LjaFGD

LjaFGD provides an integrated functional genomics resource for Lonicera japonica that combines gene annotations, a gene co‑expression network, and analysis tools to identify and analyze genes involved in secondary metabolite biosynthesis such as chlorogenic acid and luteolin.

Key Features:

• Gene Co‑expression Network: A network constructed from 77 RNA‑seq samples that highlights co‑expression relationships, including MYB and WRKY transcription factors with enzymes involved in chlorogenic acid and luteolin biosynthesis.
• Gene Annotation: Gene annotations derived by alignment against protein sequences from public databases.
• BLAST: Sequence similarity searches to identify homologous genes.
• Motif Analysis: Identification of conserved motifs within gene sequences to aid inference of regulatory elements.
• Gene Set Enrichment Analysis (GSEA): Statistical assessment of whether predefined gene sets show significant differences between biological states.
• Heatmap Analysis: Generation of heatmaps to visualize expression levels across samples or conditions.
• JBrowse: Genome browser visualization of genomic data and gene structures.

Scientific Applications:

• Transcription Factor Network Analysis: Investigation of MYB and WRKY co‑expression patterns with biosynthetic enzymes.
• Metabolic Pathway Analysis: Study of pathways for secondary metabolite biosynthesis, including chlorogenic acid and luteolin.
• Gene Functional Characterization: Case study application to flavonol synthase 1 (LjFLS1) for functional investigation.

Methodology:

Construction of a gene co‑expression network from 77 RNA‑seq samples; gene annotation via alignment to protein sequences from public databases; and computational analyses including BLAST, motif analysis, GSEA, heatmap generation, and JBrowse visualization.