Abstract
BackgroundThe 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.DescriptionThe 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.ConclusionThe 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:
Highlights
The Lepidoptera Spodoptera frugiperda is a pest which causes widespread economic damage on a variety of crop plants
For example,S. frugiperda is well known through its famous Sf21 cell line and its Sf9 subclone [3] which is used for numerous heterologous protein productions
2-5- GO assignment of the Expressed Sequence Tags (ESTs) sequences in the SPODOBASE To define the function of the contigs and singletons present in the SPODOBASE, we used the Gene Ontology (GO) controlled vocabulary [34], and more GOSlim, a subset of GO terms, which provides a higher level of annotations and allows a more global view of the dataset
Summary
The SPODOBASE represent a major contribution to the genomics of Spodoptera frugiperda. Together with BAC library, existence of various cell lines and expression systems, this makes of S. frugiperda of the most advanced models among agricultural pests in terms of genomic resources. SPODOBASE contains EST sequences that are cleaned, clusterized and annotated. These informations are available to serve insect research community, provide better understanding of the Lepidoptera physiology and identify new molecules targeted against Lepidoptera pests that could be used as safe biopesticides for sustainable agriculture. They have been deposited in dbEST database (accession numbers for midgut library: DV075863 to DV080045 and DY786624 to DY7927772; fat body library: DY773453 to DY780623; hemocytes: DY773453 to DY780623; Sf9 cell line library: DY895775 to DY901596).
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