1
|
Li X, Zhang T, Jiang L, Fan G. Evaluation of Suitable Reference Genes for Quantitative Real-Time PCR in Various Tissues of Apocynum venetum. Genes (Basel) 2024; 15:231. [PMID: 38397220 PMCID: PMC10888412 DOI: 10.3390/genes15020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/27/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Apocynum venetum L. is an economically valuable plant with tolerance to drought and salinity. Its leaves are utilized in tea production and pharmaceuticals, while the stem bark serves as a high-quality fiber material. To gain insights into the gene expression patterns of A. venetum using quantitative real-time PCR (qRT-PCR), it is crucial to identify appropriate reference genes. This study selected nine candidate genes, including α-tubulin (TUA), β-tubulin (TUB), actin (ACT), cyclophilin (CYP), elongation factor-1α (EF-1α), the B family of regulatory subunits of protein phosphatase (PPP2R2, PPP2R3, and PPP2R5), and phosphoglycerate kinase (PGK), to determine the most appropriate reference genes in the leaf, stem, and root tissues of A. venetum. A comprehensive ranking by geNorm, NormFinder, BestKeeper, and RefFinder software and Venn diagrams was used to screen more stable reference genes in different tissues. The two most stable reference genes were CYP and TUA in leaves, PGK and PPP2R3 in stems, and TUA and EF-1α in roots, respectively. The relative expression values of the four genes involved in proline metabolism under polyethylene glycol treatment were used to validate the screened reference genes, and they exhibited highly stable expression levels. These findings represent the first set of stable reference genes for future gene expression studies in A. venetum. They significantly contribute to enhancing the accuracy and reliability of gene expression analyses in this economically important plant species.
Collapse
Affiliation(s)
- Xiaoshuang Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| | - Tingting Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| | - Li Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Guizhi Fan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| |
Collapse
|
2
|
He L, Wang JY, Su QJ, Chen ZH, Xie F. Selection and validation of reference genes for RT-qPCR in ophiocordyceps sinensis under different experimental conditions. PLoS One 2024; 19:e0287882. [PMID: 38319940 PMCID: PMC10846742 DOI: 10.1371/journal.pone.0287882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/14/2023] [Indexed: 02/08/2024] Open
Abstract
The Chinese caterpillar mushroom, Ophiocordyceps sinensis (O. sinensis), is a rarely medicinal fungus in traditional chinese herbal medicine due to its unique medicinal values, and the expression stability of reference genes is essential to normalize its gene expression analysis. In this study, BestKeeper, NormFinder and geNorm, three authoritative statistical arithmetics, were applied to evaluate the expression stability of sixteen candidate reference genes (CRGs) in O. sinensis under different stress [low temperature (4°C), light treatment (300 lx), NaCl (3.8%)] and different development stages (mycelia, primordia and fruit bodies) and formation of morphologic mycelium (aeriasubstrate, hyphae knot mycelium). The paired variation values indicated that two genes could be enough to accurate standardization exposed to different conditions of O.sinensis. Among these sixteen CRGs, 18S ribosomal RNA (18S rRNA) and beta-Tubulin (β-TUB) showed the topmost expression stability in O.sinensis exposed to all conditions, while glutathione hydrolase proenzym (GGT) and Phosphoglucose isomerase (PGI) showed the least expression stability. The optimal reference gene in different conditions was various. β-TUB and Ubiquitin (UBQ) were identified as the two most stable genes in different primordia developmental stage, while phosphoglucomutase (PGM) with elongation factor 1-alpha (EF1-α) and 18S rRNA with UBQ were the most stably expressed for differentially morphologic mycelium stages and different stresses, respectively. These results will contribute to more accurate evaluation of the gene relative expression levels in O.sinensis under different conditions using the optimal reference gene in real-time quantitative PCR (RT-qPCR) analysis.
