammel S, Higgins DG, Bagagli E, Wolfe KH, Butler G.

PLoS Genet. 2016 Nov 2;12(11):e1006404. doi: 10.1371/journal.pgen.1006404. eCollection 2016 Nov.


Comparative genomics of biotechnologically important yeasts.

Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk HP, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):9882-7. doi: 10.1073/pnas.1603941113. Epub 2016 Aug 17.


Centromeres of the Yeast Komagataella phaffii (Pichia pastoris) Have a Simple Inverted-Repeat Structure.

Coughlan AY, Hanson SJ, Byrne KP, Wolfe KH.

Genome Biol Evol. 2016 Aug 27;8(8):2482-92. doi: 10.1093/gbe/evw178.


Correction: The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis.

Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedűsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T.

PLoS Genet. 2016 Jul 14;12(7):e1006202. doi: 10.1371/journal.pgen.1006202. eCollection 2016 Jul.


The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis.

Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedűsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T.

PLoS Genet. 2015 Oct 30;11(10):e1005626. doi: 10.1371/journal.pgen.1005626. eCollection 2015 Oct. Erratum in: PLoS Genet. 2016 Jul;12(7):e1006202.


Origin of the Yeast Whole-Genome Duplication.

Wolfe KH.

PLoS Biol. 2015 Aug 7;13(8):e1002221. doi: 10.1371/journal.pbio.1002221. eCollection 2015 Aug.


Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres.

Kobayashi N, Suzuki Y, Schoenfeld LW, Müller CA, Nieduszynski C, Wolfe KH, Tanaka TU.

Curr Biol. 2015 Aug 3;25(15):2026-33. doi: 10.1016/j.cub.2015.06.023. Epub 2015 Jul 9.


Clade- and species-specific features of genome evolution in the Saccharomycetaceae.

Wolfe KH, Armisén D, Proux-Wera E, ÓhÉigeartaigh SS, Azam H, Gordon JL, Byrne KP.

FEMS Yeast Res. 2015 Aug;15(5):fov035. doi: 10.1093/femsyr/fov035. Epub 2015 Jun 10.


Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus Group I and II strains.

Monerawela C, James TC, Wolfe KH, Bond U.

FEMS Yeast Res. 2015 Mar;15(2). pii: fou008. doi: 10.1093/femsyr/fou008.


Cdc42p-interacting protein Bem4p regulates the filamentous-growth mitogen-activated protein kinase pathway.

Pitoniak A, Chavel CA, Chow J, Smith J, Camara D, Karunanithi S, Li B, Wolfe KH, Cullen PJ.

Mol Cell Biol. 2015 Jan;35(2):417-36. doi: 10.1128/MCB.00850-14. Epub 2014 Nov 10.


Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system.

Hanson SJ, Byrne KP, Wolfe KH.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4851-8. doi: 10.1073/pnas.1416014111. Epub 2014 Oct 27.


SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes.

Óhéigeartaigh SS, Armisén D, Byrne KP, Wolfe KH.

J Bacteriol. 2014 Jun;196(11):2030-42. doi: 10.1128/JB.01368-13. Epub 2014 Mar 21.


Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution.

Maguire SL, Wang C, Holland LM, Brunel F, Neuvéglise C, Nicaud JM, Zavrel M, White TC, Wolfe KH, Butler G.

PLoS Genet. 2014 Jan;10(1):e1004076. doi: 10.1371/journal.pgen.1004076. Epub 2014 Jan 16.


Comparative genome analysis and gene finding in Candida species using CGOB.

Maguire SL, ÓhÉigeartaigh SS, Byrne KP, Schröder MS, O'Gaora P, Wolfe KH, Butler G.

Mol Biol Evol. 2013 Jun;30(6):1281-91. doi: 10.1093/molbev/mst042. Epub 2013 Mar 13.


Evolutionary mobility of the ribosomal DNA array in yeasts.

Proux-Wéra E, Byrne KP, Wolfe KH.

Genome Biol Evol. 2013;5(3):525-31. doi: 10.1093/gbe/evt022.


A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach.

Proux-Wéra E, Armisén D, Byrne KP, Wolfe KH.

BMC Bioinformatics. 2012 Sep 17;13:237. doi: 10.1186/1471-2105-13-237.


Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.

Riccombeni A, Vidanes G, Proux-Wéra E, Wolfe KH, Butler G.

