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The generation of sequencing data for the hemiascomycetous yeast random sequence tag project was performed using the procedures established at GENOSCOPE. These procedures include a series of protocols for the sequencing reactions, using infra-red labelled primers, performed on both ends of the plasmid inserts in the same reaction tube, and their analysis on automated DNA sequencers. They also include a package of computer programs aimed at detecting potential assignation errors, selecting good quality sequences and estimating their useful length.

Comparative sequence analysis is widely used to infer gene function and study genome evolution and requires proper ortholog identification across different genomes. We have developed a program for the Identification of Orthologs in one-to-one relationship by Neighborhood and Similarity (IONS) between closely related species. The algorithm combines two levels of evidence to determine co-ancestrality at the genome scale: sequence similarity and shared neighborhood. The method was initially designed to provide anchor points for syntenic blocks within the Génolevures project concerning nine hemiascomycetous yeasts (about 50,000 genes) and is applicable to different input databases. Comparison based on use of a Rand index shows that the results are highly consistent with the pillars of the Yeast Gene Order Browser, a manually curated database. Compared with SYNERGY, another algorithm reporting homology relationships, our method's main advantages are its automation and the absence of dataset-dependent parameters, facilitating consistent integration of newly released genomes.

This paper reports the genomic analysis of strain CBS732 of Zygosaccharomyces rouxii, a homothallic diploid yeast. We explored the sequences of 4934 random sequencing tags of about 1 kb in size and compared them to the Saccharomyces cerevisiae gene products. Approximately 2250 nuclear genes, 57 tRNAs, the rDNA locus, the endogenous pSR1 plasmid and 15 mitochondrial genes were identified. According to 18S and 25S rRNA cladograms and to synteny analysis, Z. rouxii could be placed among the S. cerevisiae sensu lato yeasts.

This paper reports the genomic analysis of the strain CBS7064 of Pichia sorbitophila, a homothallic diploid yeast. We sequenced 4829 random sequence tags of about 1 kb and compared them to the Saccharomyces cerevisiae gene products. Approximately 1300 nuclear genes, 22 tRNAs, the rDNA locus, and six mitochondrial genes have been identified. The analysis of the rDNA genes has permitted to classify this organism close to the Candida species. Accession numbers from AL414896 to AL419724 at EMBL databank.