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. 2016 Aug 30;113(35):9882-7.
doi: 10.1073/pnas.1603941113. Epub 2016 Aug 17.

Comparative genomics of biotechnologically important yeasts

Robert Riley  1 , Sajeet Haridas  1 , Kenneth H Wolfe  2 , Mariana R Lopes  3 , Chris Todd Hittinger  4 , Markus Göker  5 , Asaf A Salamov  1 , Jennifer H Wisecaver  6 , Tanya M Long  7 , Christopher H Calvey  8 , Andrea L Aerts  1 , Kerrie W Barry  1 , Cindy Choi  1 , Alicia Clum  1 , Aisling Y Coughlan  2 , Shweta Deshpande  1 , Alexander P Douglass  2 , Sara J Hanson  2 , Hans-Peter Klenk  9 , Kurt M LaButti  1 , Alla Lapidus  1 , Erika A Lindquist  1 , Anna M Lipzen  1 , Jan P Meier-Kolthoff  5 , Robin A Ohm  1 , Robert P Otillar  1 , Jasmyn L Pangilinan  1 , Yi Peng  1 , Antonis Rokas  6 , Carlos A Rosa  10 , Carmen Scheuner  5 , Andriy A Sibirny  11 , Jason C Slot  12 , J Benjamin Stielow  13 , Hui Sun  1 , Cletus P Kurtzman  14 , Meredith Blackwell  15 , Igor V Grigoriev  16 , Thomas W Jeffries  17
Affiliations

Comparative genomics of biotechnologically important yeasts

Robert Riley et al. Proc Natl Acad Sci U S A. .

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.

Keywords: bioenergy; biotechnological yeasts; genetic code; genomics; microbiology.

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Conflict of interest statement

C.H.C. and T.W.J. are employees of Xylome Corporation, which is developing nonconventional yeasts for biotechnological applications.

Figures

Fig. 1.
Fig. 1.
Phylogenetic tree inferred from the MARE-filtered supermatrix (364,126 aligned amino acid residues) using maximum likelihood (ML) and rooted with Batrachochytrium. Organisms sequenced in this study are shown in bold. Numbers on the branches indicate ML and maximum parsimony (MP) bootstrap support values for the MARE-filtered (red), full (blue), and core genes (green) supermatrices. Values less than 60% are shown as dashes; dots indicate branches with maximum support under all settings.
Fig. 2.
Fig. 2.
CUG-Ala genetic code inferred from amino acids aligned to yeast CUG codons based on 700 orthologous groups of orthologous proteins. Blue-shaded boxes indicate the number of CUG-encoded amino acid positions in the ortholog set. Green-shaded boxes indicate the fraction of each organism’s CUG-encoded positions aligned to each amino acid.
Fig. 3.
Fig. 3.
Distribution of metabolic traits and their genes. For d-xylose, galactose, methanol, and l-rhamnose, numbered boxes indicate the numbers of predicted pathway genes. Genes for d-xylose, galactose, methanol, and l-rhamnose metabolism were identified by homology to characterized sequences (Materials and Methods).
See this image and copyright information in PMC

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