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Zhang J, He X, Zhou J, Dong Z, Yu H, Tang Q, Yuan L, Peng S, Zhong X, He Y. Selection and Verification of Standardized Reference Genes of Angelica dahurica under Various Abiotic Stresses by Real-Time Quantitative PCR. Genes (Basel) 2024; 15:79. [PMID: 38254968 PMCID: PMC10815136 DOI: 10.3390/genes15010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. Real-time quantitative PCR (RT-qPCR) is widely employed as the predominant method for investigating gene expression. In order to ensure the precise determination of target gene expression outcomes in RT-qPCR analysis, it is imperative to employ stable reference genes. In this study, a total of 11 candidate reference genes including SAND family protein (SAND), polypyrimidine tract-binding protein (PTBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), TIP41-like protein (TIP41), cyclophilin 2 (CYP2), elongation factor 1 α (EF1α), ubiquitin-protein ligase 9 (UBC9), tubulin β-6 (TUB6), thioredoxin-like protein YLS8 (YLS8), and tubulin-α (TUBA) were selected from the transcriptome of A. dahurica. Subsequently, three statistical algorithms (geNorm, NormFinder, and BestKeeper) were employed to assess the stability of their expression patterns across seven distinct stimulus treatments. The outcomes obtained from these analyses were subsequently amalgamated into a comprehensive ranking using RefFinder. Additionally, one target gene, phenylalanine ammonia-lyase (PAL), was used to confirm the effectiveness of the selected reference genes. According to the findings of this study, the two most stable reference genes for normalizing the expression of genes in A. dahurica are TIP41 and UBC9. Overall, our research has determined the appropriate reference genes for RT-qPCR in A. dahurica and provides a crucial foundation for gene screening and identifying genes associated with the biosynthesis of active ingredients in A. dahurica.
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Affiliation(s)
- Jing Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xinyi He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Jun Zhou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Zhuang Dong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Han Yu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Lei Yuan
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Siqing Peng
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xiaohong Zhong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Yuedong He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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Mu D, Shao Y, He J, Zhu L, Qiu D, Wilson IW, Zhang Y, Pan L, Zhou Y, Lu Y, Tang Q. Evaluation of Reference Genes for Normalizing RT-qPCR and Analysis of the Expression Patterns of WRKY1 Transcription Factor and Rhynchophylline Biosynthesis-Related Genes in Uncaria rhynchophylla. Int J Mol Sci 2023; 24:16330. [PMID: 38003520 PMCID: PMC10671239 DOI: 10.3390/ijms242216330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Uncaria rhynchophylla (Miq.) Miq. ex Havil, a traditional medicinal herb, is enriched with several pharmacologically active terpenoid indole alkaloids (TIAs). At present, no method has been reported that can comprehensively select and evaluate the appropriate reference genes for gene expression analysis, especially the transcription factors and key enzyme genes involved in the biosynthesis pathway of TIAs in U. rhynchophylla. Reverse transcription quantitative PCR (RT-qPCR) is currently the most common method for detecting gene expression levels due to its high sensitivity, specificity, reproducibility, and ease of use. However, this methodology is dependent on selecting an optimal reference gene to accurately normalize the RT-qPCR results. Ten candidate reference genes, which are homologues of genes used in other plant species and are common reference genes, were used to evaluate the expression stability under three stress-related experimental treatments (methyl jasmonate, ethylene, and low temperature) using multiple stability analysis methodologies. The results showed that, among the candidate reference genes, S-adenosylmethionine decarboxylase (SAM) exhibited a higher expression stability under the experimental conditions tested. Using SAM as a reference gene, the expression profiles of 14 genes for key TIA enzymes and a WRKY1 transcription factor were examined under three experimental stress treatments that affect the accumulation of TIAs in U. rhynchophylla. The expression pattern of WRKY1 was similar to that of tryptophan decarboxylase (TDC) under ETH treatment. This research is the first to report the stability of reference genes in U. rhynchophylla and provides an important foundation for future gene expression analyses in U. rhynchophylla. The RT-qPCR results indicate that the expression of WRKY1 is similar to that of TDC under ETH treatment. It may coordinate the expression of TDC, providing a possible method to enhance alkaloid production in the future through synthetic biology.
