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KAIKObase: An integrated silkworm genome database and data mining tool

Michihiko Shimomura1, Hiroshi Minami1, Yoshitaka Suetsugu2, Hajime Ohyanagi1, Chikatada Satoh1, Baltazar Antonio3, Yoshiaki Nagamura3, Keiko Kadono-Okuda2, Hideyuki Kajiwara3, Hideki Sezutsu2, Javaregowda Nagaraju4, Marian R Goldsmith5, Qingyou Xia6, Kimiko Yamamoto2* and Kazuei Mita2

Author Affiliations

1 Mitsubishi Space Software Co. Ltd., Takezono, Tsukuba, Ibaraki 305-0032, Japan

2 National Institute of Agrobiological Sciences, Owashi, Tsukuba, Ibaraki 305-8634, Japan

3 National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki 305-8602, Japan

4 Centre for DNA Fingerprinting & Diagnostics, Nampally, Hyderabad-500001, India

5 Biological Sciences Department, University of Rhode Island, Kingston, Rhode Island 02881-0816, USA

6 The Institute of Agricultural and Life Sciences, Chongqing University, Chongqing 400030, PR China

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BMC Genomics 2009, 10:486  doi:10.1186/1471-2164-10-486

Published: 21 October 2009

Abstract

Background

The silkworm, Bombyx mori, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, B. mori has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for B. mori were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between the two groups.

Description

Integration of the two data sets of silkworm whole-genome-shotgun sequencing by the Japanese and Chinese groups together with newly obtained fosmid- and BAC-end sequences produced the best continuity (~3.7 Mb in N50 scaffold size) among the sequenced insect genomes and provided a high degree of nucleotide coverage (88%) of all 28 chromosomes. In addition, a physical map of BAC contigs constructed by fingerprinting BAC clones and a SNP linkage map constructed using BAC-end sequences were available. In parallel, proteomic data from two-dimensional polyacrylamide gel electrophoresis in various tissues and developmental stages were compiled into a silkworm proteome database. Finally, a Bombyx trap database was constructed for documenting insertion positions and expression data of transposon insertion lines.

Conclusion

For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the silkworm proteome database and the Bombyx trap database with KAIKObase led to a high-grade, user-friendly, and comprehensive silkworm genome database which is now available from URL: http://sgp.dna.affrc.go.jp/KAIKObase/ webcite.