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DNA Research 2004 11(1):27-35; doi:10.1093/dnares/11.1.27
© 2004 by Kazusa DNA Research Institute
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The Genome Sequence of Silkworm, Bombyx mori

Kazuei Mita1,*, Masahiro Kasahara2, Shin Sasaki2, Yukinobu Nagayasu3, Tomoyuki Yamada3, Hiroyuki Kanamori4, Nobukazu Namiki4, Masanari Kitagawa5, Hidetoshi Yamashita5, Yuji Yasukochi1, Keiko Kadono-Okuda1, Kimiko Yamamoto1, Masahiro Ajimura1, Gopalapillai Ravikumar1, Michihiko Shimomura6, Yoshiaki Nagamura7, Tadasu Shin-i8, Hiroaki Abe9, Toru Shimada10, Shinichi Morishita3 and Takuji Sasaki1

1Genome Research Department, National Institute of Agrobiological Sciences 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
2Department of Computer Science, University of Tokyo 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
3Department of Computational Biology, University of Tokyo 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
4Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries 446-1 Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
5Dragon Genomics Center, TAKARA BIO Inc. 7870-15 Sakura-cho, Yokkaichi, Mie 512-1211, Japan
6Genome Project Department, Tsukuba Division, Mitsubishi Space Software Co., Ltd. 1-6-1 Takezono, Tsukuba, Ibaraki 305-8602, Japan
7DNA Bank, Genome Research Department, National Institute of Agrobiological Sciences 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
8Center for Genetic Resource Information, National Institute of Genetics 1111 Yata, Mishima, Shizuoka 411-8540, Japan
9Department of Biological Production, Tokyo University of Agriculture and Technology 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
10Department of Agricultural and Environmental Biology, University of Tokyo 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan

* To whom correspondence should be addressed. Tel. +81-29-838-6120, Fax. +81-29-838-6121, E-mail: kmita{at}nias.a.rc.go.jp

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.

Key words: silkworm; Bombyx mori; WGS; genome sequence


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