Genomic sequencing reveals four major yeast clades of biotechnological interest

One yeast, Saccharomyces cerevisiae, is used in the vast majority of the world’s bioprocesses. Its economic significance is unchallenged. S. cerevisiae, however, represents only a small slice of yeast physiological diversity. Many other yeasts, are used in lesser known, but commercially important processes that take advantage of their unique physiological and biochemical properties. Through a project conducted with the DOE Joint Genome Laboratory (JGI), we sequenced, annotated and compared 18 new yeast genomes to 11 previously sequenced yeasts, and 9 other fungi belonging to the filamentous ascomyces, basidiomyces, and other more distant fungi. Whole genome alignment of these 38 fungi revealed four distinct clades of ascomycetous yeasts and confirmed the monophyletic nature of the Taphrinomycotina. Native capacities for fermenting xylose and cellobiose were confined almost entirely to the CUG yeast clade. Highly lipogenic yeasts were found in the Dipodascascacae, and the methylotrophic yeasts clearly exhibited higher capacities for respiration.  The Saccharomycetaceae, some of which were clearly adapted for fermentative metabolism, were in a distinct but heterogeneous clade. Highly divergent yeast species showed marked losses of many enzymatic activities, which apparently occurred during their evolutionary speciation. Publication of these genomes has opened up many new yeasts to genetic and economic development.