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
1Unité Informatique de Centre, INRA-AgroM, 2 place Viala, 34060 Montpellier Cedex 2, France.
BMC Bioinformatics. 2006 Jun 23;7:322. 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.
鳞翅目昆虫草地贪夜蛾是一种对多种农作物造成广泛经济损害的害虫。它还因其著名的Sf9细胞系而广为人知，该细胞系用于大量异源蛋白的生产。草地贪夜蛾属的物种被用作抗药性模型以及研究病毒与宿主相互作用的模型。基因组学方法现在是这些昆虫生物学和病理学进一步新发展的关键步骤，并且EST测序工作的结果需要构建到数据库中，以提供一套集成的工具和信息。
来自五个独立cDNA文库的EST被存入数据库，这些文库由草地贪夜蛾的三种不同组织（血细胞、中肠和脂肪体）以及Sf9细胞系制备而成。选择这些组织是因为它们在免疫反应、发育和植物/昆虫相互作用等生物学过程中具有重要性。到目前为止，SPODOBASE包含29325条EST，这些EST经过清理并聚类为非冗余集（2294个簇和6103个单拷贝）。SPODOBASE的构建方式使得可以添加来自草地贪夜蛾或其他物种的其他EST。用户可以使用文本搜索、预格式化查询、查询助手或Blast搜索来检索信息。注释是针对NCBI、UNIPROT或家蚕EST数据库提供的，并使用GO-Slim词汇表。
SPODOBASE数据库提供了对鳞翅目昆虫草地贪夜蛾表达序列标签（EST）的集成访问。它是一个公开可用的结构化数据库，包含害虫序列，这将使科学界能够鉴定许多基因并全面克隆感兴趣的基因家族。可通过以下网址访问SPODOBASE：http://bioweb.ensam.inra.fr/spodobase 。
