Black Pepper Knowledge Base (BlackPepKB)

Black Pepper Knowledge Base (BlackPepKB) hosts genomic, transcriptomic, and functional annotation data for black pepper (Piper nigrum L.) and incorporates interactive tools for data exploration and analysis to support functional genomics research and breeding efforts.

Key Features:

• Electronic Fluorescent Pictograph (eFP) browser: Visualizes gene expression patterns across tissues and developmental stages.
• JBrowse2: Enables genome navigation.
• BLAST: Supports sequence similarity searches.
• GeneViz: Provides exon-intron gene structure visualization.
• PepperExp: Generates heatmaps of gene expression data.
• PepperClust: Performs hierarchical clustering of gene expression data.
• GO-Pep: Facilitates retrieval of Gene Ontology terms.
• SNP querying: Supports querying of single nucleotide polymorphisms.
• Transcription factor family exploration: Enables exploration of TF families in black pepper.

Scientific Applications:

• Transcription factor analysis: Supports classification and analysis of 2,503 TF-encoding genes (PnTFs) into 62 TF families, including identification of 471 intronless PnTF genes and 171 hub PnTFs through protein-protein interaction network analysis.
• Functional annotation: Enables Gene Ontology-based functional annotation of proteins, with 35,670 of 63,463 proteins (56.2%) annotated with at least one GO term.
• Gene expression analysis: Supports visualization and clustering of gene expression data across tissues and developmental stages.
• Genome navigation and sequence analysis: Facilitates genome browsing and sequence similarity searches for genomic research.
• Genetic research and molecular breeding: Provides foundational data and tools for advancing genetic research and breeding in black pepper.

Methodology:

Transcription factor-encoding genes were identified and classified into families; intronless genes were identified; protein-protein interaction network analysis was performed to identify hub TFs; Gene Ontology-based functional annotation of proteins was conducted.