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The genetic code is degenerate allowing for introduction of species specific codon utilization biases. These has been intensively studied but it is not yet clear whether they arise from mutational pressure alone or whether other forces, such as the translational efficiency, also influence it To address this question we took advantage of a unique genetic code alteration that occurred in the fungal Saccharomycotina subphylum, the so called CTG clade, which translate leucine CTG codons as serine due to a novel transfer RNA tRNACAGSer The atypical serine CTG codons are rarely used among the CTG clade species except for Candida cylindracea which uses CTGs at high level, allowing to gain further insight on how they were remodeled after the reassignment event For this, we conducted de novo whole genome sequencing, and annotation of C cylindracea. Alongside, we performed systematic alignment of yeast orthologous genes, phylogenetic reconstruction and codon evolution analysis The results showed that C cylindracea’s genome is different from the other Saccharomycotina genomes and occupies a basal position with respect to the reassignment event. Our findings support the hypothesis that CTG codon reassignment, and not only G+C pressure, exerted a strong influence on serine/leucine codon evolution in yeast. Not Published

The influence of duplicated sequences on chromosomal stability is poorly understood. To characterize chromosomal rearrangements involving duplicated sequences, we compared the organization of tandem repeats of the DUP240 gene family in 15 Saccharomyces cerevisiae strains of various origins. The DUP240 gene family consists of 10 members of unknown function in the reference strain S288C. Five DUP240 paralogs on chromosome I and two on chromosome VII are arranged as tandem repeats that are highly polymorphic in copy number and sequence. We characterized DNA sequences that are likely involved in homologous or nonhomologous recombination events and are responsible for intra- and interchromosomal rearrangements that cause the creation and disappearance of DUP240 paralogs. The tandemly repeated DUP240 genes seem to be privileged sites of gene birth and death.

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.

The identification of molecular evolutionary mechanisms in eukaryotes is approached by a comparative genomics study of a homogeneous group of species classified as Hemiascomycetes. This group includes Saccharomyces cerevisiae, the first eukaryotic genome entirely sequenced, back in 1996. A random sequencing analysis has been performed on 13 different species sharing a small genome size and a low frequency of introns. Detailed information is provided in the 20 following papers. Additional tables available on websites describe the ca. 20 000 newly identified genes. This wealth of data, so far unique among eukaryotes, allowed us to examine the conservation of chromosome maps, to identify the ‘yeast-specific’ genes, and to review the distribution of gene families into functional classes. This project conducted by a network of seven French laboratories has been designated ‘Génolevures’.

Comparative sequence analysis is widely used to infer gene function and study genome evolution and requires proper ortholog identification. We have developed a program for the inference of homology relationships and the identification of positional orthologs between closely related species. The algorithm combines two levels of evidence to determine co-ancestrality at the genome scale: sequence similarity and shared chromosomal neighborhood. The method called IONS (for Identification of Orthologs by Neigborhood and Similarity) was first applied on some transporters family or subfamily, in particular on the Pleiotropic Drug Resistant (PDR) transporters which are involved in the export of antifungals. These small scale tests allowed validating and improving the method. The algorithm was then applied to the complete genomes of nine hemiascomycetous yeasts (about 50,000 genes) studied within the Génolevures Consortium: Saccharomyces cerevisiae, Candida glabrata, Zygosaccharomyces rouxii, Kluyveromyces thermotolerans, Saccharomyces kluyveri, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii and Yarrowia lipolytica. Results were highly consistent with a manually curated database. The main advantages of the method are the automation and the absence of dataset-dependent parameterization, facilitating consistent integration of newly released genomes. The inference of homology relationships were used to study the evolution of gene’s families and for two other goals. First, subsets of positional orthologs were used as anchor points to build syntenic blocks at the genome scale. Second, subsets of homologs were used jointly with the Génolevures’ families to proceed to the propagation of functional annotation based on the hierarchical classification of the Transport Classification database (TCDB) within a total of 5,173 transporters from ten yeasts (the nine mentioned above plus Arxula adeninivorans). L’analyse comparative des séquences est largement utilisée pour inférer la fonction des gènes et étudier l’évolution des génomes. Elle requiert l’identification des gènes orthologues. Nous avons développé un programme permettant l’inférence des relations d’homologie et l’identification des orthologues positionnels entre espèces proches d’un point de vue évolutif. L’algorithme combine la similarité de séquence et le partage d’un voisinage chromosomique semblable pour déterminer la co-ancestralité. La méthode a été utilisée en premier lieu sur des familles de protéines de transport, en particulier celle des PDR responsables de résistances multiples aux fongicides. Ces tests à petite échelle ont permis de valider et d’améliorer la méthode. L’algorithme a ensuite été développé et appliqué aux génomes de neuf levures (~50.000 gènes) étudiées au sein du Consortium Génolevures : Saccharomyces cerevisiae, Candida glabrata, Zygosacharomyces rouxii, Kluyveromyces thermotolerans, Saccharomyces kluyveri, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii et Yarrowia lipolytica. Les avantages de la méthode sont son automatisation et l’absence de paramètres dépendant des données, ce qui facilite l’intégration de nouveaux génomes. A côté des études évolutives de familles de gènes, les inférences des relations d’homologie ont été utilisées pour deux finalités différentes. Premièrement, les groupes d’orthologues positionnels ont été utilisés comme point d’ancrage pour la construction de blocs de synténie à l‘échelle des génomes. Deuxièmement, les groupes d’homologues ont été utilisés avec les familles Génolevures pour réaliser la propagation de l’annotation fonctionnelle du système de classification hiérarchique TCDB au sein d’un ensemble de 5173 transporteurs appartenant à dix espèces de levures (les neufs mentionnées plus haut plus Arxul (AGRO 3) -- UCL, 2012