Collapse
Affiliation(s)
- Li He
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Jin Yi Wang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Qiang Jun Su
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Zhao He Chen
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Fang Xie
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| |
Collapse
|
3
|
Ni Y, Zhang Q, Li W, Cao L, Feng R, Zhao Z, Zhao X. Selection and validation of reference genes for normalization of gene expression in Floccularia luteovirens. Fungal Biol 2024; 128:1596-1606. [PMID: 38341265 DOI: 10.1016/j.funbio.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 02/12/2024]
Abstract
Floccularia luteovirens is one of the rare edible fungi with high nutritional value found on the Qinghai-Tibet Plateau. However, research at the molecular level on this species is currently constrained due to the lack of reliable reference genes for this species. Thirteen potential reference genes (ACT, GAPDH, EF-Tu, SAMDC, UBI, CLN1, β-TUB, γ-TUB, GTP, H3, UBC, UBC-E2, and GTPBP1) were chosen for the present study, and their expression under various abiotic conditions was investigated. Stability of gene expression was tested using GeNorm, NormFinder, BestKeeper, Delta-Ct, and RefFinder. The results showed that the most suitable reference genes for salt treatment were ACT and EF-Tu. Under drought stress, γ-TUB and UBC-E2 would be suitable for normalization. Under oxidative stress, the reference genes H3 and GAPDH worked well. Under heat stress, the reference genes EF-Tu and γ-TUB were suggested. Under extreme pH stress, UBC-E2 and H3 were appropriate reference genes. Under cadmium stress, the reference genes ACT and UBC-E2 functioned well. In different tissues, H3 and GTPBP1 were appropriate reference genes. The optimal internal reference genes when analyzing all samples were H3 and SAMDC. The expression level of HSP90 was studied to further validate the applicability of the genes identified in this study.
Collapse
Affiliation(s)
- Yanqing Ni
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China.
| | - Qin Zhang
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Wensheng Li
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China.
| | - Luping Cao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
| | - Rencai Feng
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Zhiqiang Zhao
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| | - Xu Zhao
- College of Food and Biological Engineering, Chengdu University, Chengdu, 610106, Sichuan, China; Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu, 610299, Sichuan, China; Chengdu National Agricultural Science and Technology Center, Chengdu, 610299, Sichuan, China.
| |
Collapse
|
4
|
Yang J, Jiang Z, Xu Q, Liu X, Dai M, Li B, Wei J. Evaluation of suitable reference genes for expression analysis using quantitative real-time polymerase chain reaction in the parasitoid Exorista sorbillans (Diptera: Tachinidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 113:e22009. [PMID: 36879498 DOI: 10.1002/arch.22009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 05/16/2023]
Abstract
The parasitoid Exorista sorbillans (Diptera: Tachinidae) is a larval endoparasitoid of the silkworm Bombyx mori, causing severe damage to silkworm cocoon industry. It is also an important natural enemy resource of insect pests in agriculture and forestry. Despite their roles in biocontrol and pest status on sericulture, there has been limited research on the functional studies of dipteran parasitoids. Quantitative real-time polymerase chain reaction (qRT-PCR) is the most commonly used to address gene functions. Using qRT-PCR, stably expressed reference genes under different experimental conditions are required to normalize the expression of target genes. However, no information regarding suitable qRT-PCR reference genes in dipteran parasitoids has been reported. In this study, we evaluate the expression stability of nine commonly used reference genes in insects including eukaryotic translation elongation factor 1δ (eEF1δ), elongation factor 2, 18S ribosomal RNA (18S rRNA), tubulin 3, actin87, ribosomal protein 49 (RP49), ribosomal protein S15, glyceraldehyde-3-phosphate dehydrogenase, and TATA-box binding protein (TBP) in E. sorbillans under different treatments, including tissues, developmental stages, genders, feeding density and pesticide stress, using ∆Ct , BestKeeper, geNorm, Normfinder and RefFinder, respectively. The results showed that the genes RP49, eEF1δ and 18S rRNA were recommended as the most suitable reference genes in E. sorbillans across all experimental conditions. This finding provides the necessary foundation for future functional studies in E. sorbillans and its effective use in both sericulture and pest control.
