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.

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 identified 277 alternative splice forms in silkworm genes based on aligning expressed sequence tags with genomic sequences, using a transcipt assembly program. A large fraction (74%) of these alternative splices are located in protein-coding regions and alter protein products, whereas only 26% are in untranslated regions. From the alternative splices located in protein-coding regions, some (43%) affect protein domains that bind various biological molecules. The vast majority of the detected alternative forms in this study appear to be novel, and potentially affect biologically meaningful control of function in silkworm genes. Our results indicate that alternative splicing in silkworm largely produces protein diversity and functional diversity, and is a widely used mechanism for regulating gene expression.

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.

Two Bombyx mori isoforms of the gene lark, which is shown to play an important role in Drosophila circadian rhythms, were identified and named Bmlark-PA and Bmlark-PB, respectively. Bmlark-PA consists of 5 exons and encodes a protein of 343 amino acid residues which contains 3 functional domains: two RRM (RNA recognization motif) domains and an RTZF (retroviral-type zinc finger), and shares 72% identity with the Drosophila gene lark at the amino acid level. Bmlark-PB lacks the sequence between 118 and 791 nt of Bmlark-PA and codes for a protein of 68 amino acid residues, which contains no distinct functional domains. Alignments of the cDNAs of Bmlark to the genomic draft sequence of B. mori showed that the gene Bmlark had a single copy in the genome, suggesting that an alternative splicing mechanism occurs in the gene Bmlark. RT-PCR analysis indicated that Bmlark-PA was expressed only in late pupae and adult but Bmlark-PB was broadly expressed in many tissues and throughout the developmental stages from embryo to adult.