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BGI-Chicken Variation Database
Thermoanaerobacter tengcongensis Database
 
 
Silk was one of the precious commodities that created the cultural bridge between eastern and western civilizations known as the "Silk Road". It is made from the cocoon of the silkworm Bombyx mori, which was domesticated over the last 5000 years from a wild progenitor Bombyx mandarina. The silkworm B. mori is believed to be a central model for lepidopteran genomics and genetics, and second only to fruitfly (Drosophila melanogaster) as an insect model for genetic studies. As many basic physiological processes of insects are conserved through evolution, study in silkworm will help further elucidate the function of gene homologues and facilitate studies of insect domestication, morphogenesis, endocrinology, reproduction, behavior, and immunity.
At the Beijing Genomics Institute (BGI), the major genome sequencing center in China, we have produced a draft genome sequence for the silkworm B. mori. The silkworm genome sequence is an important contribution to functional genomics for the silkworm and to comparative and functional genomics for lepidopteran species. In order to facilitate the usage of most up-to-date knowledge about the silkworm genome, we develop the Silkworm Knowledgebase (SilkDB) as a highly integrated information system for silkworm data storage, retrieval, visualization, and analysis. SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, EST clusters, transposable elements (TEs), and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from B. mandarina, and a collection of genes from other lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B. mori and other lepidoptera, and between B. mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B. mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies.
 


*  首届“生物信息学方法及应用”短期培训班招生
1  Total size of B. mori genome: 428.7 Mb, including unassembled reads.
2  Latest version of B. mori sequence assembly:
    23,156 Scaffolds
    66,482 Contigs
3  Scaffold annotation:
    209 full-length cDNAs from NCBI are mapped to the scaffolds
    21,302 Genes predicted by BGI Gene Finder (BGF)
    691 BGF genes are emphasized and classified into 9 function classes
    601,225 Repeat regions
    17 ,363 UniGene assemblies from 64,038 ESTs, including:
    15,715 UniGenes of domesticated silkworm ( B. mori ) ( SwUniGene )
    1,648 UniGenes of wild silkworm ( B. mandarina ) ( FswUniGene )
    521 B. mori homologs of genes from other Lepidoptera are mapped onto 323 scaffolds.
B. mori mutants
NCBI B. mori ESTs
B. mori WGS sequences from SGP
SNPs from SWAU(Southwest Agricultural University)

 
 
  • SilkDB: a knowledgebase for silkworm biology and genomics
    Nucleic Acids Research 33, 399-402 (2005)    ( PDF )
 
   

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Supported by China National Grid Project 2002AA104250