Comparative genomics of biotechnologically important yeasts

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...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 113; no. 35; pp. 9882 - 9887
Main Authors 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.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 30.08.2016
Proceedings of the National Academy of Sciences
Subjects
Ascomycetes
Ascomycota - classification
Ascomycota - genetics
Ascomycota - metabolism
BASIC BIOLOGICAL SCIENCES
bioenergy
bioengineering
Biological Sciences
biotechnological yeasts
Biotechnology
Biotechnology - methods
Evolution, Molecular
Fungal Proteins - genetics
Fungal Proteins - metabolism
genetic code
Genetic Code - genetics
Genome, Fungal - genetics
Genomics
Genomics - methods
Heterochromatin
loci
Metabolic Networks and Pathways - genetics
microbiology
multigene family
Pachysolen tannophilus
Phylogenetics
Phylogeny
rhamnose
sequence analysis
Species Specificity
xylose
Yeast
Yeasts
Yeasts - classification
Yeasts - genetics
Yeasts - metabolism
bioenergy
microbiology
genomics
biotechnological yeasts
genetic code
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Summary: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.
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AC02-05CH11231; FC02-07ER64494
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Author contributions: A.L., C.P.K., M.B., I.V.G., and T.W.J. designed research; T.M.L., C.H.C., C.C., A.Y.C., S.D., S.J.H., H.-P.K., Y.P., A.A. Sibirny, J.B.S., C.P.K., and T.W.J. performed research; C.H.C. contributed new reagents/analytic tools; R.R., S.H., K.H.W., M.R.L., C.T.H., M.G., A.A. Salamov, J.H.W., A.L.A., K.W.B., A.C., A.P.D., K.M.L., A.L., E.A.L., A.M.L., J.P.M.-K., R.A.O., R.P.O., J.L.P., A.R., C.A.R., C.S., J.C.S., H.S., C.P.K., I.V.G., and T.W.J. analyzed data; R.R., S.H., K.H.W., C.T.H., M.G., C.P.K., M.B., I.V.G., and T.W.J. wrote the paper; and K.W.B., C.P.K., M.B., I.V.G., and T.W.J. coordinated the project.
2Present address: Microbiology, Department of Biology, Utrecht University, 3508, Utrecht, The Netherlands.
1Present address: Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg 199004, Russia.
Edited by Chris R. Somerville, University of California, Berkeley, CA, and approved July 11, 2016 (received for review March 10, 2016)
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1603941113