Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

Abstract Glycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate m...

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Autores principales:	Yuping Li, Xiaoju Liang, Xuguo Zhou, Yu An, Ming Li, Ling Yuan, Yongqing Li, Ying Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0819945d15e541b0ae1c3bf29c9fcc96
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spelling	oai:doaj.org-article:0819945d15e541b0ae1c3bf29c9fcc962021-12-02T13:34:33ZSpatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza10.1038/s41598-020-79298-82045-2322https://doaj.org/article/0819945d15e541b0ae1c3bf29c9fcc962021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-79298-8https://doaj.org/toc/2045-2322Abstract Glycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.Yuping LiXiaoju LiangXuguo ZhouYu AnMing LiLing YuanYongqing LiYing WangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yuping Li Xiaoju Liang Xuguo Zhou Yu An Ming Li Ling Yuan Yongqing Li Ying Wang Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza
description	Abstract Glycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.
format	article
author	Yuping Li Xiaoju Liang Xuguo Zhou Yu An Ming Li Ling Yuan Yongqing Li Ying Wang
author_facet	Yuping Li Xiaoju Liang Xuguo Zhou Yu An Ming Li Ling Yuan Yongqing Li Ying Wang
author_sort	Yuping Li
title	Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza
title_short	Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza
title_full	Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza
title_fullStr	Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza
title_full_unstemmed	Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza
title_sort	spatio-temporal selection of reference genes in the two congeneric species of glycyrrhiza
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/0819945d15e541b0ae1c3bf29c9fcc96
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Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

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