An enhanced gene function analysis platform for Gastrodia Elata integrating further omics data and analysis tools

Area of Science:

• Genomics and Bioinformatics
• Plant Science
• Traditional Chinese Medicine

Background:

• Gastrodia elata, a traditional Chinese medicine, has significant medicinal and dietary value.
• Increasing multi-omics data necessitates an updated platform for G. elata gene function analysis.
• Existing resources require integration of the latest genome and transcriptome data.

Purpose of the Study:

• To upgrade the Gastrodia elata Functional Annotation Platform (GelFAP) to version 3.0.
• To integrate the latest G. elata genome and transcriptome data for enhanced gene analysis.
• To provide researchers with advanced tools for studying G. elata gene functions.

Main Methods:

• Construction of co-expression networks using four G. elata genome versions.
• Integration of recent transcriptome data and annotation using multiple databases (TAIR, Uniprot, NR, Swissprot).
• Gene family identification and functional prediction using InterProScan, GhostKOALA, HMMER, iTAK, OrthoFinder, and KEGG.

Main Results:

• The upgraded GelFAP v3.0 platform includes tools for BLAST, gene set enrichment analysis, sequence extraction, JBrowse v2, multiple sequence alignment, DEG/DEM analysis, primer design, and heatmap analysis.
• Identification of GeMYB4 as a potential suppressor of flavonoid biosynthesis.
• Identification of GePAL1, a key phenylpropanoid pathway gene, with higher expression in G. elata f. glauca and co-expression with phenolic compound biosynthesis genes.

Conclusions:

• GelFAP v3.0 provides an enhanced resource for G. elata research.
• The platform facilitates the analysis of genes involved in secondary metabolite biosynthesis, stress response, and development.
• Case studies with GeMYB4 and GePAL1 demonstrate the platform's utility in uncovering gene functions.