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Affiliation(s)
- Detian Mu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Yingying Shao
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Jialong He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Lina Zhu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Iain W Wilson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT 2601, Australia
| | - Yao Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Limei Pan
- Key Laboratory of Guangxi for High-Quality Formation and Utilization of Dai-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China
| | - Yu Zhou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Ying Lu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Changsha 410208, China
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Evaluation of Candidate Reference Genes for Gene Expression Analysis in Wild Lamiophlomis rotata. Genes (Basel) 2023; 14:genes14030573. [PMID: 36980847 PMCID: PMC10048348 DOI: 10.3390/genes14030573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Lamiophlomis rotata (Benth.) Kudo is a perennial and unique medicinal plant of the Qinghai–Tibet Plateau. It has the effects of diminishing inflammation, activating blood circulation, removing blood stasis, reducing swelling, and relieving pain. However, thus far, reliable reference gene identifications have not been reported in wild L. rotata. In this study, we identified suitable reference genes for the analysis of gene expression related to the medicinal compound synthesis in wild L. rotata subjected to five different-altitude habitats. Based on the RNA-Seq data of wild L. rotata from five different regions, the stability of 15 candidate internal reference genes was analyzed using geNorm, NormFinder, BestKeeper, and RefFinder. TFIIS, EF-1α, and CYP22 were the most suitable internal reference genes in the leaves of L. rotata from different regions, while OBP, TFIIS, and CYP22 were the optimal reference genes in the roots of L. rotata. The reference genes identified here would be very useful for gene expression studies with different tissues in L. rotata from different habitats.
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Genetic Analysis of the Grapevine GATA Gene Family and Their Expression Profiles in Response to Hormone and Downy Mildew Infection. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Grapevine (Vitis. vinifera L.) is one of the most economically important fruit crops throughout the world. However, grape production is increasingly impacted by numerous diseases, including downy mildew, caused by the oomycete Plasmopara viticola. In grapevine and other plants, members of the GATA family of transcription factors play key roles in light and phytohormone signaling. However, little is known about their potential roles in biotic defense responses. As a first step, we identified 27 GATA transcription factors in grapevine and defined their transcriptional responses to three biotic stress-related phytohormones (SA, MeJA, and BR) in callus cells, and challenge with P. viticola in a downy mildew-sensitive cultivar, V. vinifera ‘Pinot noir’, and a resistant cultivar, V. piasezkii ‘Liuba-8′. Many of the VvGATA genes had higher expression at 0.5 h after hormones treatments. Moreover, a group of VvGATAs was dramatically induced in ‘Liuba-8′ at 24 post infection by P. viticola. However, the same genes were significantly repressed and showed low expression levels in ‘Pinot noir’. Additionally, VvGATA27 was located in the nucleus and had transcriptional activity. Taken together, the study identified the GATA full gene families in grapes on phylogenetic analysis and protein structure. Moreover, this study provided a basis for discussing the roles of VvGATAs in response to hormones and P. viticola infection. Our results provided evidence for the selection of candidate genes against downy mildew and lay the foundation for further investigation of VvGATA transcription factors.
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Wu Y, Zhang C, Yang H, Lyu L, Li W, Wu W. Selection and Validation of Candidate Reference Genes for Gene Expression Analysis by RT-qPCR in Rubus. Int J Mol Sci 2021; 22:ijms221910533. [PMID: 34638877 PMCID: PMC8508773 DOI: 10.3390/ijms221910533] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Due to the lack of effective and stable reference genes, studies on functional genes in Rubus, a genus of economically important small berry crops, have been greatly limited. To select the best internal reference genes of different types, we selected four representative cultivars of blackberry and raspberry (red raspberry, yellow raspberry, and black raspberry) as the research material and used RT-qPCR technology combined with three internal stability analysis software programs (geNorm, NormFinder, and BestKeeper) to analyze 12 candidate reference genes for the stability of their expression. The number of most suitable internal reference genes for different cultivars, tissues, and fruit developmental stages of Rubus was calculated by geNorm software to be two. Based on the results obtained with the three software programs, the most stable genes in the different cultivars were RuEEF1A and Ru18S. Finally, to validate the reliability of selected reference genes, the expression pattern of the RuCYP73A gene was analyzed, and the results highlighted the importance of appropriate reference gene selection. RuEEF1A and Ru18S were screened as reference genes for their relatively stable expression, providing a reference for the further study of key functional genes in blackberry and raspberry and an effective tool for the analysis of differential gene expression.
