Comparative genomics of biotechnologically important yeasts.

التفاصيل البيبلوغرافية
العنوان:	Comparative genomics of biotechnologically important yeasts.
المؤلفون:	Riley R; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Haridas S; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Wolfe KH; University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;, Lopes MR; 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;, Hittinger CT; 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;, Göker M; Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany;, Salamov AA; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Wisecaver JH; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235;, Long TM; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706; US Department of Agriculture Forest Products Laboratory, Madison, WI 53726;, Calvey CH; Xylome Corporation, Madison, WI 53719;, Aerts AL; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Barry KW; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Choi C; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Clum A; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Coughlan AY; University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;, Deshpande S; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Douglass AP; University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;, Hanson SJ; University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin 4, Ireland;, Klenk HP; 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;, LaButti KM; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Lapidus A; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Lindquist EA; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Lipzen AM; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Meier-Kolthoff JP; Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany;, Ohm RA; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Otillar RP; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Pangilinan JL; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Peng Y; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Rokas A; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235;, Rosa CA; Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil;, Scheuner C; Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, 38124 Braunschweig, Germany;, Sibirny AA; 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;, Slot JC; Department of Plant Pathology, Ohio State University, Columbus, OH 43210;, Stielow JB; 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;, Sun H; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;, Kurtzman CP; Agricultural Research Service, National Center for Agricultural Utilization Research, US Department of Agriculture, Peoria, IL 61604;, Blackwell M; Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803; Department of Biological Sciences, University of South Carolina, Columbia, SC 29208., Grigoriev IV; Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; IVGrigoriev@lbl.gov twjeffri@wisc.edu., Jeffries TW; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706; IVGrigoriev@lbl.gov twjeffri@wisc.edu.
المصدر:	Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2016 Aug 30; Vol. 113 (35), pp. 9882-7. Date of Electronic Publication: 2016 Aug 17.
نوع المنشور:	Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة:	English
بيانات الدورية:	Publisher: National Academy of Sciences Country of Publication: United States NLM ID: 7505876 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1091-6490 (Electronic) Linking ISSN: 00278424 NLM ISO Abbreviation: Proc Natl Acad Sci U S A Subsets: MEDLINE
أسماء مطبوعة:	Original Publication: Washington, DC : National Academy of Sciences
مواضيع طبية MeSH:	Biotechnology/methods , Genome, Fungal/genetics , Genomics/methods , Yeasts/genetics, Ascomycota/classification ; Ascomycota/genetics ; Ascomycota/metabolism ; Evolution, Molecular ; Fungal Proteins/genetics ; Fungal Proteins/metabolism ; Genetic Code/genetics ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Species Specificity ; Yeasts/classification ; Yeasts/metabolism
مستخلص:	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. Competing Interests: C.H.C. and T.W.J. are employees of Xylome Corporation, which is developing nonconventional yeasts for biotechnological applications.
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معلومات مُعتمدة:	United Kingdom WT_ Wellcome Trust
فهرسة مساهمة:	Keywords: bioenergy; biotechnological yeasts; genetic code; genomics; microbiology
سلسلة جزيئية:	GENBANK AECK00000000; AEHA00000000; AEUO00000000; LSGR00000000; LSKT00000000; LTAD00000000; LWKO00000000; LWUN00000000; LWUO00000000; LXPB00000000; LXPE00000000; LXTC00000000; LYBQ00000000; LYBR00000000; LYME00000000; LZCH00000000
المشرفين على المادة:	0 (Fungal Proteins)
تواريخ الأحداث:	Date Created: 20160819 Date Completed: 20180326 Latest Revision: 20230726
رمز التحديث:	20240628
مُعرف محوري في PubMed:	PMC5024638
DOI:	10.1073/pnas.1603941113
PMID:	27535936
قاعدة البيانات:	MEDLINE

الوصف
تدمد:	1091-6490
DOI:	10.1073/pnas.1603941113