SilkDB 3.0

SilkDB 3.0 provides integrated access to chromosome-level genome assemblies, transcriptome, Hi-C, and pangenome data for Bombyx mori to support genomic analysis and interpretation.

Key Features:

• Chromosome-level genome assembly: Provides a high-quality chromosome-scale assembly of the Bombyx mori genome.
• Improved coding sequences and gene sets: Contains refined coding sequence annotations and updated gene sets for increased accuracy.
• Transcriptome and expression profiles: Integrates transcriptome data and gene expression profiles across samples.
• Hi-C genome interaction maps: Includes Hi-C contact maps enabling analysis of genome 3D organization and interactions.
• Pangenome data integration: Incorporates pangenome datasets to represent genomic variation across multiple Bombyx mori accessions.
• Protein structure and gene family analyses: Provides data for protein structure inspection and gene family/orthology assessments.
• Synteny and genome organization analyses: Supports synteny comparisons and analyses of genome organization.
• Visualization tools for large-scale datasets: Supplies computational visualization capabilities for exploring integrated genomic, transcriptomic, Hi-C, and pangenome data.

Scientific Applications:

• Silkworm genomics: Enables gene discovery, annotation validation, and genome-scale studies in Bombyx mori.
• Comparative and evolutionary genomics: Supports orthology, gene family, and synteny analyses across silkworm and related insect genomes.
• Functional genomics and gene regulation: Facilitates integration of transcriptome and Hi-C data to study gene expression and regulatory interactions.
• Genetic variation and breeding research: Uses pangenome and variation data to investigate genomic diversity relevant to breeding and trait mapping.

Methodology:

Curated genomic datasets were assembled to chromosome level and annotated for coding sequences and gene sets, with integration of transcriptome, Hi-C, and pangenome data.