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SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm.

Fang Lu1, Zhaoyuan Wei1, Yongjiang Luo1

  • 1Biological Science Research Center, Southwest University, Chongqing 400715, China.

Nucleic Acids Research
|October 24, 2019
PubMed
Summary

SilkDB 3.0 offers a comprehensive, visual platform for silkworm (Bombyx mori) genome data. This updated database integrates diverse datasets, enhancing research accessibility for the insect community.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • SilkDB 2.0 was released a decade ago, necessitating an update due to extensive new silkworm data.
  • Recent advancements include genome, transcriptome, Hi-C, and pangenome data for Bombyx mori.
  • Existing resources require enhanced visualization and integration capabilities.

Purpose of the Study:

  • To present SilkDB 3.0, an upgraded visual analytic tool for exploring silkworm genome data.
  • To provide an interactive user interface for accessing and visualizing diverse silkworm biological information.
  • To serve as a valuable, updated resource for the silkworm and broader insect research community.

Main Methods:

  • Developed SilkDB 3.0 with a high-quality chromosome-level assembly of the silkworm genome.
  • Integrated and visualized data across multiple biological levels: sequence, protein structure, gene family, orthology, synteny, and genome organization.
  • Incorporated gene expression, genetic variation, and genome interaction map data.
  • Implemented a suite of visualization tools within an improved interactive user interface.

Main Results:

  • SilkDB 3.0 features a more accurate chromosome-level genome assembly and gene sets than previous versions.
  • The database provides comprehensive gene information, including sequence, structure, function, and evolutionary context.
  • Interactive visualization tools are available for exploring integrated datasets, including gene expression and genome interactions.

Conclusions:

  • SilkDB 3.0 is a significantly enhanced resource for silkworm (Bombyx mori) research.
  • The platform's integrated data and visualization tools improve accessibility and analytical capabilities.
  • This updated database will accelerate research in silkworm genomics and related insect studies.