SilkBase

SilkBase provides an integrated database of transcriptomic and genomic datasets for the domesticated silkworm, Bombyx mori, and related species to support genomic, transcriptomic, and epigenetic analyses.

Key Features:

• Complete genome and gene models: Contains the complete genome sequence of Bombyx mori and predicted gene models.
• Expressed sequence tags (ESTs) and cDNA reads: Includes ESTs and complementary DNA (cDNA) reads from 69 libraries.
• Shotgun and clone-end sequences: Integrates bacterial artificial chromosome (BAC)-end and fosmid-end sequences.
• RNA-seq datasets: Houses RNA-seq data from 10 libraries for transcriptomic profiling.
• piRNA datasets: Provides piRNA datasets from 13 libraries for small RNA and regulatory analyses.
• ChIP-seq of histone marks and HP1: Contains ChIP-seq data for nine histone modifications and HP1 proteins for epigenetic annotation.
• Comparative genomics data: Incorporates transcriptome and genome data from Bombyx mandarina, Trilocha varians, Ernolatia moorei, and Samia ricini.
• Functional element annotations: Includes annotations of functional elements such as piRNAs and histone modifications.

Scientific Applications:

• Gene function and regulation: Enables studies of gene function, regulation, and expression patterns in Bombyx mori and related species.
• Developmental biology and epigenetics: Supports investigations into developmental processes and epigenetic modifications in lepidopteran insects.
• Comparative genomics: Facilitates comparative genomic and transcriptomic analyses among closely related lepidopteran species.

Methodology:

Integration of high-throughput sequencing technologies and bioinformatics tools to assemble complete genome sequences, predict gene models, and annotate functional elements such as piRNAs and histone modifications.