plantiSMASH

plantiSMASH identifies and annotates biosynthetic gene clusters (BGCs) in plant genomes to detect and prioritize candidate pathways involved in plant specialized metabolism.

Key Features:

• Plant-Specific Detection Rules: Incorporates specialized detection rules and algorithms tailored to plant biosynthetic enzyme families to enhance identification of BGCs.
• Comparative Genomics: Facilitates comparative genomic analyses to assess evolutionary conservation and diversity of BGCs across plant species.
• Visualization Tools: Generates visualizations of BGC structure and annotation to support interpretation of gene cluster architecture and predicted functions.
• Integration with Transcriptomic Data: Integrates transcriptomic coexpression data to prioritize candidate BGCs based on coexpression patterns of predicted biosynthetic enzyme-coding genes.

Scientific Applications:

• BGC discovery in plant genomes: Applied to 48 high-quality plant genomes to reveal a diversity of candidate biosynthetic gene clusters.
• Guiding experimental characterization: Helps prioritize candidate clusters for experimental validation of gene clustering and metabolic function in plants.
• Genome mining for natural products: Supports genome mining efforts to discover plant-derived natural products by identifying candidate biosynthetic loci.

Methodology:

Extends antiSMASH with plant-specific detection rules, performs comparative genomic analyses, integrates transcriptomic coexpression data, and generates visualizations of identified BGCs.