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

Comparative genomics of biotechnologically important yeasts.

Author information

1
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
2
University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;
3
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;
4
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;
5
Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany;
6
Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235;
7
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706; US Department of Agriculture Forest Products Laboratory, Madison, WI 53726;
8
Xylome Corporation, Madison, WI 53719;
9
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;
10
Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil;
11
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;
12
Department of Plant Pathology, Ohio State University, Columbus, OH 43210;
13
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;
14
Agricultural Research Service, National Center for Agricultural Utilization Research, US Department of Agriculture, Peoria, IL 61604;
15
Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208.
16
Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; IVGrigoriev@lbl.gov twjeffri@wisc.edu.
17
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706; IVGrigoriev@lbl.gov twjeffri@wisc.edu.

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.

KEYWORDS:

bioenergy; biotechnological yeasts; genetic code; genomics; microbiology

PMID:
27535936
PMCID:
PMC5024638
[Available on 2017-02-28]
DOI:
10.1073/pnas.1603941113
[Indexed for MEDLINE]
Free PMC Article

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