Comparative genomics of biotechnologically important yeasts
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- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598,
- University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland,
- 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,
- 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,
- Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany,
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235,
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706,, US Department of Agriculture Forest Products Laboratory, Madison, WI 53726,
- Xylome Corporation, Madison, WI 53719,
- 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,
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil,
- 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,
- Department of Plant Pathology, Ohio State University, Columbus, OH 43210,
- 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,
- Agricultural Research Service, National Center for Agricultural Utilization Research, US Department of Agriculture, Peoria, IL 61604,
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803,, Department of Biological Sciences, University of South Carolina, Columbia, SC 29208
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706,
Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here in this paper, 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. In conclusion, these data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.
- Research Organization:
- Univ. of Wisconsin, Madison, WI (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- Grant/Contract Number:
- AC02-05CH11231; FC02-07ER64494
- OSTI ID:
- 1298331
- Alternate ID(s):
- OSTI ID: 1469564
- Journal Information:
- Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Vol. 113 Journal Issue: 35; ISSN 0027-8424
- Publisher:
- Proceedings of the National Academy of SciencesCopyright Statement
- Country of Publication:
- United States
- Language:
- English
Web of Science
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