Silkworm genome sequencing

A threefold shotgun sequencing of the silkworm (Bombyx mori) genome was performed to obtain a draft sequence and establish a basic resource for comprehensive genome analysis. The sequence data derived from whole-genome shotgun (WGS) sequencing were assembled into 49,345 scaffolds that span a total length of 514 Mb including gaps and 387 Mb without gaps. Analysis of the WGS data revealed that the silkworm genome contains many repetitive sequences with an average length of less than 500 bp derived from truncated transposons, which are interspersed at 2.5- to 3-kb intervals throughout the genome. This pattern suggests that silkworm may have an active mechanism that promotes removal of transposons from the genome. We also found evidence for insertions of mitochondrial DNA fragments at 9 sites. A search for Bombyx orthologs to Drosophila genes controlling sex determination in the WGS data revealed 11 Bombyx genes and suggested that the sex-determining systems differ profoundly between the two species.