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Jiang J, Mu C, Bai Y, Cheng W, Geng R, Xu J, Dou Y, Cheng Z, Gao J. Selection and Validation of Reference Genes in Dendrocalamus brandisii for Quantitative Real-Time PCR. PLANTS (BASEL, SWITZERLAND) 2024; 13:2363. [PMID: 39273847 DOI: 10.3390/plants13172363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 08/15/2024] [Accepted: 08/21/2024] [Indexed: 09/15/2024]
Abstract
Dendrocalamus brandisii (Munro) Kurz is a sympodial bamboo species with a wide distribution in tropical and subtropical regions. Due to its remarkable regenerative ability and exceptional flavor, this species plays a pivotal role in bolstering the economies of numerous nations across these regions. We recently published a high-quality genome of this species. To date, no study results have identified the optimal reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) normalization in Dendrocalamus brandisii. qRT-PCR offers a highly accurate and effective approach to analyzing gene expression. However, the precision of the resulting quantitative data hinges on the correct choice of reference genes. Twenty-one potential reference genes were identified from the D. brandisii transcriptomes. Their expression in 23 samples, including 8 different tissue organs and 15 samples of D. brandisii under various treatment conditions, were evaluated through qRT-PCR. Subsequently, four software programs-Delta CT, geNorm, NormFinder, and RefFinder-were employed to compare their expression stability. The results revealed that the selection of optimal reference genes varied based on the particular organ and condition being examined. EF-1-α-2 consistently exhibits the most stable expression across diverse tissues, while ACTIN-1, TUBULIN-1, and EF-1-α-2 were the most consistent reference genes in roots, culms, and leaves under various treatments, respectively. In this study, we identified and characterized appropriate internal genes utilized for calibrating qRT-PCR analyses of D. brandisii across different tissue organs and under various treatments. This research will provide key insights for advancing the study of gene functionality and molecular biology in D. brandisii and related species.
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Affiliation(s)
- Jutang Jiang
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yucong Bai
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Ruiman Geng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Junlei Xu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Yuping Dou
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China
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Feng K, Yang ZY, Yan YJ, Sun N, Zhou ZQ, Liu JL, Zhao SP, Wu P, Li LJ. Selection of suitable reference genes for qPCR normalization in different developmental stages of Oenanthe javanica. FRONTIERS IN PLANT SCIENCE 2023; 14:1287589. [PMID: 38205019 PMCID: PMC10777208 DOI: 10.3389/fpls.2023.1287589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024]
Abstract
Gene expression analysis is widely used to unravel molecular regulatory mechanisms and identify key genes in plants. Appropriate reference gene is an important prerequisite to ensure the accuracy and reliability of qPCR analysis results. Water dropwort is a plant of the Oenanthe genus in the Apiaceae family, which has high economic benefits. However, the underlying molecular regulatory mechanisms in the growth and development of water dropwort have not been fully understood and the appropriate reference genes in different developmental stages of water dropwort not yet reported. In this study, 10 candidate reference genes (ACTIN, PP2A, SAND, EF-1α, GAPDH, UBQ, MIP, TBP, RPS-18, eIF-4α) were identified and cloned from Oenanthe javanica. The qPCR primers of candidate reference genes were designed and verified. Four statistical algorithms, geNorm, NormFinder, BestKeeper and RefFinder were used to evaluate the expression stability of 10 candidate reference genes in different developmental stages of water dropwort. The results showed that TBP and UBQ were the most stable genes in different developmental stages of water dropwort, while GAPDH was the most unstable gene. The normalization of EXP1 genes at different developmental stages further confirmed the reliability of internal reference genes. The results of this study provide a theoretical basis for selecting appropriate internal reference genes in different developmental stages of water dropwort. This study also provides technical support and reliable basis for the expression analysis of key genes in different developmental stages of water dropwort.
