title: Comparative genomics of biotechnologically important yeasts.
abstract: Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Robert
authors.initials: R
authors.lastname: Riley
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Sajeet
authors.initials: S
authors.lastname: Haridas
authors.affiliation: University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wolfe
authors.affiliation: Laboratory of Genetics, Genetics/Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706; Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil;
authors.forename: Mariana R
authors.initials: MR
authors.lastname: Lopes
authors.affiliation: Laboratory of Genetics, Genetics/Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706; Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726;
authors.forename: Chris Todd
authors.initials: CT
authors.lastname: Hittinger
authors.affiliation: Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany;
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Asaf A
authors.initials: AA
authors.lastname: Salamov
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235;
authors.forename: Jennifer H
authors.initials: JH
authors.lastname: Wisecaver
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706; US Department of Agriculture Forest Products Laboratory, Madison, WI 53726;
authors.forename: Tanya M
authors.initials: TM
authors.lastname: Long
authors.affiliation: Xylome Corporation, Madison, WI 53719;
authors.forename: Christopher H
authors.identifier: 0000-0002-7330-4983
authors.initials: CH
authors.lastname: Calvey
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Andrea L
authors.initials: AL
authors.lastname: Aerts
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Kerrie W
authors.initials: KW
authors.lastname: Barry
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Cindy
authors.initials: C
authors.lastname: Choi
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Alicia
authors.initials: A
authors.lastname: Clum
authors.affiliation: University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;
authors.forename: Aisling Y
authors.initials: AY
authors.lastname: Coughlan
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Shweta
authors.initials: S
authors.lastname: Deshpande
authors.affiliation: University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Douglass
authors.affiliation: University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;
authors.forename: Sara J
authors.initials: SJ
authors.lastname: Hanson
authors.affiliation: Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany; School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom;
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Kurt M
authors.initials: KM
authors.lastname: LaButti
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Erika A
authors.initials: EA
authors.lastname: Lindquist
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Anna M
authors.initials: AM
authors.lastname: Lipzen
authors.affiliation: Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany;
authors.forename: Jan P
authors.initials: JP
authors.lastname: Meier-Kolthoff
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Robin A
authors.initials: RA
authors.lastname: Ohm
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Robert P
authors.initials: RP
authors.lastname: Otillar
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Jasmyn L
authors.initials: JL
authors.lastname: Pangilinan
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Yi
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235;
authors.forename: Antonis
authors.identifier: 0000-0002-7248-6551
authors.initials: A
authors.lastname: Rokas
authors.affiliation: Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil;
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Rosa
authors.affiliation: Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany;
authors.forename: Carmen
authors.initials: C
authors.lastname: Scheuner
authors.affiliation: Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv 79005, Ukraine; Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow 35-601, Poland;
authors.forename: Andriy A
authors.initials: AA
authors.lastname: Sibirny
authors.affiliation: Department of Plant Pathology, Ohio State University, Columbus, OH 43210;
authors.forename: Jason C
authors.initials: JC
authors.lastname: Slot
authors.affiliation: Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany; Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre, Royal Netherlands Academy of Arts and Sciences, 3508 AD, Utrecht, The Netherlands;
authors.forename: J Benjamin
authors.initials: JB
authors.lastname: Stielow
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Hui
authors.initials: H
authors.lastname: Sun
authors.affiliation: Agricultural Research Service, National Center for Agricultural Utilization Research, US Department of Agriculture, Peoria, IL 61604;
authors.forename: Cletus P
authors.initials: CP
authors.lastname: Kurtzman
authors.affiliation: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208.
authors.forename: Meredith
authors.initials: M
authors.lastname: Blackwell
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; IVGrigoriev@lbl.gov twjeffri@wisc.edu.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706; IVGrigoriev@lbl.gov twjeffri@wisc.edu.
authors.forename: Thomas W
authors.identifier: 0000-0001-7408-4065
authors.initials: TW
authors.lastname: Jeffries
mesh_terms: D001203:Ascomycota / Q000145:classification / Q000235:genetics / Q000378:metabolism; D001709:Biotechnology / Q000379:methods*; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D005815:Genetic Code / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D010802:Phylogeny; D013045:Species Specificity; D015003:Yeasts / Q000145:classification / Q000235:genetics* / Q000378:metabolism
chemical_list: D005656:Fungal Proteins
keywords: bioenergy; biotechnological yeasts; genetic code; genomics; microbiology