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Genomic and Functional Diversity of Yeasts

Cécile Neuvéglise

DivY

 Genomic and functional diversity of Yeasts

Team leader:  Cécile Neuvéglise

Research Projects / Thematics

The aim of DivY is to use comparative genomics to i) characterize genome diversity and to deduce the main mechanisms involved in yeast evolution, ii) to understand yeast metabolism with two applications: lipid metabolism and mRNA metabolism, and iii) to characterize the diversity of yeast and their relationships in different environments: grape musts, cheese and insect larvae.

Functional and evolutionary genomics

  • Reconstruction of ancestral chromosome architecture and gene repertoires in the genus Lachancea

We used the Lachancea clade as a model to develop tools for genome sequencing, gene annotation (structural and functional), comparative genomics and to make available our data (GRYC). We sequenced and annotated the whole genome of 9 species and reannotated those of 3 reference strains. Comparison of genome organization revealed unusual chromosomal rearrangements such as the migration of the rDNA cluster or the separation of the silenced mating-type cassettes. Together with the team of Gilles Fischer we were able to reconstruct the chromosomal architecture of the ancestors at each evolutionary node with their gene repertoires, and to deduce the main evolutionary mechanisms including the impact of transposable elements on chromosome modeling.

  • Reconstruction of the evolutionary scenario of genes involved in the lipid metabolism

We investigate species of the Yarrowia clade by comparative physiology, genomics and transcriptomics to understand the evolution of the lipid metabolism and the evolutionary events that led to the current organization of their genomes. It appears that several gene families have undergone expansions or contractions, but the common ancestor already had one member of each gene family, suggesting that it was probably also an oleaginous yeast.

  • mRNA metabolism

In contrast to most Saccharomycotina species, Y. lipolytica still possesses a lot of spliceosomal introns. We thus decided to study the evolution of the mRNA metabolism, especially the non-sense mediated mRNA decay (NMD) pathway, which targets mRNA with premature termination codons usually generated by intron retention or alternative splicing. In link with the NMD, we showed that the exon-junction complex that is deposited on mRNA after splicing, and which has been lost in Saccharomyces cerevisiae, still exists in basal species of the Saccharomycotina tree and is functional in Y. lipolytica.

Alternative models to study yeast lipid metabolism

We look for species, which in contrast to Y. lipolytica, are able to grow on a large spectrum of sugars for the production of lipids from alternative industrial substrates. After revision of their taxonomy, it appears that wild strains of Blastobotrys adeninivorans and B. raffinosifermentans, known as biotechnological yeasts, have the capacity to synthesize and store lipids up to 30% of their cell dry weight from various sugars. We are using comparative genomics and genetic tools to modify their genomes and to reorientate their metabolisms for an increased lipid production.

Diversity of yeasts in various environments

To move forward on the topic of biodiversity and evolution of yeast, we decided to characterize the diversity of yeast and their relationships in different environments.

In collaboration with the INRA ADEL team, we study the bacteria and yeast content of grape musts. We are focusing on four Hanseniaspora species, which are frequently isolated in vineyards and whose genetic relationships had to be clarified. MLST analyses and genome sequencing approaches are in progress to validate species delineation and characterize genetic exchanges between species, such as introgressions and horizontal gene transfers, which may give them selective advantages and contribute to their adaptive evolution.

We also investigate insect-associated yeasts, which contribute to the assimilation of complex compounds such as xylan in the insect gut. Our insect harvests allowed us to identify multiple new species, some of which with interesting enzymatic activities.

Finally, through the MetaPDOcheese project, we investigate the factors shaping the microbial communities in traditional cheeses.

Publications

Team members

DivY team

Fundings

INRA
ANR
toulouse-white-biotechnology
APT

See also

GRYC, a website dedicated to yeast genomes