Section: Application Domains

Function and history of yeast genomes

Yeasts provide an ideal subject matter for the study of eukaryotic microorganisms. From an experimental standpoint, the yeast Saccharomyces cerevisiae is a model organism amenable to laboratory use and very widely exploited, resulting in an astonishing array of experimental results. From a genomic standpoint, yeasts from the hemiascomycete class provide a unique tool for studying eukaryotic genome evolution on a large scale. With their relatively small and compact genomes, yeasts offer a unique opportunity to explore eukaryotic genome evolution by comparative analysis of several species.

• Yeasts are widely used as cell factories, for the production of beer, wine and bread and more recently of various metabolic products such as vitamins, ethanol, citric acid, lipids, etc.

• Yeasts can assimilate hydrocarbons (genera Candida, Yarrowia and Debaryomyces), depolymerise tannin extracts (Zygosaccharomyces rouxii) and produce hormones and vaccines in industrial quantities through heterologous gene expression.

• Several yeast species are pathogenic for humans, especially Candida albicans, Candida glabrata, Candida tropicalis and the Basidiomycete Cryptococcus neoformans.

The hemiascomycetous yeasts represent a homogeneous phylogenetic group of eukaryotes with a relatively large diversity at the physiological and ecological levels. Comparative genomic studies within this group have proved very informative [33] , [48] , [47] , [35] , [50] , [30] , [31] , [6] .

Magnome applies its methods for comparative genomics and knowledge engineering to the yeasts through the ten-year old Génolevures program (GDR 2354 CNRS), devoted to large-scale comparisons of yeast genomes with the aim of addressing basic questions of molecular evolution. We developed the software tools used by the CNRS's genolevures.org web site. For example, Magnome 's Magus system for simultaneous genome annotation combines semi-supervised classification and rule-based inference in a collaborative web-based system that explicitly uses comparative genomics to simultaneously analyse groups of related genomes.