July 7, 2019  |  

Comparative genomics of biotechnologically important yeasts.

Authors: 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

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.

Journal: Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1603941113
Year: 2016

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