Collapse
Affiliation(s)
- Jin Yang
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Zhe Jiang
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Qian Xu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Xinyi Liu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Minli Dai
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Bing Li
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, China
- Sericulture Institute of Soochow University, Suzhou, Jiangsu, China
| | - Jing Wei
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, China
- Sericulture Institute of Soochow University, Suzhou, Jiangsu, China
| |
Collapse
|
5
|
Zheng H, Zhao H, Zhang X, Liang Z, He Q. Systematic Identification and Validation of Suitable Reference Genes for the Normalization of Gene Expression in Prunella vulgaris under Different Organs and Spike Development Stages. Genes (Basel) 2022; 13:1947. [PMID: 36360184 PMCID: PMC9689956 DOI: 10.3390/genes13111947] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 08/01/2023] Open
Abstract
The quantitative real-time PCR (qRT-PCR) is an efficient and sensitive method for determining gene expression levels, but the accuracy of the results substantially depends on the stability of the reference gene (RG). Therefore, choosing an appropriate reference gene is a critical step in normalizing qRT-PCR data. Prunella vulgaris L. is a traditional Chinese medicine herb widely used in China. Its main medicinal part is the fruiting spike which is termed Spica Prunellae. However, thus far, few studies have been conducted on the mechanism of Spica Prunellae development. Meanwhile, no reliable RGs have been reported in P. vulgaris. The expression levels of 14 candidate RGs were analyzed in this study in various organs and at different stages of Spica Prunellae development. Four statistical algorithms (Delta Ct, BestKeeper, NormFinder, and geNorm) were utilized to identify the RGs' stability, and an integrated stability rating was generated via the RefFinder website online. The final ranking results revealed that eIF-2 was the most stable RG, whereas VAB2 was the least suitable as an RG. Furthermore, eIF-2 + Histon3.3 was identified as the best RG combination in different periods and the total samples. Finally, the expressions of the PvTAT and Pv4CL2 genes related to the regulation of rosmarinic acid synthesis in different organs were used to verify the stable and unstable RGs. The stable RGs in P. vulgaris were originally identified and verified in this work. This achievement provides strong support for obtaining a reliable qPCR analysis and lays the foundation for in-depth research on the developmental mechanism of Spica Prunellae.
Collapse
Affiliation(s)
- Hui Zheng
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Hongguang Zhao
- Tasly Botanical Pharmaceutical Co., Ltd., Shangluo 726000, China
| | - Xuemin Zhang
- Tasly R&D Institute, Tasly Holding Group Co., Ltd., Tianjin 300410, China
| | - Zongsuo Liang
- Shaoxing Academy of Biomedicine, Zhejiang Sci-Tech University, Shaoxing 312000, China
| | - Qiuling He
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Science and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| |
Collapse
|
6
|
Cheng SS, Ku YS, Cheung MY, Lam HM. Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification. FRONTIERS IN PLANT SCIENCE 2022; 13:1001920. [PMID: 36247637 PMCID: PMC9557097 DOI: 10.3389/fpls.2022.1001920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Arabidopsis thaliana has been used regularly as a model plant in gene expression studies on transcriptional reprogramming upon pathogen infection, such as that by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), or when subjected to stress hormone treatments including jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has been extensively employed to quantitate these gene expression changes. However, the accuracy of the quantitation is largely dependent on the stability of the expressions of reference genes used for normalization. Recently, RNA sequencing (RNA-seq) has been widely used to mine stably expressed genes for use as references in RT-qPCR. However, the amplification step in RNA-seq creates an intrinsic bias against those genes with relatively low expression levels, and therefore does not provide an accurate quantification of all expressed genes. In this study, we employed mass spectrometry-based label-free quantification (LFQ) in proteomic analyses to identify those proteins with abundances unaffected by Pst DC3000 infection. We verified, using RT-qPCR, that the levels of their corresponding mRNAs were also unaffected by Pst DC3000 infection. Compared to commonly used reference genes for expression studies in A. thaliana upon Pst DC3000 infection, the candidate reference genes reported in this study generally have a higher expression stability. In addition, using RT-qPCR, we verified that the mRNAs of the candidate reference genes were stably expressed upon stress hormone treatments including JA, SA, and ABA. Results indicated that the candidate genes identified here had stable expressions upon these stresses and are suitable to be used as reference genes for RT-qPCR. Among the 18 candidate reference genes reported in this study, many of them had greater expression stability than the commonly used reference genes, such as ACT7, in previous studies. Here, besides proposing more appropriate reference genes for Arabidopsis expression studies, we also demonstrated the capacity of mass spectrometry-based LFQ to quantify protein abundance and the possibility to extend protein expression studies to the transcript level.
