ASAP: a platform for gene functional analysis in Angelica sinensis

Area of Science:

• Genomics and Bioinformatics
• Medicinal Plant Research
• Systems Biology

Background:

• Angelica sinensis (Danggui) is a medicinal orchid with diverse therapeutic applications.
• Understanding gene function is crucial for unlocking its medicinal potential.
• Chromosome-level genomes and multiomics data offer new avenues for gene function exploration.

Purpose of the Study:

• To construct a coexpression network for Angelica sinensis using genomic and transcriptomic data.
• To develop an integrated platform for comprehensive gene functional analysis in A. sinensis.
• To provide researchers with essential tools and data for exploring A. sinensis gene functions.

Main Methods:

• Genomic and transcriptomic data were utilized to build a coexpression network.
• Gene annotation was performed using multiple databases (NR, TAIR, trEMBL, UniProt, SwissProt).
• Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were achieved using InterProScan and GhostKOALA.
• Gene family prediction was conducted using iTAK, HMMER, OrholoFinder, and KEGG annotation.
• A platform integrating data and analysis tools (BLAST, GSEA, Heatmap, JBrowse, Sequence Extraction) was developed.

Main Results:

• A coexpression network for A. sinensis was successfully constructed.
• Comprehensive gene annotations and functional predictions were obtained.
• An integrated platform, ASAP, was established, offering diverse analytical tools and data resources.

Conclusions:

• The ASAP platform facilitates gene functional analysis in Angelica sinensis.
• ASAP provides a valuable, integrated resource for researchers studying A. sinensis.
• This platform enhances the exploration of gene functions in medicinal plants.