SPODOBASE: an EST database for the lepidopteran crop pest Spodoptera

• Published in: BMC bioinformatics Vol. 7; no. 1; p. 322
• Main Authors: Nègre, Vincent, Hôtelier, Thierry, Volkoff, Anne-Nathalie, Gimenez, Sylvie, Cousserans, François, Mita, Kazuei, Sabau, Xavier, Rocher, Janick, López-Ferber, Miguel, d'Alençon, Emmanuelle, Audant, Pascaline, Sabourault, Cécile, Bidegainberry, Vincent, Hilliou, Frédérique, Fournier, Philippe
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 23.06.2006; BioMed Central; BMC
• Subjects: Animals; Biochemistry, Molecular Biology; Bombyx mori; Cluster Analysis; Computational Biology - methods; Contig Mapping; Databases, Genetic; DNA, Complementary - metabolism; Expressed Sequence Tags; Gene Library; Lepidoptera; Life Sciences; Molecular Sequence Data; Sequence Alignment; Sequence Analysis, DNA; Software; Spodoptera - genetics; Spodoptera frugiperda; Tissue Distribution
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/1471-2105-7-322

The Lepidoptera Spodoptera frugiperda is a pest which causes widespread economic damage on a variety of crop plants. It is also well known through its famous Sf9 cell line which is used for numerous heterologous protein productions. Species of the Spodoptera genus are used as model for pesticide resistance and to study virus host interactions. A genomic approach is now a critical step for further new developments in biology and pathology of these insects, and the results of ESTs sequencing efforts need to be structured into databases providing an integrated set of tools and informations. The ESTs from five independent cDNA libraries, prepared from three different S. frugiperda tissues (hemocytes, midgut and fat body) and from the Sf9 cell line, are deposited in the database. These tissues were chosen because of their importance in biological processes such as immune response, development and plant/insect interaction. So far, the SPODOBASE contains 29,325 ESTs, which are cleaned and clustered into non-redundant sets (2294 clusters and 6103 singletons). The SPODOBASE is constructed in such a way that other ESTs from S. frugiperda or other species may be added. User can retrieve information using text searches, pre-formatted queries, query assistant or blast searches. Annotation is provided against NCBI, UNIPROT or Bombyx mori ESTs databases, and with GO-Slim vocabulary. The SPODOBASE database provides integrated access to expressed sequence tags (EST) from the lepidopteran insect Spodoptera frugiperda. It is a publicly available structured database with insect pest sequences which will allow identification of a number of genes and comprehensive cloning of gene families of interest for scientific community. SPODOBASE is available from URL: http://bioweb.ensam.inra.fr/spodobase.