Abstract
Gastrodia elata, also named Tianma, is a valuable traditional Chinese herbal medicine. It has numerous important pharmacological roles such as in sedation and lowering blood pressure and as anticonvulsant and anti-aging, and it also has effects on the immune and cardiovascular systems. The whole genome sequencing of G. elata has been completed in recent years, which provides a strong support for the construction of the G. elata gene functional analysis platform. Therefore, in our research, we collected and processed 39 transcriptome data of G. elata and constructed the G. elata gene co-expression networks, then we identified functional modules by the weighted correlation network analysis (WGCNA) package. Furthermore, gene families of G. elata were identified by tools including HMMER, iTAK, PfamScan, and InParanoid. Finally, we constructed a gene functional analysis platform for G. elata1. In our platform, we introduced functional analysis tools such as BLAST, gene set enrichment analysis (GSEA), and cis-elements (motif) enrichment analysis tool. In addition, we analyzed the co-expression relationship of genes which might participate in the biosynthesis of gastrodin and predicted 19 mannose-binding lectin antifungal proteins of G. elata. We also introduced the usage of the G. elata gene function analysis platform (GelFAP) by analyzing CYP51G1 and GFAP4 genes. Our platform GelFAP may help researchers to explore the gene function of G. elata and make novel discoveries about key genes involved in the biological processes of gastrodin.
Highlights
Gastrodia elata, a kind of perennial herb of Orchidaceae, is one of the traditional Chinese herbal medicines
Exploring the function of genes that can catalyze the synthesis of gastrodin from the cytochrome P450 (CYP450) and UGT gene family will help to explore the molecular mechanism of gastrodin biosynthesis
We identified the functional modules of G. elata co-expression network and further annotated their functions via gene set enrichment analysis
Summary
A kind of perennial herb of Orchidaceae, is one of the traditional Chinese herbal medicines. G. elata Gene Functional Analysis Platform lectin antifungal proteins of G. elata (GAFPs) play important roles in its growth during G. elata and A. mellea, establishing a stable symbiotic association (Yuan et al, 2018). Whole genome sequencing had been completed in typical model plants and crops, and many species even owned their gene function analysis platforms, which were established by the integration of multiple omics data. Wang et al (2020) analyzed the genomics data of 13 species in 9 genera of Malvaceae, such as genome-wide association analysis site (GWAS) information and single nucleotide mutation site (SNP) information, as well as a total of 374 sets of transcriptomic and proteomic data, and established a functional genomic hub for Malvaceae plants, which provided a powerful online analysis tool for scientists to carry out mallow family gene function analysis. We constructed a G. elata gene function analysis platform (GelFAP) with analysis tools, such as BLAST, GSEA, and cis-element enrichment analysis tools, which will help to further explore the novel functions of genes in G. elata
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