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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #325677

Research Project: Genomic Analyses and Management of Agricultural and Industrial Microbial Genetic Resources and Associated Information

Location: Mycotoxin Prevention and Applied Microbiology Research

Title: Comparative genomics of biotechnologically important yeasts

Author
item RILEY, ROBERT - Department Of Energy Joint Genome
item HARIDAS, SAJEET - Department Of Energy Joint Genome
item WOLFE, KENNETH - University College Dublin
item LOPES, MARIANA - University Of Wisconsin
item HITTINGER, CHRIS - University Of Wisconsin
item GOKER, MARKUS - Leibniz Institute
item SALAMOV, ASAF - Department Of Energy Joint Genome
item WISECAVER, JEN - Vanderbilt University
item LONG, TANYA - University Of Wisconsin
item Kurtzman, Cletus

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/11/2016
Publication Date: 8/30/2016
Publication URL: http://handle.nal.usda.gov/10113/5695398
Citation: Riley, R., Haridas, S., Wolfe, K.H., Lopes, M.R., Hittinger, C.T., Goker, M., Salamov, A.A., Wisecaver, J.H., Long, T.M., Kurtzman, C.P., et al. 2016. Comparative genomics of biotechnologically important yeasts. Proceedings of the National Academy of Sciences. 113(35):9882-9887.

Interpretive Summary: Yeasts are commonly identified from DNA “barcode” sequences, but these sequences are usually too short to determine relationships among species. In an effort to understand if unique metabolic properties of biotechnologically important yeasts are found only among closely related species, the genomes of 16 yeasts of biotechnological and taxonomic importance were sequenced and analyzed. Certain unique properties, such as ability to grow on methanol, are found only among closely related species. These data demonstrate that genome sequences can be used to predict metabolic properties among species, which will allow selection of yeasts to address specific problems in biotechnology and agriculture.

Technical 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.