Collapse
|
7
|
Transcriptomic and Non-Targeted Metabolomic Analyses Reveal the Flavonoid Biosynthesis Pathway in Auricularia cornea. Molecules 2022; 27:molecules27072334. [PMID: 35408732 PMCID: PMC9000485 DOI: 10.3390/molecules27072334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
Flavonoids, which are abundant in plants, are recognized for their antioxidant and anticancer roles in clinical applications. However, little is known about the molecular basis of flavonoid biosynthesis in fungi. In this study, we found that inclusion of leachate of Korshinsk peashrub (Caragana korshinskii) in the fermentation medium increased the total flavonoid content of the edible fungus Auricularia cornea by 23.6% relative to that grown in a control medium. Combined transcriptomic and non-targeted metabolomic analysis of the flavonoid biosynthesis pathway in A. cornea illustrated that there are important metabolites in the phenylpropanoid, coumarin and isoflavonoid biosynthesis pathways. In addition, we found that certain homologous genes encode phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO) and chalcone isomerase (CHI) in these biosynthesis pathways. These results, in this study, provide a new line for studying the regulation of flavonoid production in edible fungi.
Collapse
|
8
|
Fu N, Li J, Wang M, Ren L, Zong S, Luo Y. Identification and Validation of Reference Genes for Gene Expression Analysis in Different Development Stages of Amylostereum areolatum. Front Microbiol 2022; 12:827241. [PMID: 35095826 PMCID: PMC8790227 DOI: 10.3389/fmicb.2021.827241] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 12/29/2022] Open
Abstract
A strict relationship exists between the Sirex noctilio and the Amylostereum areolatum, which is carried and spread by its partner. The growth and development of this symbiotic fungus is key to complete the life history of the Sirex woodwasp. Real-time quantitative polymerase chain reaction (RT-qPCR) is used to measure gene expression in samples of A. areolatum at different growth stages and explore the key genes and pathways involved in the growth and development of this symbiotic fungus. To obtain accurate RT-qPCR data, target genes need to be normalized by reference genes that are stably expressed under specific experimental conditions. In our study, the stability of 10 candidate reference genes in symbiotic fungal samples at different growth and development stages was evaluated using geNorm, NormFinder, BestKeeper, delta Ct methods, and RefFinder. Meanwhile, laccase1 was used to validate the stability of the selected reference gene. Under the experimental conditions of this study, p450, CYP, and γ-TUB were identified as suitable reference genes. This work is the first to systematically evaluate the reference genes for RT-qPCR results normalization during the growth of this symbiotic fungus, which lays a foundation for further gene expression experiments and understanding the symbiotic relationship and mechanism between S. noctilio and A. areolatum.
Collapse
Affiliation(s)
- Ningning Fu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Jiaxing Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ming Wang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Shixiang Zong
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| |
Collapse
|
9
|
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] [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.
Collapse
|
10
|
Chen MD, Wang B, Li YP, Zeng MJ, Liu JT, Ye XR, Zhu HS, Wen QF. Reference gene selection for qRT-PCR analyses of luffa (Luffa cylindrica) plants under abiotic stress conditions. Sci Rep 2021; 11:3161. [PMID: 33542253 PMCID: PMC7862638 DOI: 10.1038/s41598-021-81524-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Selecting suitable internal reference genes is an important prerequisite for the application of quantitative real-time PCR (qRT-PCR). However, no systematic studies have been conducted on reference genes in luffa. In this study, seven reference genes were selected, and their expression levels in luffa plants exposed to various simulated abiotic stresses [i.e., cold, drought, heat, salt, H2O2, and abscisic acid (ABA) treatments] were analyzed by qRT-PCR. The stability of the reference gene expression levels was validated using the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. The results indicated that EF-1α was the most stably expressed and suitable reference gene overall and for the heat, cold, and ABA treatments. Additionally, UBQ expression was stable following the salt treatment, whereas TUB was identified as a suitable reference gene for H2O2 and drought treatments. The reliability of the selected reference genes was verified by analyzing the expression of copper/zinc superoxide dismutase (Cu/Zn-SOD) gene in luffa. When the most unstable reference genes were used for data normalizations, the resulting expression patterns had obvious biases when compared with the expression patterns for the most ideal reference genes used alone or combined. These results will be conducive to more accurate quantification of gene expression levels in luffa.