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Affiliation(s)
- Kai Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Zhi-Yuan Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Ya-Jie Yan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Nan Sun
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Zi-Qi Zhou
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Jia-Lu Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Shu-Ping Zhao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Peng Wu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Liang-Jun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri−Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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Liu Q, Wang S, Wen J, Chen J, Sun Y, Dong S. Genome-wide identification and analysis of the WRKY gene family and low-temperature stress response in Prunus sibirica. BMC Genomics 2023; 24:358. [PMID: 37370033 DOI: 10.1186/s12864-023-09469-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND WRKY transcription factors are a prominent gene family in plants, playing a crucial role in various biological processes including development, metabolism, defense, differentiation, and stress response. Although the WRKY gene family has been extensively studied and analysed in numerous plant species, research on Prunus sibirica's WRKY genes (PsWRKY) remains lacking. RESULTS This study analysed the basic physicochemical properties, phylogeny, gene structure, cis-acting elements, and Gene ontology (GO) annotation of PsWRKY gene family members using bioinformatics methods based on the whole-genome data of P. sibirica. In total, 55 WRKYs were identified in P. sibirica and were heterogeneously distributed on eight chromosomes. Based on the phylogenetic analysis, these WRKYs were classified into three major groups: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III. Members of different subfamilies have different cis-acting elements, conserved motifs, and intron-exon structures, indicating functional heterogeneity of the WRKY family. Prediction of subcellular localisation indicated that PsWRKYs were mainly located in the nucleus. Twenty pairs of duplicated genes were identified, and segmental duplication events may play an important role in PsWRKY gene family expansion. Analysis of the Ka/Ks ratio showed that the PsWRKY family's homologous genes were primarily purified by selection. Additionally, GO annotation analysis showed that the WRKY gene family was mainly involved in responses to stimuli, immune system processes, and reproductive processes. Furthermore, quantitative real-time PCR (qRT-PCR) analysis showed that 23 PsWRKYs were highly expressed in one or more tissues (pistils and roots) and PsWRKYs showed specific expression patterns under different low-temperature stress conditions. CONCLUSIONS Our results provide a scientific basis for the further exploration and functional validation of WRKYs in P. sibirica.
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Affiliation(s)
- Quangang Liu
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Shipeng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Jiaxing Wen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Jianhua Chen
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Yongqiang Sun
- College of Forestry, Shenyang Agricultural University, Shenyang, China
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - Shengjun Dong
- College of Forestry, Shenyang Agricultural University, Shenyang, China.
- Key Laboratory for Silviculture of Liaoning Province, Shenyang Agricultural University, Shenyang, China.
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Lu L, Tang Y, Xu H, Qian Y, Tao J, Zhao D. Selection and verification of reliable internal reference genes in stem development of herbaceous peony ( Paeonia lactiflora Pall.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:773-782. [PMID: 37520813 PMCID: PMC10382430 DOI: 10.1007/s12298-023-01325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 08/01/2023]
Abstract
Herbaceous peony (Paeonia lactiflora Pall.) has emerged in the cut flower market due to its beautiful appearance. The bending flower stems caused by a lack of mechanical strength is the main problem restricting the development of the cut P. lactiflora industry. So it is of great worth to reveal the basis of stem development changes in P. lactiflora to improve its cut flower quality. Quantitative research on gene expression characteristics can provide clues for understanding their biological functions, and the screening of relatively stable expression genes is a prerequisite for the quantitative study of gene expression characteristics. Thus, it is necessary to find appropriate genes during stem development so as to analyze the qRT‒PCR results. In this study, 10 genes were screened, and these genes expressed stably in stems of different stem strengths at three different developmental stages. Then, their expressions were evaluated by RefFinder, BestKeeper, NormFinder, and GeNorm programs. The results demonstrated that γ-tubulin (γ-TUB) was the most suitable gene, followed by α-tubulin (α-TUB) and β-D-glucosidase (β-GUS), whereas histone H3 (His) was the least suitable gene. Besides, the temporal and spatial expression characteristics of PlCOMT1, the key gene concerned with the synthesis of cell wall fillers in P. lactiflora, were also used to evaluate the suitability of genes. Consequently, γ-TUB and α-TUB are the two best combinations during stem development, and their combination can be used for the stem development of P. lactiflora. These findings will provide a reference for the selection of genes related to stem development and the study of molecular mechanisms related to stem development in P. lactiflora. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01325-5.
