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Zou K, Wang T, Guan M, Liu Y, Li J, Liu Y, Du J, Wu D. Identification and Evaluation of qRT-PCR Reference Genes in Melanaphis sacchari. INSECTS 2024; 15:522. [PMID: 39057255 DOI: 10.3390/insects15070522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 06/26/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024]
Abstract
Appropriate reference genes must be selected for accurate qRT-PCR data to conduct a thorough gene expression analysis in the sorghum aphid (Melanaphis sacchari, Hemiptera, Aphididae). This approach will establish a foundation for gene expression analysis and determines the efficacy of RNA interference in the sorghum aphid. Nine potential reference genes, including Actin, 18S, GAPDH, RPL7, EF-1α, EF-1β, 28S, HSP70, and TATA, were assessed under various experimental conditions to gauge their suitability based on qRT-PCR Ct values. The stability of these candidate reference genes in diverse experimental setups was analyzed employing several techniques, including the ΔCt comparative method, geNorm, Normfinder, BestKeeper, and RefFinder. The findings revealed that the quantity of ideal reference genes ascertained by the geNorm method for diverse experimental conditions remained consistent. For the developmental stages of the sorghum aphid, RPL7 and 18S proved to be the most dependable reference genes, whereas GAPDH and EF-1β were recommended as the most stable reference genes for different tissues. In experiments involving wing dimorphism, EF-1α and GAPDH were identified as the optimal reference gene pair. Under varying temperatures, EF-1α and EF-1β were found to be the most dependable gene pair. For studies focusing on insecticide susceptibility, 18S and TATA emerged as the most stable candidate reference genes. Across all experimental conditions, EF-1α and EF-1β was the optimal combination of reference genes in the sorghum aphid. This research has pinpointed stable reference genes that can be utilized across various treatments, thereby enhancing gene expression studies and functional genomics research on the sorghum aphid.
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Affiliation(s)
- Kunliang Zou
- College of Agriculture, Anhui Science and Technology University, Chuzhou 233100, China
| | - Tonghan Wang
- College of Agriculture, Anhui Science and Technology University, Chuzhou 233100, China
| | - Minghui Guan
- Anhui Province International Joint Research Center of Forage Bio-Breeding, Chuzhou 233100, China
- College of Resources and Environment, Anhui Science and Technology University, Chuzhou 233100, China
| | - Yang Liu
- College of Resources and Environment, Anhui Science and Technology University, Chuzhou 233100, China
| | - Jieqin Li
- College of Agriculture, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Province International Joint Research Center of Forage Bio-Breeding, Chuzhou 233100, China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Province International Joint Research Center of Forage Bio-Breeding, Chuzhou 233100, China
| | - Junli Du
- College of Agriculture, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Province International Joint Research Center of Forage Bio-Breeding, Chuzhou 233100, China
| | - Degong Wu
- College of Agriculture, Anhui Science and Technology University, Chuzhou 233100, China
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Zhang S, Zhu E, Wang Z, Zhong Y, Zha X, Ji H, Meng Q. Evaluation of suitable reference genes for expression profile analyses of target genes in the coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2024; 114:57-66. [PMID: 38180086 DOI: 10.1017/s0007485323000615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae), is a major destructive insect pest of coffee, which impacts the coffee crops negatively. As a draft genome has been completed for this insect, most molecular studies on gene transcriptional levels under different experimental conditions will be conducted using real-time reverse-transcription quantitative polymerase chain reactions (RT-qPCR). However, the lack of suitable internal reference genes will affect the accuracy of RT-qPCR results. In this study, the expression stability of nine candidate reference genes was evaluated under different developmental stages, temperature stress, and Beauveria bassiana infection. Data analyses were completed by four commonly used programs, BestKeeper, NormFinder, geNorm, and RefFinder. The result showed that RPL3 and EF1α combination were recommended as the most stable reference genes for developmental stages. EF1α and RPS3a combination were the top two stable reference genes for B. bassiana infection. RPS3a and RPL3 combination performed as the optimal reference genes both in temperature stress and all samples. Our results should provide a good foundation for the expression profile analyses of target genes in the future, especially for molecular studies on insect genetic development, temperature adaptability, and immune mechanism to entomogenous fungi in H. hampei.
