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 Taming of the Silkworm: Silkworms, Bombyx mori , represent one of the few domesticated insects, having been domesticated over 10,000 years ago. Xia et al. (p. 433 , published online 27 August) sequenced 29 domestic and 11 wild silkworm lines and identified genes that were most likely to be selected during domestication. These genes represent those that enhance silk production, reproduction, and growth. Furthermore, silkworms were probably only domesticated once from a large progenitor population, rather than on multiple occasions, as has been observed for other domesticated animals.

We designed and constructed a genome-wide microarray with 22,987 70-mer oligonucleotides covering the presently known and predicted genes in the silkworm genome, and surveyed the gene expression in multiple silkworm tissues on day 3 of the fifth instar. Clusters of tissue-prevalent and tissue-specific genes and genes that are differentially expressed in different tissues were identified, and they reflect well major tissue-specific functions on the molecular level. The data presented in this study provide a new resource for annotating the silkworm genome.

The SilkDB is an open-access database for genome biology of the silkworm (Bombyx mori). Since the draft sequence was completed and the SilkDB was first released 5 years ago, we have collaborated with other groups to make much remarkable progress on silkworm genome research, such as the completion of a new high-quality assembly of the silkworm genome sequence as well as the construction of a genome-wide microarray to survey gene expression profiles. To accommodate these new genomic data and house more comprehensive genomic information, we have reconstructed SilkDB database with new web interfaces. In the new version (v2.0) of SilkDB, we updated the genomic data, including genome assembly, gene annotation, chromosomal mapping, orthologous relationship and experiment data, such as microarray expression data, Expressed Sequence Tags (ESTs) and corresponding references. Several new tools, including SilkMap, Silkworm Chromosome Browser (SCB) and BmArray, are developed to access silkworm genomic data conveniently. SilkDB is publicly available at the new URL of http://www.silkdb.org.