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Affiliation(s)
- Lili Lu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yuhan Tang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Huajie Xu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yi Qian
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jun Tao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Daqiu Zhao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, 225009 Jiangsu China
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Liu H, Liu J, Chen P, Zhang X, Wang K, Lu J, Li Y. Selection and Validation of Optimal RT-qPCR Reference Genes for the Normalization of Gene Expression under Different Experimental Conditions in Lindera megaphylla. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112185. [PMID: 37299163 DOI: 10.3390/plants12112185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/18/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Lindera megaphylla, a broad-leaved evergreen that is used as a landscape ornamental plant and medicinal plant, is an ecologically important and dominant tree species. However, little is known about the molecular mechanisms of its growth, development, and metabolism. The selection of suitable reference genes is critical for molecular biological analyses. To date, no research on reference genes as a foundation for gene expression analysis has been undertaken in L. megaphylla. In this study, 14 candidate genes were selected from the transcriptome database of L. megaphylla for RT-qPCR assay under different conditions. Results showed that helicase-15 and UBC28 were most stable in different tissues of seedlings and adult trees. For different leaf developmental stages, the best combination of reference genes was ACT7 and UBC36. UBC36 and TCTP were the best under cold treatment, while PAB2 and CYP20-2 were the best under heat treatment. Finally, a RT-qPCR assay of LmNAC83 and LmERF60 genes were used to further verify the reliability of selected reference genes above. This work is the first to select and evaluate the stability of reference genes for the normalization of gene expression analysis in L. megaphylla and will provide an important foundation for future genetic studies of this species.
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Affiliation(s)
- Hongli Liu
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Jing Liu
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Peng Chen
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Xin Zhang
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Ke Wang
- Zhengzhou Botanical Garden, Zhengzhou 450042, China
| | - Jiuxing Lu
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
| | - Yonghua Li
- International Union Laboratory of Landscape Architecture of Henan, College of Landscape Architecture and Arts, Henan Agricultural University, Zhengzhou 450003, China
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Wang G, Guan SL, Zhu N, Li Q, Chong X, Wang T, Xuan J. Comprehensive Genomic Analysis of SnRK in Rosaceae and Expression Analysis of RoSnRK2 in Response to Abiotic Stress in Rubus occidentalis. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091784. [PMID: 37176842 PMCID: PMC10181103 DOI: 10.3390/plants12091784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The sucrose nonfermenting 1-related protein kinase (SnRK) plays an important role in responding to abiotic stresses by phosphorylating the target protein to regulate various signaling pathways. However, little is known about the characteristics, evolutionary history, and expression patterns of the SnRK family in black raspberry (Rubus occidentalis L.) or other Rosaceae family species. In this study, a total of 209 SnRK genes were identified in 7 Rosaceae species and divided into 3 subfamilies (SnRK1, SnRK2, and SnRK3) based on phylogenetic analysis and specific motifs. Whole-genome duplication (WGD) and dispersed duplication (DSD) were considered to be major contributions to the SnRK family expansion. Purifying selection was the primary driving force in the SnRK family evolution. The spatial expression indicated that the RoSnRK genes may play important roles in different tissues. In addition, the expression models of 5 RoSnRK2 genes in response to abiotic stresses were detected by qRT-PCR. The proteins encoded by RoSnRK2 genes localize to the cytoplasm and nucleus in order to perform their respective functions. Taken together, this study provided an analysis of the SnRK gene family expansion and evolution, and contributed to the current knowledge of the function of 5 RoSnRK2 genes, which in turn expanded understanding of the molecular mechanisms of black raspberry responses to abiotic stress.
