GreenPhyl : Phylogenomic resources for comparative and functional genomics

Conte Matthieu, Perin Christophe, Laporte Marie-Angélique, Droc Gaëtan, Aluome Christelle, Guignon Valentin, Lanau Nadège, Sempere Guilhem, Rouard Mathieu. 2010. GreenPhyl : Phylogenomic resources for comparative and functional genomics. In : Final program and abstracts of the 2nd International Symposium on Genomics of Plant Genetic Resources, Bologna, Italy, 24-27 April 2010. Rome : Bioversity International, Résumé, 103. International Symposium on Genomics of Plant Genetic Resources. 2, Bologne, Italie, 24 Avril 2010/27 Avril 2010.

Résumé : With the increasing number of plant genomes being sequenced, a major objective is to transfer accurate annotation from characterized sequences to uncharacterized sequences. GreenPhyl (Conte et al., 2008, Nucleic Acid Research, 36: D991-8) is a tool for plant comparative genomics that predicts the function of genes based on their evolutionary relationship with genes of known function. The database (version 2) comprises protein sequences of 16 plant species fully sequenced including socio-economically important crops like rice, sorghum and maize that were grouped into gene families using similarity-based methods. GreenPhyl contains approximately 13,000 gene families being annotated, computational analyzes and external cross-references (InterPro, KEGG, Swiss-Prot, Pubmed) related to all gene members. Once manually annotated (i.e. properly named and classified), gene families are finally processed by phylogenetic analyses to distinguish orthologous and paralogous gene. Orthologous genes descend from the last common ancestor through speciation and most probably encode proteins with a similar function in different species. In addition, the website offers a range of user-friendly tools to query the data. These resources will be particularly helpful to molecular biologist for gene discovery and gene function inference. We believe that a better understanding of genome evolution will contribute to elucidate the genetic basis of important agronomic traits and therefore facilitate ongoing plant breeding efforts.(Texte intégral)

Classification Agris : F30 - Génétique et amélioration des plantes

Auteurs et affiliations

• Conte Matthieu, Bioversity International (FRA)
• Perin Christophe, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0002-2469-310X
• Laporte Marie-Angélique, Bioversity International (FRA)
• Droc Gaëtan, CIRAD-BIOS-UMR DAP (FRA) ORCID: 0000-0003-1849-1269
• Aluome Christelle, Bioversity International (FRA)
• Guignon Valentin, Bioversity International (FRA)
• Lanau Nadège, CIRAD-BIOS-UMR DAP (FRA)
• Sempere Guilhem ORCID: 0000-0001-7429-2091
• Rouard Mathieu, Bioversity International (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/558717/)

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