Abstract
SilkDB is an open-accessibility database and powerful platform that provides comprehensive information on the silkworm (Bombyx mori) genome. Since SilkDB 2.0 was released 10 years ago, vast quantities of data about multiple aspects of the silkworm have been generated, including genome, transcriptome, Hi-C and pangenome. To visualize data at these different biological levels, we present SilkDB 3.0 (https://silkdb.bioinfotoolkits.net), a visual analytic tool for exploring silkworm data through an interactive user interface. The database contains a high-quality chromosome-level assembly of the silkworm genome, and its coding sequences and gene sets are more accurate than those in the previous version. SilkDB 3.0 provides a view of the information for each gene at the levels of sequence, protein structure, gene family, orthology, synteny, genome organization and gives access to gene expression information, genetic variation and genome interaction map. A set of visualization tools are available to display the abundant information in the above datasets. With an improved interactive user interface for the integration of large data sets, the updated SilkDB 3.0 database will be a valuable resource for the silkworm and insect research community.
Highlights
The silkworm, Bombyx mori, which was domesticated during the last ∼5000 years from a wild progenitor, Bombyx mandarina, is one of the most economically important insects and the foundation of sericulture
The silkworm has many basic physiological processes typical of insects, which have been conserved through insect evolution, and a considerable number of genes that are homologous to those of humans; it has been widely used in various life science studies [2]
SilkDB was published in the Nucleic Acids Research database issue in 2005 [6], and its updated version (SilkDB 2.0) was released in 2010 [7]
Summary
The silkworm, Bombyx mori, which was domesticated during the last ∼5000 years from a wild progenitor, Bombyx mandarina, is one of the most economically important insects and the foundation of sericulture. Though these databases have added to the available resources for silkworm genomic research, no platform yet incorporates multiple levels of silkworm data and provides integrated search, analysis, and visualization features through a single portal. The database contains a large amount of transcriptome data for exploring silkworm gene expression in different tissues.
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