Collapse
Affiliation(s)
- Min-dong Chen
- grid.418033.d0000 0001 2229 4212Fujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Vegetable Research Center, Fujian Engineering Research Center for Vegetables, Fuzhou, 350013 Fujian China
| | - Bin Wang
- grid.418033.d0000 0001 2229 4212Fujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Vegetable Research Center, Fujian Engineering Research Center for Vegetables, Fuzhou, 350013 Fujian China
| | - Yong-ping Li
- grid.418033.d0000 0001 2229 4212Fujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Vegetable Research Center, Fujian Engineering Research Center for Vegetables, Fuzhou, 350013 Fujian China
| | - Mei-juan Zeng
- grid.418033.d0000 0001 2229 4212Fujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Vegetable Research Center, Fujian Engineering Research Center for Vegetables, Fuzhou, 350013 Fujian China
| | - Jian-ting Liu
- grid.418033.d0000 0001 2229 4212Fujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Vegetable Research Center, Fujian Engineering Research Center for Vegetables, Fuzhou, 350013 Fujian China
| | - Xin-ru Ye
- grid.418033.d0000 0001 2229 4212Fujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Vegetable Research Center, Fujian Engineering Research Center for Vegetables, Fuzhou, 350013 Fujian China
| | - Hai-sheng Zhu
- grid.418033.d0000 0001 2229 4212Fujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Vegetable Research Center, Fujian Engineering Research Center for Vegetables, Fuzhou, 350013 Fujian China
| | - Qing-fang Wen
- grid.418033.d0000 0001 2229 4212Fujian Key Laboratory of Vegetable Genetics and Breeding, Crops Research Institute, Fujian Academy of Agricultural Sciences, Vegetable Research Center, Fujian Engineering Research Center for Vegetables, Fuzhou, 350013 Fujian China
| |
Collapse
|
11
|
Wang G, Cheng H, Li M, Zhang C, Deng W, Li T. Selection and validation of reliable reference genes for Tolypocladium guangdongense gene expression analysis under differentially developmental stages and temperature stresses. Gene 2020; 734:144380. [PMID: 31978511 DOI: 10.1016/j.gene.2020.144380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/16/2019] [Accepted: 01/16/2020] [Indexed: 01/23/2023]
Abstract
Tolypocladium guangdongense, formerly known as Cordyceps guangdongensis, is a widely cultivated fungus of the Cordyceps s.l. species that has been investigated over the last 12 years. It has the potential to be used in a number of applications in the health and pharmaceutical industries for it has shown its high nutritional and medicinal values according to previous animal studies. qRT-PCR (quantitative reverse transcription polymerase chain reaction) is extensively used to analyze the expression pattern and molecular mechanisms of functional genes under differentially experimental conditions. The expression stability of reference genes used for normalization determines the reliability of qRT-PCR results, indicating the importance of selection and validation of reference genes before gene expression analysis. In the present study, three statistical algorithms, geNorm, NormFinder and BestKeeper, were used for analyzing the expression stability of nineteen candidate reference genes (CRGs) in T. guangdongense. Investigation were carried out under differentially experimental conditions, which included differentially developmential stages (mycelia, primordia, young and mature fruiting bodies), different carbon sources, cold and heat stresses. The results showed that histone H4 and tubulin beta chain 2 (β-tub2) were the most and least stable genes, respectively, across all the experimental samples. Moreover, analysis of individual data sets exhibited different stability and expression profiles of reference genes. The vacuolar protein sorting gene VPS was the most stable gene expressed under the differentially developmental stages and temperature stresses, whereas H4 was the most stably expressed gene under different carbon sources. Therefore, it can be proposed that VPS and H4 are the preferred reference genes for normalization of gene expression under different experimental conditions. The results of our present study will enable more accurate evaluation of gene expression in T. guangdongense using the optimal reference gene for qRT-PCR analysis.
Collapse
Affiliation(s)
- Gangzheng Wang
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China
| | - Huijiao Cheng
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China; South China Agricultural University, Guangzhou 510642, China
| | - Min Li
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China; College of Agriculture and Animal Husbandry, Tibet University, Nyingchi 860000, Tibet, China
| | - Chenghua Zhang
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China.
| | - Wangqiu Deng
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China.
| | - Taihui Li
- Guangdong Institute of Microbiology, Guangdong Academy of Sciences, State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangzhou 510070, China.
| |
Collapse
|