title: 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.
authors.affiliation: Genome Research Department, National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan. kmita@nias.affrc.go.jp
authors.forename: Kazuei
authors.initials: K
authors.lastname: Mita
authors.forename: Masahiro
authors.initials: M
authors.lastname: Kasahara
authors.forename: Shin
authors.initials: S
authors.lastname: Sasaki
authors.forename: Yukinobu
authors.initials: Y
authors.lastname: Nagayasu
authors.forename: Tomoyuki
authors.initials: T
authors.lastname: Yamada
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.forename: Masanari
authors.initials: M
authors.lastname: Kitagawa
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Yamashita
authors.forename: Yuji
authors.initials: Y
authors.lastname: Yasukochi
authors.forename: Keiko
authors.initials: K
authors.lastname: Kadono-Okuda
authors.forename: Kimiko
authors.initials: K
authors.lastname: Yamamoto
authors.forename: Masahiro
authors.initials: M
authors.lastname: Ajimura
authors.forename: Gopalapillai
authors.initials: G
authors.lastname: Ravikumar
authors.forename: Michihiko
authors.initials: M
authors.lastname: Shimomura
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
authors.forename: Tadasu
authors.initials: T
authors.lastname: Shin-I
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Abe
authors.forename: Toru
authors.initials: T
authors.lastname: Shimada
authors.forename: Shinichi
authors.initials: S
authors.lastname: Morishita
authors.forename: Takuji
authors.initials: T
authors.lastname: Sasaki
mesh_terms: D000818:Animals; D012831:Bombyx / Q000235:genetics*; D019295:Computational Biology; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D015723:Gene Library; D016678:Genome