The Silkworm Knowledgebase (SilkDB) is a webbased repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a 6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, 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. SilkDB is publicly accessible at http://silkworm.genomics.org.cn.

We report a draft sequence for the genome of the domesticated silkworm (Bombyx mori), covering 90.9% of all known silkworm genes. Our estimated gene count is 18,510, which exceeds the 13,379 genes reported for Drosophila melanogaster. Comparative analyses to fruitfly, mosquito, spider, and butterfly reveal both similarities and differences in gene content.

The fat body plays key roles in metabolism and sustenance of growth throughout the life of a silkworm, and thus represents a model tissue for studying development and metamorphosis. Analysis of 18480 ESTs derived from larval and pupal fat body cDNA libraries allowed characterization of gene expression patterns in the fat body during metamorphosis. By Phrap assembling, 6814 estimated transcription units (TUs) were generated, 2673 of which contained 60% of the total ESTs and represented 1366 distinctive known genes. These genes were classified into 14 categories based on their known or putative functions, and most were found to be involved in metabolism and cell defense. Further comparative analysis of the expression profiles revealed that the gene expression patterns in the larval fat body strikingly differed from those in the pupal fat body. From this, we identified a subset of genes potentially associated with metamorphic events such as the formation or destruction of specific tissues, and simultaneously confirmed the stage-specific expression patterns of several identified genes using RT-PCR examination. This work will provide a valuable resource for studying regulatory mechanisms associated with fat body developmental changes and silkworm metamorphosis.

家蚕小卵突变体（Small egg mutant，sm），其卵体积仅及正常卵的2/3，不能受精而致死。因其卵母细胞不能正常吸收卵黄原蛋白（Vg），人们认为其原因可能是卵黄原蛋白受体基因（VgR）突变所致。本研究首先通过克隆筛选和基因组序列分析，获得了2564 bp含有pbvA的家蚕卵黄原蛋白受体基因（BmVgR）片段。将该基因片段的预测蛋白与其它物种的VgR/YPR和低密度脂蛋白受体（LDLR）家族比较，发现该基因具有LDLR家族的基本结构特征。其次，经RT-ECR检测，结果表明BmVgR在sm的不同时期的卵母细胞中都能正常转录。最后，分别对sm不同发育时期的体液和卵的总蛋白进行SDSPAGE分析，发现该突变体的卵母细胞不能正常摄取体液蛋白（包括Vg）。综合分析，sm不能正常摄取Vg，可能并不是VgR的功能异常导致，而是与滤泡细胞异常有关

We made use of 81,635 expressed sequence tags (ESTs) derived from 12 different cDNA libraries of the silkworm, Bombyx mori, inbred strain Dazao (P50), to identify high-quality candidate single nucleotide polymorphisms (SNPs). By PHRAP assembling, 12,980 contigs containing 11,537 contigs assembled by more than one read were obtained, and 101 candidate SNPs and 27 single base insertions/deletions were identified from 117 contigs assembled from 1576 high-quality reads base-called with PHRED and screened on the basis of the neighborhood quality standard (NQS). Simultaneously, we also predicted 40 SNPs in coding regions (cSNPs), of which 26 were predicted to lead to amino acid non-synonymous variations and 14 synonymous substitutions. Also, the 1.66:1 ratio of transition/transversion is different from that of other insects. As the first SNP analysis of a Lepidoptera, B. mori, the single nucleotide polymorphic density is estimated to be 1:3 103 by sequence diversity. This analysis shows that expressed sequences from multiple libraries may provide an abundant source of comparative reads to mine for cSNPs from the silkworm genome.