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Related Experiment Video

Updated: Jun 19, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
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KAIKObase: an integrated silkworm genome database and data mining tool.

Michihiko Shimomura1, Hiroshi Minami, Yoshitaka Suetsugu

  • 1Mitsubishi Space Software Co Ltd, Takezono, Tsukuba, Ibaraki, Japan. shimomur@mi.mss.co.jp

BMC Genomics
|October 22, 2009
PubMed
Summary

The silkworm genome has been significantly improved through merged sequencing data and integrated databases, enhancing its utility for biomedical research. This comprehensive resource, KAIKObase, aids functional studies and genetic analysis of Bombyx mori.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Insect Molecular Biology

Background:

  • Bombyx mori (silkworm) is crucial for silk production and as a bioreactor for recombinant proteins.
  • Previous genome sequencing efforts lacked sufficient data for accurate annotation.
  • A joint collaboration merged datasets from Chinese and Japanese projects.

Purpose of the Study:

  • To create a comprehensive and integrated silkworm genome database.
  • To improve the quality and contiguity of the silkworm genome assembly.
  • To facilitate functional genomics studies in Bombyx mori.

Main Methods:

  • Integrated whole-genome shotgun sequencing data with fosmid and BAC-end sequences.
  • Constructed physical maps (BAC contigs) and genetic maps (SNP linkage).
  • Compiled proteomic data and transposon insertion data into specialized databases.

Main Results:

  • Achieved high continuity (~3.7 Mb N50 scaffold size) and 88% nucleotide coverage of the silkworm genome.
  • Developed KAIKObase, an integrated database with multiple viewers and search systems.
  • Successfully integrated proteome and transposon data into KAIKObase.

Conclusions:

  • KAIKObase provides a user-friendly and comprehensive resource for silkworm genome research.
  • The integrated database enhances the utility of genomic, genetic, and proteomic data.
  • This resource supports advanced functional studies and applications of Bombyx mori.