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GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis
Glycyrrhiza uralensis (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 G. uralensis has been completed, which will help to lay the foundation for the stu...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9039005/ https://www.ncbi.nlm.nih.gov/pubmed/35495163 http://dx.doi.org/10.3389/fgene.2022.823966 |
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author | Yang, Jiaotong Yan, Hengyu Liu, Yue Da, Lingling Xiao, Qiaoqiao Xu, Wenying Su, Zhen |
author_facet | Yang, Jiaotong Yan, Hengyu Liu, Yue Da, Lingling Xiao, Qiaoqiao Xu, Wenying Su, Zhen |
author_sort | Yang, Jiaotong |
collection | PubMed |
description | Glycyrrhiza uralensis (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 G. uralensis 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 G. uralensis and constructed the G. uralensis gene co-expression network. We then annotated gene functions of G. uralensis via aligning with public databases. Furthermore, gene families of G. uralensis 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 G. uralensis (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 CYP88D6, CYP72A154, and bAS 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 G. uralensis and thus discover more key genes involved in the biosynthetic pathway of active ingredients. |
format | Online Article Text |
id | pubmed-9039005 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-90390052022-04-27 GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis Yang, Jiaotong Yan, Hengyu Liu, Yue Da, Lingling Xiao, Qiaoqiao Xu, Wenying Su, Zhen Front Genet Genetics Glycyrrhiza uralensis (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 G. uralensis 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 G. uralensis and constructed the G. uralensis gene co-expression network. We then annotated gene functions of G. uralensis via aligning with public databases. Furthermore, gene families of G. uralensis 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 G. uralensis (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 CYP88D6, CYP72A154, and bAS 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 G. uralensis and thus discover more key genes involved in the biosynthetic pathway of active ingredients. Frontiers Media S.A. 2022-04-12 /pmc/articles/PMC9039005/ /pubmed/35495163 http://dx.doi.org/10.3389/fgene.2022.823966 Text en Copyright © 2022 Yang, Yan, Liu, Da, Xiao, Xu and Su. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Genetics Yang, Jiaotong Yan, Hengyu Liu, Yue Da, Lingling Xiao, Qiaoqiao Xu, Wenying Su, Zhen GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis |
title | GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis
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title_full | GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis
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title_fullStr | GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis
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title_full_unstemmed | GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis
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title_short | GURFAP: A Platform for Gene Function Analysis in Glycyrrhiza Uralensis
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title_sort | gurfap: a platform for gene function analysis in glycyrrhiza uralensis |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9039005/ https://www.ncbi.nlm.nih.gov/pubmed/35495163 http://dx.doi.org/10.3389/fgene.2022.823966 |
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