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Affiliation(s)
- Yaqiong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
| | - Chunhong Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
| | - Haiyan Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
| | - Lianfei Lyu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing 210037, China
- Correspondence: (W.L.); (W.W.); Tel.: +86-25-8542-8531 (W.L.); +86-25-8434-7063 (W.W.)
| | - Wenlong Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Qian Hu Hou Cun No. 1, Nanjing 210014, China; (Y.W.); (C.Z.); (H.Y.); (L.L.)
- Correspondence: (W.L.); (W.W.); Tel.: +86-25-8542-8531 (W.L.); +86-25-8434-7063 (W.W.)
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Evaluation of Angelica decursiva reference genes under various stimuli for RT-qPCR data normalization. Sci Rep 2021; 11:18993. [PMID: 34556773 PMCID: PMC8460625 DOI: 10.1038/s41598-021-98434-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 08/17/2021] [Indexed: 11/23/2022] Open
Abstract
Angelica decursiva is one of the lending traditional Chinese medicinal plants producing coumarins. Notably, several studies have focused on the biosynthesis and not the RT-qPCR (quantitative real-time reverse transcription polymerase chain reaction) study of coumarins. This RT-qPCR technique has been extensively used to investigate gene expression levels in plants and the selection of reference genes which plays a crucial role in standardizing the data form the RT-qPCR analysis. In our study, 11 candidate reference genes were selected from the existing transcriptome data of Angelica decursiva. Here, four different types of statistical algorithms (geNorm, NormFinder, BestKeeper, and Delta Ct) were used to calculate and evaluate the stability of gene expression under different external treatments. Subsequently, RefFinder analysis was used to determine the geometric average of each candidate gene ranking, and to perform comprehensive index ranking. The obtained results showed that among all the 11 candidate reference genes, SAND family protein (SAND), protein phosphatase 2A gene (PP2A), and polypyrimidine tract-binding protein (PTBP) were the most stable reference genes, where Nuclear cap binding protein 2 (NCBP2), TIP41-like protein (TIP41), and Beta-6-tubulin (TUBA) were the least stable genes. To the best of our knowledge, this work is the first to evaluate the stability of reference genes in the Angelica decursiva which has provided an important foundation on the use of RT-qPCR for an accurate and far-reaching gene expression analysis in this medicinal plant.
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Identification and selection of reference genes for gene expression analysis by quantitative real-time PCR in Suaeda glauca's response to salinity. Sci Rep 2021; 11:8569. [PMID: 33883657 PMCID: PMC8060425 DOI: 10.1038/s41598-021-88151-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
Quantitative real-time polymerase chain reaction (qPCR) using a stable reference gene is widely used for gene expression research. Suaeda glauca L. is a succulent halophyte and medicinal plant that is extensively used for phytoremediation and extraction of medicinal compounds. It thrives under high-salt conditions, which promote the accumulation of high-value secondary metabolites. However, a suitable reference gene has not been identified for gene expression standardization in S. glauca under saline conditions. Here, 10 candidate reference genes, ACT7, ACT11, CCD1, TUA5, UPL1, PP2A, DREB1D, V-H+-ATPase, MPK6, and PHT4;5, were selected from S. glauca transcriptome data. Five statistical algorithms (ΔCq, geNorm, NormFinder, BestKeeper, and RefFinder) were applied to determine the expression stabilities of these genes in 72 samples at different salt concentrations in different tissues. PP2A and TUA5 were the most stable reference genes in different tissues and salt treatments, whereas DREB1D was the least stable. The two reference genes were sufficient to normalize gene expression across all sample sets. The suitability of identified reference genes was validated with MYB and AP2 in germinating seeds of S. glauca exposed to different NaCl concentrations. Our study provides a foundational framework for standardizing qPCR analyses, enabling accurate gene expression profiling in S. glauca.
