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Title: Comparative genomics of biotechnologically important yeasts

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.
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [4] ;  [5] ;  [1] ;  [6] ;  [7] ; ORCiD logo [8] ;  [1] ;  [1] ;  [1] ;  [1] ;  [2] ;  [1] ;  [2] ;  [2] ;  [9] ;  [1] more »;  [1] ;  [1] ;  [1] ;  [5] ;  [1] ;  [1] ;  [1] ;  [1] ; ORCiD logo [6] ;  [10] ;  [5] ;  [11] ;  [12] ;  [13] ;  [1] ;  [14] ;  [15] ;  [1] ; ORCiD logo [4] « less
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. University College Dublin Conway Institute, School of Medicine, University College Dublin, Dublin (Ireland)
  3. Univ. of Wisconsin, Madison, WI (United States); Universidade Federal de Minas Gerais, Belo Horizonte, MG (Brazil). Departamento de Microbiologia, Instituto de Ciências Biológicas
  4. Univ. of Wisconsin, Madison, WI (United States)
  5. Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, Braunschweig (Germany)
  6. Vanderbilt Univ., Nashville, TN (United States)
  7. Univ. of Wisconsin, Madison, WI (United States); US Department of Agriculture Forest Products Laboratory, Madison, WI (United States)
  8. Xylome Corporation, Madison, WI (United States)
  9. Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, Braunschweig (Germany); Newcastle University (United Kingdom)
  10. Universidade Federal de Minas Gerais, Belo Horizonte, MG (Brazil). Departamento de Microbiologia, Instituto de Ciências Biológicas
  11. National Academy of Sciences of Ukraine, Lviv (Ukraine); University of Rzeszow (Poland)
  12. The Ohio State Univ., Columbus, OH (United States)
  13. Deutsche Sammlung von Mikroorganismen und Zellkulturen German Collection of Microorganisms and Cell Cultures, Leibniz Institute, Braunschweig (Germany); Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre, Royal Netherlands Academy of Arts and Sciences, Utrecht (The Netherlands)
  14. Agricultural Research Service, National Center for Agricultural Utilization Research, US Department of Agriculture, Peoria, IL (United States)
  15. Louisiana State Univ., Baton Rouge, LA (United States); Univ. of South Carolina, Columbia, SC (United States)
Publication Date:
Grant/Contract Number:
AC02-05CH11231; FC02-07ER64494
Type:
Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 113; Journal Issue: 35; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Research Org:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; genomics; bioenergy; biotechnological yeasts; genetic code; microbiology
OSTI Identifier:
1298331
Alternate Identifier(s):
OSTI ID: 1469564

Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H., Lopes, Mariana R., Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A., Wisecaver, Jennifer H., Long, Tanya M., Calvey, Christopher H., Aerts, Andrea L., Barry, Kerrie W., Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y., Deshpande, Shweta, Douglass, Alexander P., Hanson, Sara J., Klenk, Hans-Peter, LaButti, Kurt M., Lapidus, Alla, Lindquist, Erika A., Lipzen, Anna M., Meier-Kolthoff, Jan P., Ohm, Robin A., Otillar, Robert P., Pangilinan, Jasmyn L., Peng, Yi, Rokas, Antonis, Rosa, Carlos A., Scheuner, Carmen, Sibirny, Andriy A., Slot, Jason C., Stielow, J. Benjamin, Sun, Hui, Kurtzman, Cletus P., Blackwell, Meredith, Grigoriev, Igor V., and Jeffries, Thomas W.. Comparative genomics of biotechnologically important yeasts. United States: N. p., Web. doi:10.1073/pnas.1603941113.
Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H., Lopes, Mariana R., Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A., Wisecaver, Jennifer H., Long, Tanya M., Calvey, Christopher H., Aerts, Andrea L., Barry, Kerrie W., Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y., Deshpande, Shweta, Douglass, Alexander P., Hanson, Sara J., Klenk, Hans-Peter, LaButti, Kurt M., Lapidus, Alla, Lindquist, Erika A., Lipzen, Anna M., Meier-Kolthoff, Jan P., Ohm, Robin A., Otillar, Robert P., Pangilinan, Jasmyn L., Peng, Yi, Rokas, Antonis, Rosa, Carlos A., Scheuner, Carmen, Sibirny, Andriy A., Slot, Jason C., Stielow, J. Benjamin, Sun, Hui, Kurtzman, Cletus P., Blackwell, Meredith, Grigoriev, Igor V., & Jeffries, Thomas W.. Comparative genomics of biotechnologically important yeasts. United States. doi:10.1073/pnas.1603941113.
Riley, Robert, Haridas, Sajeet, Wolfe, Kenneth H., Lopes, Mariana R., Hittinger, Chris Todd, Göker, Markus, Salamov, Asaf A., Wisecaver, Jennifer H., Long, Tanya M., Calvey, Christopher H., Aerts, Andrea L., Barry, Kerrie W., Choi, Cindy, Clum, Alicia, Coughlan, Aisling Y., Deshpande, Shweta, Douglass, Alexander P., Hanson, Sara J., Klenk, Hans-Peter, LaButti, Kurt M., Lapidus, Alla, Lindquist, Erika A., Lipzen, Anna M., Meier-Kolthoff, Jan P., Ohm, Robin A., Otillar, Robert P., Pangilinan, Jasmyn L., Peng, Yi, Rokas, Antonis, Rosa, Carlos A., Scheuner, Carmen, Sibirny, Andriy A., Slot, Jason C., Stielow, J. Benjamin, Sun, Hui, Kurtzman, Cletus P., Blackwell, Meredith, Grigoriev, Igor V., and Jeffries, Thomas W.. 2016. "Comparative genomics of biotechnologically important yeasts". United States. doi:10.1073/pnas.1603941113.
@article{osti_1298331,
title = {Comparative genomics of biotechnologically important yeasts},
author = {Riley, Robert and Haridas, Sajeet and Wolfe, Kenneth H. and Lopes, Mariana R. and Hittinger, Chris Todd and Göker, Markus and Salamov, Asaf A. and Wisecaver, Jennifer H. and Long, Tanya M. and Calvey, Christopher H. and Aerts, Andrea L. and Barry, Kerrie W. and Choi, Cindy and Clum, Alicia and Coughlan, Aisling Y. and Deshpande, Shweta and Douglass, Alexander P. and Hanson, Sara J. and Klenk, Hans-Peter and LaButti, Kurt M. and Lapidus, Alla and Lindquist, Erika A. and Lipzen, Anna M. and Meier-Kolthoff, Jan P. and Ohm, Robin A. and Otillar, Robert P. and Pangilinan, Jasmyn L. and Peng, Yi and Rokas, Antonis and Rosa, Carlos A. and Scheuner, Carmen and Sibirny, Andriy A. and Slot, Jason C. and Stielow, J. Benjamin and Sun, Hui and Kurtzman, Cletus P. and Blackwell, Meredith and Grigoriev, Igor V. and Jeffries, Thomas W.},
abstractNote = {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.},
doi = {10.1073/pnas.1603941113},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 35,
volume = 113,
place = {United States},
year = {2016},
month = {8}
}

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