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Affiliation(s)
- Shaohua Zhang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Enhang Zhu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Zheng Wang
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, The First Batch of Key Disciplines On Public Health in Chongqing, Department of Disinfection and Vector Control, Chongqing Center for Disease Control and Prevention, Chongqing 40042, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Yaofeng Zhong
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Xuezong Zha
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Hengqing Ji
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, The First Batch of Key Disciplines On Public Health in Chongqing, Department of Disinfection and Vector Control, Chongqing Center for Disease Control and Prevention, Chongqing 40042, P.R. China
| | - Qianqian Meng
- Institute of Agricultural Resources and Environment, Chongqing Academy of Agricultural Sciences, Chongqing 40042, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
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Wang L, Liu Q, Guo P, Gao Z, Chen D, Zhang T, Ning J. Evaluation of Reference Genes for Quantitative Real-Time PCR Analysis in the Bean Bug, Riptortus pedestris (Hemiptera: Alydidae). INSECTS 2023; 14:960. [PMID: 38132633 PMCID: PMC10743553 DOI: 10.3390/insects14120960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Quantitative real-time PCR (qRT-PCR) is widely accepted as a precise and convenient method for quantitatively analyzing the expression of functional genes. The data normalization strongly depends upon stable reference genes. The bean bug, Riptortus pedestris (Hemiptera: Alydidae), is a significant pest of leguminous crops and broadly distributed across Southeast Asia. In this study, a total of 16 candidate reference genes (RPL32, RPS23, SDHA, UBQ, UCCR, GST, TATA-box, HSP70, GAPDH, RPL7A, SOD, RPS3, Actin, α-tubulin, AK, and EF1) were carefully chosen in R. pedestris, and their expression levels were assessed across various conditions, including different developmental stages, diverse tissues, temperature treatments, adult age, molting time, and mating status. Following this, the stability of these reference genes was evaluated using four algorithms (ΔCt, GeNorm, NormFinder, and BestKeeper). Ultimately, the comprehensive rankings were determined using the online tool RefFinder. Our results demonstrate that the reference gene for qRT-PCR analysis in R. pedestris is contingent upon the specific experimental conditions. RPL7A and EF1 are optimal reference genes for developmental stages. Furthermore, α-tubulin and EF1 exhibit the most stable expression across various adult tissues. RPL32 and RPL7A exhibit the most stable expression for adult age. For nymph age, RPL32 and SOD display the most stable expression. For temperature conditions, RPS23 and RPL7A were identified as the most suitable for monitoring gene expression. Lastly, we verified the practicability of evaluating expression levels of odorant-binding protein 37 (RpedOBP37) and cytochrome P450 6a2 (RpedCYP6) throughout developmental stages, tissues, and temperature conditions. These findings are a significant addition to the qRT-PCR analysis studies on R. pedestris, serving as a fundamental groundwork for future investigations on stable reference genes in R. pedestris as well as other organisms.
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Affiliation(s)
- Liuyang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (Q.L.)
| | - Qingyu Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (Q.L.)
| | - Pei Guo
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding 071000, China; (P.G.); (Z.G.); (D.C.)
| | - Zhanlin Gao
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding 071000, China; (P.G.); (Z.G.); (D.C.)
| | - Dan Chen
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding 071000, China; (P.G.); (Z.G.); (D.C.)
| | - Tao Zhang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding 071000, China; (P.G.); (Z.G.); (D.C.)
| | - Jun Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (Q.L.)
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Martín-Pérez T, Köhsler M, Walochnik J. Evaluation and validation of reference genes for RT-qPCR gene expression in Naegleria gruberi. Sci Rep 2023; 13:16748. [PMID: 37798308 PMCID: PMC10555999 DOI: 10.1038/s41598-023-43892-3] [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: 05/26/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023] Open
Abstract
Naegleria gruberi is a free-living amoeboflagellate commonly found in freshwater and in soils around the world. It is a non-pathogenic relative of Naegleria fowleri, which is the etiologic agent of Primary Amoebic Meningoencephalitis (PAM). PAM occurs world-wide and it is considered a rare disease, but its fatality rate is high (96%) mainly because of delay in initiation of treatment due to misdiagnosis and lack of a specific treatment. The analysis of gene expression by quantitative real-time PCR in N. gruberi could be a highly efficient means to understand the pathogenicity of N. fowleri and also to find drug targets. Accurate RT-qPCR analysis requires correct normalization of gene expression data using reference genes (RG), whose expression should be constant under different experimental conditions. In this study, six genes, representing the most frequently used housekeeping genes, were selected for evaluation as reference genes in N. gruberi. The expression and stability of these genes was evaluated employing four algorithms (geNorm, NormFinder, BestKeeper and RefFinder). This work shows significant variations of the stability of RGs depending on the algorithms employed and on the experimental conditions (i.e. logarithmic, stationary, heat-shock and oxidative stress). The geNorm, NormFinder and RefFinder analysis of all the experimental conditions in combination revealed that ACT and G6PD were the most stable RGs. While BestKeeper analysis showed that 18S and TBP were the most stable RGs. Moreover, normalization of HSP90 gene expression with the most stable RGs resulted in an upregulation whereas when the normalization was done with the unstable RGs, the gene expression was not reliable. Hence, the implications of this study are relevant to gene expression studies in N. gruberi.
