Génolevures is a large-scale comparative genomics project between Saccharomyces cerevisiae and other yeast species representative of the various branches of the Hemiascomycetous class. We sequence and manually curate both complete genomes and random genomic libraries.

Génolevures addresses basic questions concerning molecular evolution: species-specific and class-specific genes, distribution of genes among functional families, rate of divergence, mechanisms of chromosome shuffling. With their relative small genome size, yeasts offer a unique opportunity for exploring eukaryotic genome evolution by comparative analysis of several species.

The method used to annotate the complete genomes of Génolevures is based on automatic prediction, BLAST results on Saccharomyces cerevisiae and manual curation. The method used to annotate the RSTs of Génolevures is mainly based on BLAST results on Saccharomyces cerevisiae.

Reference:

• Dujon B et al., Nature 430(6995):35-44, 2004
• FEBS Letters Special Issue, 487(1), 2000

Genome annotation was carried out by using the CAAT-Box system [Frangeul L et al., Bioinformatics 20(5):790-797, 2004].
Automatic predictions were manually curated and each open reading frame (ORF) was classified as coding (CDS), non-coding (false ORF) or pseudogene according to Génolevures annotation standards.The codon usage matrix used to screen for ORFs was trained on a sample of coding and non-coding sequences, initially produced by automatic identification and subsequently using curated CDS. Annotation was performed iteratively across successive sequence assemblies (each file is conserved if no sequence edition occurs; it is replaced otherwise).
In a final stage, 291 small ORFs missed by the automatic procedures were identified with the help of the protein family classification (each protein of incomplete families was used as a tBLASTn query against all remaining intergenic sequences).
Introns were identified from consensus splice sites and branch points and from comparisons to S. cerevisiae.
Genes encoding tRNA molecules were identified.
All other non-coding RNA molecules, rRNAs, transposons, centromeres and telomeric repeats were identified by sequence comparisons and manual curation.

High quality sequencing, high coverage and manual finishing allowed us to obtain an exhaustive catalog of chromosomal elements. Table 1 of the Nature article (2004):



For more information, see Dujon B et al., Nature 430(6995):35-44, 2004

The method, called nine-SONS, for detection of ortholog genes is based on the search for syntenic homologs from the protein families across nine yeast species (contact P. Baret for details). In case of ambiguity due to tandem gene duplication, the message "unresolved orthology due to tandem or other duplication in syntenic block" is shown. If a protoploid species (which ancestor has not undergone Whole Genome Duplication) contains more than 2 homologs from the same protein family, a warning message "strict determination not possible; homologs must be refined manually" is issued in place of the ortholog list. The 9 species used in this method are Saccharomyces cerevisiae, Candida glabrata, Zygosaccharomyces rouxii, Kluyveromyces thermotolerans, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii, Yarrowia lipolytica.