AspWood

AspWood analyzes high-resolution RNA-Seq and genomic data to annotate carbohydrate-active enzymes (CAZymes) and expansins and to characterize their organ-specific expression, co-expression networks, and regulons in Populus species for studies of polysaccharide biosynthesis and wood formation.

Key Features:

• Re-Annotation of CAZyme Genes: Re-annotates CAZyme and expansin genes in the Populus trichocarpa genome, identifying 1914 genes across 101 families.
• Expression Analysis: Identifies organ-specific expression in Populus with approximately 1797 genes expressed in at least one organ.
• Comparative Genomics: Compares CAZyme gene family copy numbers between Populus and Arabidopsis thaliana to highlight species-specific differences.
• Co-Expression Network Analysis: Performs co-expression network analysis in wood-forming tissues to elucidate transcriptional coordination and the transition from primary to secondary cell wall formation in Populus tremula.
• Regulon Clustering: Clusters transcripts into potential regulons to map gene regulatory networks involved in cell wall biosynthesis and development.
• Identification of Candidate Enzymes: Identifies candidate enzymes implicated in polysaccharide biosynthesis, alongside uncharacterized genes and transcription factors specific to tissues as targets for modifying secondary cell wall production.

Scientific Applications:

• Biomass Research: Links CAZyme function and expression to polysaccharide composition to inform woody biomass utilization for renewable energy and industrial applications.
• Genetic Engineering: Provides candidate genes and regulatory networks for genetic modification aimed at improving wood quality and secondary cell wall production.
• Comparative Plant Biology: Enables comparative analyses between Populus and Arabidopsis thaliana to investigate evolutionary adaptation of cell wall-related gene families.

Methodology:

Integrates high-resolution RNA-Seq with genomic and transcriptomic data, applies co-expression network analysis and regulon clustering, and performs in silico functional characterization of CAZymes based on expression patterns and predicted functions.