From AphidBase and Lepido-DB to an Information System for Insect Plant pest genomics studies.

Abstract : Genome annotation includes any features mapped on the genome, including protein coding genes and their multiples mRNA, pseudogenes, transposons and repeats, non-coding RNAs, SNPs, or similarities to other genomes. While many of these features can be automatically locally predicted by sophisticated software packages based on sequence or structure comparisons, setting up centralized a boinformatic warehouse is crucial to organize, display, and distribute all these data, and facilitates their handling by non skilled bio-analyst. It also provides the opportunity to unite a broad community for curating gene models and gathering manual and functional annotations, which is an essential step to attain a basal data quality. AphidBase (http://www.aphidbase.org) is a comprehensive information system dedicated to aphids. It has been set up to safely centralize, manage, mine, disseminate and promulgate data generated by International Aphid Genomics Consortium (IAGC). It allowed an international community dispersed at many sites to produce a robust and comprehensive annotation of the pea aphid genome. Lepido-DB (http://www.inra.fr/lepidodb) is a centralized bioinformatic resource that was first developed to facilitate the comparative genomics of two major lepidopteran pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, by the analyzis of syntenic relationships and genome rearrangements of 15 pairs of BACs sequences and their corresponding colinear regions extracted from 10 Bombyx mori chromosomes. These systems were constructed using open source software tools from the Generic Model Organism Database (GMOD, http://www.gmod.org) including several Chado instances and genome browsers (Gbrowse and Cmap), gene and protein reports, Apollo, an application for the manual curation, and various other tools such as a a blast search and a full text search facilities. At a a larger scope, ensuing the AphidBase and LepidoDB experience, this system will be extended to definitely support complete genomes sequencing or resequencing, annotation projects, or any other project based on deep sequencing strategies (expression profiling by RNA-Seq, variability studies, ChIP-Seq, ...) for various Insect pest species. And, to ensure that all these resources were fully exploited by the community, this expansion would be accompanied by gathering many new biological data such as phenotypes, ontologies and atlas.
Type de document :
Communication dans un congrès
1st Workshop on Information System for Insect Pest, Nov 2009, Rennes, France. 2009
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https://hal.inria.fr/inria-00435823
Contributeur : Fabrice Legeai <>
Soumis le : mardi 24 novembre 2009 - 18:43:38
Dernière modification le : mercredi 16 mai 2018 - 11:23:28

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  • HAL Id : inria-00435823, version 1

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Fabrice Legeai, Jean-Pierre Gauthier, François Cousserans, Emmanuelle D'Alençon, Olivier Collin, et al.. From AphidBase and Lepido-DB to an Information System for Insect Plant pest genomics studies.. 1st Workshop on Information System for Insect Pest, Nov 2009, Rennes, France. 2009. 〈inria-00435823〉

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