GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis

• Published in: Frontiers in genetics Vol. 13; p. 823966
• Main Authors: Yang, Jiaotong, Yan, Hengyu, Liu, Yue, Da, Lingling, Xiao, Qiaoqiao, Xu, Wenying, Su, Zhen
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 12-04-2022
• Subjects: co-expression network; gene function analyses; Genetics; Glycyrrhiza uralensis; glycyrrhizin; Platform; gene function analyses; Glycyrrhiza uralensis; Platform; glycyrrhizin; co-expression network
• ISSN: 1664-8021; 1664-8021
• DOI: 10.3389/fgene.2022.823966

(Licorice), which belongs to Leguminosae, is famous for the function of pharmacologic action and natural sweetener with its dried roots and rhizomes. In recent years, the whole-genome sequence of
has been completed, which will help to lay the foundation for the study of gene function. Here, we integrated the available genomic and transcriptomic data of
and constructed the
gene co-expression network. We then annotated gene functions of
aligning with public databases. Furthermore, gene families of
were predicted by tools including iTAK (Plant Transcription factor and Protein kinase Identifier and Classifier), HMMER (hidden Markov models), InParanoid, and PfamScan. Finally, we constructed a platform for gene function analysis in
(GURFAP, www.gzybioinfoormatics.cn/GURFAP). For analyzed and predicted gene function, we introduced various tools including BLAST (Basic local alignment search tool), GSEA (Gene set enrichment analysis), Motif, Heatmap, and JBrowse. Our analysis based on this platform indicated that the biosynthesis of glycyrrhizin might be regulated by MYB and bHLH. We also took
,
and
gene in the synthesis pathway of glycyrrhizin as examples to demonstrate the reliability and availability of our platform. Our platform GURFAP will provide convenience for researchers to mine the gene function of
and thus discover more key genes involved in the biosynthetic pathway of active ingredients.