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Affiliation(s)
- Guoming Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Sophia Lee Guan
- College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, MD 20742, USA
| | - Nan Zhu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Tao Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Jiping Xuan
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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Yu J, Wang R, Ma W, Lei S, Zhu M, Yang G. Pectate Lyase Gene VvPL1 Plays a Role in Fruit Cracking of Table Grapes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1643-1654. [PMID: 36638364 DOI: 10.1021/acs.jafc.2c05996] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Fruit cracking seriously affects the commercial value of table grapes. To explore whether cell wall disassembly influences grape berry cracking, first, the differences in the cell wall metabolism were compared between cracking-resistant "Shennongjinhuanghou" (SN) and cracking-susceptible "Xiangfei" (XF) varieties. Our results showed that cell wall disassembly events were extremely different between "SN" and "XF." The cracking-resistant "SN" had a higher pectinmethylesterase activity in the early stage and lower polygalacturonase, β-galactosidase, pectate lyase, and cellulase activities from veraison, cooperatively yielding higher ionically bound pectin, covalently bound pectin, hemicellulose, and lower water-soluble pectin, leading to a stronger skin break force and elasticity and conferring "SN" with higher cracking resistance. Furthermore, the function of the VvPL1 gene in fruit cracking was verified by heterologously transforming tomatoes. The transgenic experiment showed that overexpressed fruits had a higher activity of pectate lyase from the breaking stage and a lower level of covalently bound pectin, ionically bound pectin, cellulose, and hemicellulose and a higher level of water-soluble pectin at the red ripe stage, which resulted in a significantly reduced skin break force and flesh firmness and increased fruit cracking incidences. In conclusion, our results demonstrated that the cracking susceptibility of the grape berry is closely related to cell wall disassembly events and VvPL1 plays an important role in fruit cracking.
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Affiliation(s)
- Jun Yu
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi417000, Hunan, China
| | - Rong Wang
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
| | - Wentao Ma
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
| | - Shumin Lei
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
| | - Mingtao Zhu
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi417000, Hunan, China
| | - Guoshun Yang
- College of Horticulture, Hunan Agricultural University, Nongda Road No. 1, Furong District, Changsha410128, Hunan, China
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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.
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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
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Yi S, Lu H, Tian C, Xu T, Song C, Wang W, Wei P, Gu F, Liu D, Cai Y, Han B. Selection of Suitable Reference Genes for Gene Expression Normalization Studies in Dendrobium huoshanense. Genes (Basel) 2022; 13:genes13081486. [PMID: 36011396 PMCID: PMC9408602 DOI: 10.3390/genes13081486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrobium huoshanense is a kind of precious herb with important medicinal and edible value in China, which is widely used in traditional Chinese medicine for various diseases. Recent studies have paid close attention to the genetic expression of the biosynthetic pathway of the main active components (polysaccharides, alkaloids, and flavonoids), and real-time polymerase chain reaction (qPCR) is one of the most widely used methods for doing so. However, so far, no reference gene selections have been reported in D. huoshanense. In this study, 15 reference gene candidates (GAPDH, eIF, EF-1α, PP2A, UBCE, RPL5, TBP, APT1, MDH, PTBP3, PEPC, CYP71, NCBP2, TIP41, and F-box) were selected and evaluated for their expression stability in D. huoshanense under various experimental conditions, including in different tissues (root, stem, and leaf), abiotic stresses (oxidative, drought, cold, and UV), and hormone treatment (methyl jasmonate) using three statistical programs (geNorm, NormFinder, and BestKeeper). Then, the RefFinder program was employed to comprehensively validate the stability of the selected reference genes. Finally, the expression profiles of the CESA and GMPP genes were further analyzed, and these results indicated that TBP, NCBP2, and CYP71 were the top three most stable reference genes after comprehensive comparison, which could be used as stable reference genes for normalizing the genes expression in D. huoshanense. This study described here provides the first data regarding on reference gene selection in D. huoshanense, which will be extremely beneficial for future research on the gene expression normalization in D. huoshanense.
