Apport de la synténie pour l'identification des orthologues chez les levures : méthodologie et application à l'étude de l'évolution des transporteurs
(2012)
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- Authors
- Supervisors
- Baret, Philippe
- Abstract
- (en) 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).
- Affiliations
Citations
Seret, M.-L. (2012). Apport de la synténie pour l’identification des orthologues chez les levures : méthodologie et application à l’étude de l’évolution des transporteurs. https://hdl.handle.net/2078.5/160905