The Genome Sequence of Silkworm, Bombyx mori

Abstract

We performed threefold shotgun sequencing of the silkworm (Bombyx mori) genome to obtain a draft sequence and establish a basic resource for comprehensive genome analysis. By using the newly developed RAMEN assembler, 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. Because the genome size of the silkworm is estimated to be 530 Mb, almost 97% of the genome has been organized in scaffolds, of which 75% has been sequenced. By carrying out a BLAST search for 50 characteristic Bombyx genes and 11,202 non-redundant expressed sequence tags (ESTs) in a Bombyx EST database against the WGS sequence data, we evaluated the validity of the sequence for elucidating the majority of silkworm genes. Analysis of the WGS data revealed that the silkworm genome contains many repetitive sequences with an average length of <500 bp. These repetitive sequences appear to have been 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.

Diversity of aminopeptidases, derived from four lepidopteran gene duplications, and polycalins expressed in the midgut of Helicoverpa armigera: Identification of proteins binding the δ-endotoxin, Cry1Ac of Bacillus thuringiensis

“…The only lepidopteran for which extensive genome sequence data is available is B. mori (Mita et al, 2004;Xia et al, 2004). Four APNs from B. mori have been reported previously (Entrez gene IDs: BmAPN1, 692563;BmAPN2, 692370;BmAPN3, 100127057;BmAPN4, 100127099), in contrast to the seven from H. armigera reported here.…”

“…The mRNA sequence of the polycalin of B. mori spans several contigs in the partially assembled bombyx genome, but there is no evidence for the existence of more than a single copy of this gene (Mita et al, 2004;Xia et al, 2004). Mauchamp et al (2006) did not observe any differential splicing in B. mori but recognised the potential for this to occur and called for further investigation.…”

Genetic mapping of Z chromosome and identification of W chromosome-specific markers in the silkworm, Bombyx mori

“…nih.gov), expressed sequence tags (ESTs) from SilkBase (http:// www.ab.a.u-tokyo.ac.jp/silkbase, Mita et al, 2003), Zlinked BAC clones , and whole genome shotgun (WGS) sequence data (http://www.ddbj.nig. ac.jp/whatsnew/040423-e.html, Mita et al, 2004). PCR amplification was performed in a 10 ml volume containing 10 mM Tris-HCl, pH 8.3, 1.5 mM MgCl 2 , 1mM dNTPs, 0.1 U of AmpliTaq Gold (Perkin Elmer), 4 mM primer, and 10-20 ng of genomic DNA.…”

Genomic resources for invertebrate vectors of human pathogens, and the role of VectorBase

“…The list can be extended to include animal and plant vectors: the pea aphid Acyrthosiphon pisum (Gauthier et al, 2007) is currently being sequenced and the tick Boophilus microplus, affecting cattle and horses (Guerrero et al, 2006) is awaiting funding. Other non-vector insects already sequenced contribute to our ability to annotate and understand vector genomes: the honey bee Apis mellifera (Consortium, 2006), the silk worm Bombyx mori (Mita et al, 2004) and the agricultural pest, the red flour beetle Tribolium castaneum (Brown et al, 2003;Wang et al, 2007). The future in vectors of human pathogen research looks very exciting.…”