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Affiliation(s)
- Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Haibo Lu
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Chuanjun Tian
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Cheng Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Peipei Wei
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Fangli Gu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Dong Liu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (Y.C.); (B.H.); Tel.: +86-564-3307060 (B.H.)
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
- Correspondence: (Y.C.); (B.H.); Tel.: +86-564-3307060 (B.H.)
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Zhang Y, Zeng L, Wei Y, Zhang M, Pan W, Sword GA, Yang F, Chen F, Wan G. Reliable reference genes for gene expression analyses under the hypomagnetic field in a migratory insect. Front Physiol 2022; 13:954228. [PMID: 36003646 PMCID: PMC9393789 DOI: 10.3389/fphys.2022.954228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Manipulating the hypomagnetic field (HMF), which is the absence or significant weakening (<5 μT) of the geomagnetic field (GMF), offers a unique tool to investigate magnetic field effects on organismal physiology, development, behavior and life history. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) has been utilized to study changes in gene expression associated with exposure to the HMF. However, selecting appropriate reference genes (RGs) with confirmed stable expression across environments for RT-qPCR is often underappreciated. Using three algorithms (BestKeeper, NormFinder, and GeNorm), we investigated the expression stability of eight candidate RGs when exposed to the HMF condition versus local GMF during developmental from juveniles to adults in the migratory insect pest, the brown planthopper Nilaparvata lugens. During the nymphal stage, RPL5 & α-TUB1, EF1-α & ARF1, RPL5 & AK, EF1-α & RPL5, and ARF1 & AK were suggested as the most stable RG sets in the 1st to 5th instars, respectively. For 1- to 3-day-old adults, AK & ARF1, AK & α-TUB1, AK & ARF1 and EF1-α & RPL5, AK & α-TUB1, AK & EF1-α were the optimal RG sets for macropterous and brachypterous females, respectively. ACT1 & RPL5, RPL5 & EF1-α, α-TUB1 & ACT1 and EF1-α & RPL5, ARF1 & ACT1, ACT1 & ARF1 were the optimal RG sets for macropterous and brachypterous males, respectively. These results will facilitate accurate gene expression analyses under the HMF in N. lugens. The verification approach illustrated in this study highlights the importance of identifying reliable RGs for future empirical studies of magnetobiology (including magnetoreception) that involve magnetic field intensity as a factor.
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Affiliation(s)
- Ying Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Health & Crop Safety, Nanjing Agricultural University, Nanjing, China
| | - Luying Zeng
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Health & Crop Safety, Nanjing Agricultural University, Nanjing, China
| | - Yongji Wei
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Health & Crop Safety, Nanjing Agricultural University, Nanjing, China
| | - Ming Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Health & Crop Safety, Nanjing Agricultural University, Nanjing, China
| | - Weidong Pan
- Beijing Key Laboratory of Bioelectromagnetics, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing, China
| | - Gregory A. Sword
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Fei Yang
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Fajun Chen
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Health & Crop Safety, Nanjing Agricultural University, Nanjing, China
| | - Guijun Wan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Plant Health & Crop Safety, Nanjing Agricultural University, Nanjing, China
- *Correspondence: Guijun Wan,
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Li J, Fu N, Ren L, Luo Y. Identification and Validation of Reference Genes for Gene Expression Analysis in Monochamus saltuarius Under Bursaphelenchus xylophilus Treatment. Front Physiol 2022; 13:882792. [PMID: 35547586 PMCID: PMC9082747 DOI: 10.3389/fphys.2022.882792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