PLoS One. 2012;7(4):e35750. doi: 10.1371/journal.pone.0035750. Epub 2012 Apr 26.


Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents.

Gordon JL, Armisén D, Proux-Wéra E, ÓhÉigeartaigh SS, Byrne KP, Wolfe KH.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20024-9. doi: 10.1073/pnas.1112808108. Epub 2011 Nov 28.


Mechanisms of chromosome number evolution in yeast.

Gordon JL, Byrne KP, Wolfe KH.

PLoS Genet. 2011 Jul;7(7):e1002190. doi: 10.1371/journal.pgen.1002190. Epub 2011 Jul 21.


Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments.

OhÉigeartaigh SS, Armisén D, Byrne KP, Wolfe KH.

BMC Genomics. 2011 Jul 26;12:377. doi: 10.1186/1471-2164-12-377.


Evolutionary Origins of the Fumonisin Secondary Metabolite Gene Cluster in Fusarium verticillioides and Aspergillus niger.

Khaldi N, Wolfe KH.

Int J Evol Biol. 2011;2011:423821. doi: 10.4061/2011/423821. Epub 2011 May 23.


Physiological and metabolic diversity in the yeast Kluyveromyces marxianus.

Lane MM, Burke N, Karreman R, Wolfe KH, O'Byrne CP, Morrissey JP.

Antonie Van Leeuwenhoek. 2011 Nov;100(4):507-19. doi: 10.1007/s10482-011-9606-x. Epub 2011 Jun 15.


Localized hypermutation and associated gene losses in legume chloroplast genomes.

Magee AM, Aspinall S, Rice DW, Cusack BP, Sémon M, Perry AS, Stefanović S, Milbourne D, Barth S, Palmer JD, Gray JC, Kavanagh TA, Wolfe KH.

Genome Res. 2010 Dec;20(12):1700-10. doi: 10.1101/gr.111955.110. Epub 2010 Oct 26. Erratum in: Genome Res. 2014 Jun;24(6):1052.


Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres.

Lynch DB, Logue ME, Butler G, Wolfe KH.

Genome Biol Evol. 2010;2:572-83. doi: 10.1093/gbe/evq042. Epub 2010 Jul 8.


SMURF: Genomic mapping of fungal secondary metabolite clusters.

Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, Fedorova ND.

Fungal Genet Biol. 2010 Sep;47(9):736-41. doi: 10.1016/j.fgb.2010.06.003. Epub 2010 Jun 8.


RNAi in budding yeast.

Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, Fink GR, Bartel DP.

Science. 2009 Oct 23;326(5952):544-550. doi: 10.1126/science.1176945. Epub 2009 Sep 10.


Evolutionary capture of viral and plasmid DNA by yeast nuclear chromosomes.

Frank AC, Wolfe KH.

Eukaryot Cell. 2009 Oct;8(10):1521-31. doi: 10.1128/EC.00110-09. Epub 2009 Aug 7.


Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.

Gordon JL, Byrne KP, Wolfe KH.

PLoS Genet. 2009 May;5(5):e1000485. doi: 10.1371/journal.pgen.1000485. Epub 2009 May 15.


Complete chloroplast genome sequence of a major allogamous forage species, perennial ryegrass (Lolium perenne L.).

Diekmann K, Hodkinson TR, Wolfe KH, van den Bekerom R, Dix PJ, Barth S.

DNA Res. 2009 Jun;16(3):165-76. doi: 10.1093/dnares/dsp008. Epub 2009 May 4.


Elaboration, diversification and regulation of the Sir1 family of silencing proteins in Saccharomyces.

Gallagher JE, Babiarz JE, Teytelman L, Wolfe KH, Rine J.

Genetics. 2009 Apr;181(4):1477-91. doi: 10.1534/genetics.108.099663. Epub 2009 Jan 26.


No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes.

Williams TA, Wolfe KH, Fares MA.

Mol Biol Evol. 2009 Feb;26(2):445-50. doi: 10.1093/molbev/msn267. Epub 2008 Nov 26.


Turning a hobby into a job: how duplicated genes find new functions.

Conant GC, Wolfe KH.

Nat Rev Genet. 2008 Dec;9(12):938-50. doi: 10.1038/nrg2482. Review.


Elusive origins of the extra genes in Aspergillus oryzae.

Khaldi N, Wolfe KH.

PLoS One. 2008 Aug 22;3(8):e3036. doi: 10.1371/journal.pone.0003036.

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