AUTHOR=Yang Jiaotong , Xiao Qiaoqiao , Xu Jiao , Da Lingling , Guo Lanping , Huang Luqi , Liu Yue , Xu Wenying , Su Zhen , Yang Shiping , Pan Qi , Jiang Weike , Zhou Tao 

TITLE=GelFAP: Gene Functional Analysis Platform for Gastrodia elata

JOURNAL=Frontiers in Plant Science

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2020.563237

DOI=10.3389/fpls.2020.563237

ISSN=1664-462X

ABSTRACT=<p><italic>Gastrodia elata</italic>, 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 <italic>G. elata</italic> has been completed in recent years, which provides a strong support for the construction of the <italic>G. elata</italic> gene functional analysis platform. Therefore, in our research, we collected and processed 39 transcriptome data of <italic>G. elata</italic> and constructed the <italic>G. elata</italic> gene co-expression networks, then we identified functional modules by the weighted correlation network analysis (WGCNA) package. Furthermore, gene families of <italic>G. elata</italic> were identified by tools including HMMER, iTAK, PfamScan, and InParanoid. Finally, we constructed a gene functional analysis platform for <italic>G. elata</italic><sup><xref ref-type="fn" rid="footnote1">1</xref></sup>. In our platform, we introduced functional analysis tools such as BLAST, gene set enrichment analysis (GSEA), and <italic>cis-</italic>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 <italic>G. elata</italic>. We also introduced the usage of the <italic>G. elata</italic> gene function analysis platform (GelFAP) by analyzing <italic>CYP51G1</italic> and <italic>GFAP4</italic> genes. Our platform GelFAP may help researchers to explore the gene function of <italic>G. elata</italic> and make novel discoveries about key genes involved in the biological processes of gastrodin.</p>