A special mutual relationship exists between the pine wood nematode (PWN) Bursaphelenchus xylophilus and its vector beetles of genus Monochamus, which enables PWN to spread, at the same time provides longhorned beetles with more weak hosts. PWN are attracted to the pupal chambers and then carried inside the trachea of beetle adults, which is a necessary part to complete the B. xylophilus infection cycle. The growth and immune responses of the vector beetle will affect this carrying process, however, they were rarely studied in Monochamus saltuarius. Real-time quantitative polymerase chain reaction (RT-qPCR), one of the most common methods for quantitative gene expression analysis, was performed to explore the key genes and pathways involved in the growth, development and immune responses of M. saltuarius at different developmental stages associated with infection of PWN and PWN treatment conditions. To enhance the accuracy of RT-qPCR data, the expression of target genes needs to be normalized with reference genes, which are stably expressed under varied experimental conditions. In our study, the stability of 14 candidate reference genes in M. saltuarius samples at different developmental stages associated with infection of PWN or PWN treatment conditions was evaluated using delta Ct, geNorm, NormFinder, BestKeeper and RefFinder algorithms. Moreover, KLF gene was used to validate the stability of the selected reference genes. Under experimental conditions of this study, RPL7 and TER were suitable reference genes at different developmental stages associated with infection of PWN. RPL7 and RPS5 were considered the most stable reference genes in the pupae treated with PWN. RPS5 and SNX6 could be used as reference genes in the adults treated with PWN. RPL7, EF1-γ, and RPS5 could be used as stable reference genes in all the samples. This work is the first to evaluate reference genes in M. saltuarius, laying a foundation for further gene expression experimental procedures and understanding the phoretic relationship between M. saltuarius and B. xylophilus.
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Affiliation(s)
- Jiaxing Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ningning Fu
- 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
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
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Wang S, Zhang S. Selection of the Reference Gene for Expression Normalization in Salsola ferganica under Abiotic Stress. Genes (Basel) 2022; 13:genes13040571. [PMID: 35456377 PMCID: PMC9029158 DOI: 10.3390/genes13040571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/01/2023] Open
Abstract
Salsola ferganica is a natural desert herbaceous plant in the arid area of western and northwestern China. Because of its salt tolerance and drought resistance, it is of great significance in desert afforestation and sand-fixing capacity. There has been much research on the genes involved in plants under desert stresses in recent years. The application of the best internal reference genes for standardization was a critical procedure in analyzing the gene expression under different types. Even so, the reference gene has not been reported in the application of gene expression normalization of S. ferganica. In this study, nine reference genes (TUA-1726, TUA-1760, TUB, GAPDH, ACT, 50S, HSC70, APT, and U-box) in S. ferganica were adopted and analyzed under six different treatments (ABA, heat, cold, NaCl, methyl viologen (MV), and PEG). The applicability of candidate genes was evaluated by statistical software, including geNorm, NormFinder, BestKeeper, and RefFinder, based on their stability values in all the treatments. These results indicated that the simultaneous selection of two stable reference genes would fully standardize the optimization of the normalization research. To verify the feasibility of the above internal reference genes, the CT values of AP2/ERF transcription factor family genes were standardized using the most (ACT) and least (GAPDH) stable reference genes in S. ferganica seedlings under six abiotic stresses. The research showed that HSC70 and U-box were the most appropriate reference genes in ABA stressed samples, and ACT and U-box genes were the optimal references for heat-stressed samples. TUA-1726 and U-box showed the smallest value in gene expression levels of cold treatment. The internal reference groups of the best applicability for the other samples were U-box and ACT under NaCl treatment, ACT and TUA-1726 under MV stress, HSC70 and TUB under PEG treatment, and ACT in all samples. ACT and U-box showed higher stability than the other genes based on the comprehensive stability ranking of RefFinder, as determined by the geometric mean in this study. These results will contribute to later gene expression studies in other closely related species and provide an important foundation for gene expression analysis in S. ferganica.
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Affiliation(s)
- Shuran Wang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
| | - Sheng Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China;
- College of Forestry, Northwest A&F University, Xianyang 712100, China
- Correspondence:
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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.
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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
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