title: Genomics and the making of yeast biodiversity.
abstract: Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies.
authors.affiliation: Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: cthittinger@wisc.edu.
authors.forename: Chris Todd
authors.initials: CT
authors.lastname: Hittinger
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
authors.forename: Antonis
authors.initials: A
authors.lastname: Rokas
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Feng-Yan
authors.initials: FY
authors.lastname: Bai
authors.affiliation: State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; Shanghai Key Laboratory of Molecular Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China.
authors.forename: Teun
authors.initials: T
authors.lastname: Boekhout
authors.affiliation: UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
authors.forename: Paula
authors.initials: P
authors.lastname: Gonçalves
authors.affiliation: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Thomas W
authors.initials: TW
authors.lastname: Jeffries
authors.affiliation: Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors.forename: Jacek
authors.initials: J
authors.lastname: Kominek
authors.affiliation: Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada.
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Lachance
authors.affiliation: Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA), UNComahue-CONICET, Bariloche, Argentina.
authors.forename: Diego
authors.initials: D
authors.lastname: Libkind
authors.affiliation: Department of Microbiology, ICB, Federal University of Minas Gerais, C.P. 486, Belo Horizonte, MG 31270-901, Brazil.
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Rosa
authors.affiliation: UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal.
authors.forename: José Paulo
authors.initials: JP
authors.lastname: Sampaio
authors.affiliation: Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL, USA.
authors.forename: Cletus P
authors.initials: CP
authors.lastname: Kurtzman
mesh_terms: D001483:Base Sequence; D044822:Biodiversity; D002176:Candida albicans / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D016681:Genome, Fungal / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D012441:Saccharomyces cerevisiae / Q000235:genetics*