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Yin X, He T, Yi K, Zhao Y, Hu Y, Liu J, Zhang X, Meng L, Wang L, Liu H, Li Y, Cui G. Comprehensive evaluation of candidate reference genes for quantitative real-time PCR-based analysis in Caucasian clover. Sci Rep 2021; 11:3269. [PMID: 33558610 PMCID: PMC7870939 DOI: 10.1038/s41598-021-82633-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 01/19/2021] [Indexed: 11/08/2022] Open
Abstract
The forage species Caucasian clover (Trifolium ambiguum M. Bieb.), a groundcover plant, is resistant to both cold and drought. However, reference genes for qRT-PCR-based analysis of Caucasian clover are lacking. In this study, 12 reference genes were selected on the basis of transcriptomic data. These genes were used to determine the most stably expressed genes in various organs of Caucasian clover under cold, salt and drought stress for qRT-PCR-based analysis. Reference gene stability was analyzed by geNorm, NormFinder, BestKeeper, the ∆Ct method and RefFinder. Under salt stress, RCD1 and PPIL3 were the most stable reference genes in the leaves, and NLI1 and RCD1 were the most stable references genes in the roots. Under low-temperature stress, APA and EFTu-GTP were the most stable reference genes in the leaves, and the RCD1 and NLI2 genes were highly stable in the roots. Under 10% PEG-6000 stress, NLI1 and NLI2 were highly stable in the leaves, and RCD1 and PPIL3 were the most stable in the roots. Overall, RCD1 and NLI2 were the most stable reference genes in organs under normal conditions and across all samples. The most and least stable reference genes were validated by assessing their appropriateness for normalization via WRKY genes.
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Affiliation(s)
- Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Taotao He
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Kun Yi
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yihang Zhao
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yao Hu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Jiaxue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Xiaomeng Zhang
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Lingdong Meng
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Lina Wang
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Haoyue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yonggang Li
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China.
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He Y, Zhong X, Jiang X, Cong H, Sun H, Qiao F. Characterisation, expression and functional analysis of PAL gene family in Cephalotaxus hainanensis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:461-470. [PMID: 33027750 DOI: 10.1016/j.plaphy.2020.09.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Phenylalanine ammonia lyase (PAL) is the first committed step in the formation of phenylpropanoids, and catalyses the deamination of L-phenylalanine (L-Phe) to yield cinnamic acid. While PALs are common in plants, PAL genes involved in alkaloid biosynthesis in Cephalotaxus hainanensis have never been described. To obtain better knowledge of PAL genes and their number and function involved in Cephalotaxus alkaloid biosynthesis four PAL genes were screened and cloned. In vitro enzymatic analysis showed that all four PAL recombinant proteins could convert L-Phe to product trans-cinnamic acid, and showed strict substrate specificity. Moreover, the expression profiles of four ChPALs were analysed using qRT-PCR, which showed that they had higher transcript levels in roots and stems, and that different ChPALs displayed different response sensitivities and change patterns in response to stimuli. Several metabolic compounds were measured in stimulated leaves using UPLC-MS, and indicating the concentration of Cephalotaxus alkaloids and cinnamic acid in leaves subjected to different conditions. These concentrations increased significantly after treatment with 100 mM NaCl, 100 mM mannitol, 100 μM SA and 10 μM ABA. The expression levels of four PAL genes showed indications of upregulation after treatment. These results supply an important foundation for further research on candidate genes involved in the biosynthesis of Cephalotaxus alkaloids.
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Affiliation(s)
- Yuedong He
- College of Horticulture, Hunan Agricultural University, Changsha, China; Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture / Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiaohong Zhong
- College of Horticulture, Hunan Agricultural University, Changsha, China
| | - Xuefei Jiang
- Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources / College of Horticulture, Hainan University (HNU), Haikou, China
| | - Hanqing Cong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture / Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Huapeng Sun
- College of Horticulture, Hunan Agricultural University, Changsha, China; Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture / Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
| | - Fei Qiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement in Southern China, Ministry of Agriculture / Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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10
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Selvakesavan RK, Franklin G. Nanoparticles Affect the Expression Stability of Housekeeping Genes in Plant Cells. Nanotechnol Sci Appl 2020; 13:77-88. [PMID: 32884247 PMCID: PMC7431599 DOI: 10.2147/nsa.s265641] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/30/2020] [Indexed: 02/05/2023] Open
Abstract
Purpose We report on the expression stability of several housekeeping/reference genes that can be used in the normalization of target gene expression in quantitative real-time PCR (qRT-PCR) analysis of plant cells challenged with metal nanoparticles (NPs). Materials and Methods Uniform cell suspension cultures of Hypericum perforatum were treated with 25 mg/l silver and gold NPs (14-15 nm in diameter). Cells were collected after 0.5, 4.0, and 12 h. The total RNA isolated from the cells was analyzed for the stability of ACT2, ACT3, ACT7, EF1-α, GAPDH, H2A, TUB-α, TUB-β, and 18S rRNA genes using qRT-PCR. The cycle threshold (Ct) values of the genes were analyzed using the geNorm, NormFinder, BestKeeper, and RefFinder statistical algorithms to rank gene stability. The stability of the top-ranked genes was validated by normalizing the expression of HYP1. Results The expression of the tested housekeeping genes varied with treatment duration and NP types. EF1-α in gold NP treatment and TUB-α and EF1-α in silver NP treatment ranked among the top three positions. However, none of the genes retained their top ranking with time and across NP types. Conclusion EF1-α can be used as a reference for treatment involving both silver and gold NPs in H. perforatum cells. TUB-α can be used only for silver NP-treated cells. The expression instability of most of the housekeeping genes highlights the importance of systematic standardization of reference genes for NP treatment conditions to draw proper conclusions on the target gene expression.
