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Comparative genomics of biotechnologically important yeasts

Journal Article · · Proceedings of the National Academy of Sciences of the United States of America
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  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 Bacteriology, University of Wisconsin–Madison, Madison, WI 53706,
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Significance

The highly diverse Ascomycete yeasts have enormous biotechnological potential. Collectively, these yeasts convert a broad range of substrates into useful compounds, such as ethanol, lipids, and vitamins, and can grow in extremes of temperature, salinity, and pH. We compared 29 yeast genomes with the goal of correlating genetics to useful traits. In one rare species, we discovered a genetic code that translates CUG codons to alanine rather than canonical leucine. Genome comparison enabled correlation of genes to useful metabolic properties and showed the synteny of the mating-type locus to be conserved over a billion years of evolution. Our study provides a roadmap for future biotechnological exploitations.

Research Organization:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Organization:
USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
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 Journal Issue: 35 Vol. 113; ISSN 0027-8424
Publisher:
Proceedings of the National Academy of SciencesCopyright Statement
Country of Publication:
United States
Language:
English

References (44)

Transformation of a glucose negative mutant ofPachysolen tannophilus with a plasmid carrying the cloned hexokinase PII gene fromSaccharomyces cerevisiae journal September 1989
Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts journal March 2004
Lipid production from Yarrowia lipolytica Po1g grown in sugarcane bagasse hydrolysate journal October 2011
The genetic code of the fungal CTG clade journal August 2011
Genomics and the making of yeast biodiversity journal December 2015
Characterisation of the gene cluster for l-rhamnose catabolism in the yeast Scheffersomyces (Pichia) stipitis journal January 2012
New insights into galactose metabolism by Schizosaccharomyces pombe: Isolation and characterization of a galactose-assimilating mutant journal February 2011
The supermatrix approach to systematics journal January 2007
The codon CUG is read as serine in an asporogenic yeast Candida cylindracea journal September 1989
Ribosome-mediated incorporation of a non-standard amino acid into a peptide through expansion of the genetic code journal April 1992
Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis journal March 2007
Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts journal July 2014
Yeast evolutionary genomics journal July 2010
The non‐standard genetic code of Candida spp.: an evolving genetic code or a novel mechanism for adaptation? journal October 1997
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts journal September 2004
High-quality draft assemblies of mammalian genomes from massively parallel sequence data journal December 2010
Comparative genomics of xylose-fermenting fungi for enhanced biofuel production journal July 2011
Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locus Saccharomyces cerevisiae system journal October 2014
Temperature and host preferences drive the diversification of Saccharomyces and other yeasts: a survey and the discovery of eight new yeast species journal March 2015
Clade- and species-specific features of genome evolution in the Saccharomycetaceae journal June 2015
Molecular Phylogeny of Sequenced Saccharomycetes Reveals Polyphyly of the Alternative Yeast Codon Usage journal July 2014
Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples journal October 2009
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence journal March 1997
An efficient algorithm for large-scale detection of protein families journal April 2002
Enzyme-specific profiles for genome annotation: PRIAM journal November 2003
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension journal May 2011
MycoCosm portal: gearing up for 1000 fungal genomes journal December 2013
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs journal February 2008
A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes journal May 2016
Relationships among genera of the Saccharomycotina ( Ascomycota ) from multigene phylogenetic analysis of type species journal February 2013
Emerging applications of the methylotrophic yeasts journal December 1990
Activating and Elucidating Metabolism of Complex Sugars in Yarrowia lipolytica journal December 2015
Endogenous Xylose Pathway in Saccharomyces cerevisiae journal June 2004
Reinventing Heterochromatin in Budding Yeasts: Sir2 and the Origin Recognition Complex Take Center Stage journal July 2011
A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cerevisiae. journal January 1987
The Genome Sequence of Methanohalophilus mahii SLP T Reveals Differences in the Energy Metabolism among Members of the Methanosarcinaceae Inhabiting Freshwater and Saline Environments journal January 2010
A molecular timescale of eukaryote evolution and the rise of complex multicellular life journal January 2004
Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae journal January 2014
Inversion of the Chromosomal Region between Two Mating Type Loci Switches the Mating Type in Hansenula polymorpha journal November 2014
The Evolution of Fungal Metabolic Pathways journal December 2014
Codivergence of Mycoviruses with Their Hosts journal July 2011
Multilocus Phylogenetic Study of the Scheffersomyces Yeast Clade and Characterization of the N-Terminal Region of Xylose Reductase Gene journal June 2012
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology journal November 2012
The Reacquisition of Biotin Prototrophy in Saccharomyces cerevisiae Involved Horizontal Gene Transfer, Gene Duplication and Gene Clustering journal December 2007

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
bioenergy
biotechnological yeasts
genetic code
genomics
microbiology