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Affiliation(s)
| | - Gregory Franklin
- Institute of Plant Genetics of the Polish Academy of Sciences, Poznan 60-479, Poland
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Xing G, Liu K, Li W, Li J, Xing C, Yuan H, Yang J. Evaluation of internal reference genes in Auxenochlorella protothecoides under continuous heterotrophic culture conditions at normal, low and high temperatures. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Identification and Selection of Reference Genes for Quantitative Transcript Analysis in Corydalis yanhusuo. Genes (Basel) 2020; 11:genes11020130. [PMID: 32012754 PMCID: PMC7074024 DOI: 10.3390/genes11020130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/19/2020] [Accepted: 01/23/2020] [Indexed: 01/07/2023] Open
Abstract
Corydalis yanhusuo is a medicinal plant frequently used in traditional Chinese medicine, which has effective medical effects in many aspects. Real-time polymerase chain reaction (RT-PCR) has been one of the most widely used methods in biosynthesis research due to its high sensitivity and quantitative properties in gene expression analysis. To obtain accurate normalization, reference genes are often selected in advance; however, no reference genes are available in C. yanhusuo. Herein, 12 reference gene candidates, named cyclophilin 2 (CYP2), elongation factor 1-α (EF1-α), protein phosphatase 2 (PP2A), SAND protein family (SAND), polypyrimidine tract-binding protein (PTBP), TIP41-like protein (TIP41), lyceraldehyde-3-phosphate hydrogenase (GAPDH), ubiquitin-conjugating enzyme 9 (UBC9), cyclophilin 1 (CYP1), tubulin beta (TUBA), thioredoxin (YLS8), and polyubiquitin 10 (UBQ10), were selected for stability analysis. After being treated with hormone, UV, salt, metal, oxidative, drought, cold (4 °C), and hot stresses (40 °C), the qRT-PCR data of the selected genes was analyzed with NormFinder, geNorm, and BestKeeper. The result indicated that GAPDH, SNAD, and PP2A were the top three most stable reference genes under most treatments. This study selected and validated reliable reference genes in C. yanhusuo under various environmental conditions, which can provide great help for future research on gene expression normalization in C. yanhusuo.
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Selection of the Reference Gene for Expression Normalization in Papaver s omniferum L. under Abiotic Stress and Hormone Treatment. Genes (Basel) 2020; 11:genes11020124. [PMID: 31979407 PMCID: PMC7074096 DOI: 10.3390/genes11020124] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/21/2023] Open
Abstract
Papaver somniferum L. is an important medical plant that produces analgesic drugs used for the pain caused by cancers and surgeries. Recent studies have focused on the expression genes involved in analgesic drugs biosynthesis, and the real-time quantitative polymerase chain reaction (RT-qPCR) technique is the main strategy. However, no reference genes have been reported for gene expression normalization in P. somniferum. Herein, nine reference genes (actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclophilin 2 (CYP2), elongation factor 1-alpha (EF-1α), glyceraldehyde-3-phosphate dehydrogenase 2, cytosolic (GAPC2), nuclear cap-binding protein subunit 2 (NCBP2), protein phosphatase 2A (PP2A), TIP41-like protein (TIP41), and tubulin beta chain (TUB)) of P. somniferum were selected and analyzed under five different treatments (cold, drought, salt, heavy metal, and hormone stress). Then, BestKeeper, NormFinder, geNorm, and RefFinder were employed to analyze their gene expression stability. The results reveal that NCBP2 is the most stable reference gene under various experimental conditions. The work described here is the first report regarding on reference gene selection in P. somniferum, which could be used for the accurate normalization of the gene expression involved in analgesic drug biosynthesis.
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