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Affiliation(s)
- Tania Martín-Pérez
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria.
| | - Martina Köhsler
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria
| | - Julia Walochnik
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, 1090, Vienna, Austria
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Evaluation of Reference Genes for Real-Time Quantitative PCR Analysis in Tissues from Bumble Bees ( Bombus Terrestris) of Different Lines. Int J Mol Sci 2022; 23:ijms232214371. [PMID: 36430847 PMCID: PMC9692494 DOI: 10.3390/ijms232214371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Bumble bees are important alternative pollinators and model insects due to their highly developed sociality and colony management. In order to better understand their molecular mechanisms, studies focusing on the genetic and molecular aspects of their development and behavior are needed. Although quantitative real-time polymerase chain reaction (qRT-PCR) can be used to quantify the relative expression of target genes, internal reference genes (which are stably expressed across different lines and tissues) must first be identified to ensure the accurate normalization of target genes. In order to contribute to molecular studies on bumble bees, we used Bombus terrestris to determine the expression stability of eight reference genes (β-actin (ACT), Arginine Kinase (AK), Phospholipase A2 (PLA2), Elongation factor 1 alpha (EF-1), Ribosomal proteins (S5, S18, S28) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH)) in five different lines and several tissues (ovary, thorax, fat body, and head) using RT-qPCR procedures and four analysis programs (RefFinder, NormFinder, BestKeeper, and geNorm). In general, the S28, S5, and S18 ribosomal protein genes and the PLA2 and EF-1 genes showed the highest stability and were therefore identified as suitable reference genes for the bumble bee species and their defined lines and tissues. Our results also emphasized the need to evaluate the stability of candidate reference genes for any differently designed lines and tissue conditions in bumble bee species.
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Validation of quantitative real-time PCR reference genes and spatial expression profiles of detoxication-related genes under pesticide induction in honey bee, Apis mellifera. PLoS One 2022; 17:e0277455. [DOI: 10.1371/journal.pone.0277455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
Recently, pesticides have been suggested to be one of the factors responsible for the large-scale decline in honey bee populations, including colony collapse disorder. The identification of the genes that respond to pesticide exposure based on their expression is essential for understanding the xenobiotic detoxification metabolism in honey bees. For the accurate determination of target gene expression by quantitative real-time PCR, the expression stability of reference genes should be validated in honey bees exposed to various pesticides. Therefore, in this study, to select the optimal reference genes, we analyzed the amplification efficiencies of five candidate reference genes (RPS5, RPS18, GAPDH, ARF1, and RAD1a) and their expression stability values using four programs (geNorm, NormFinder, BestKeeper, and RefFinder) across samples of five body parts (head, thorax, gut, fat body, and carcass) from honey bees exposed to seven pesticides (acetamiprid, imidacloprid, flupyradifurone, fenitrothion, carbaryl, amitraz, and bifenthrin). Among these five candidate genes, a combination of RAD1a and RPS18 was suggested for target gene normalization. Subsequently, expression levels of six genes (AChE1, CYP9Q1, CYP9Q2, CYP9Q3, CAT, and SOD1) were normalized with a combination of RAD1a and RPS18 in the different body parts from honey bees exposed to pesticides. Among the six genes in the five body parts, the expression of SOD1 in the head, fat body, and carcass was significantly induced by six pesticides. In addition, among seven pesticides, flupyradifurone statistically induced expression levels of five genes in the fat body.
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Liu Z, Xiao J, Xia Y, Wu Q, Zhao C, Li D. Selection and validation of reference genes for RT-qPCR-based analyses of Anastatus japonicus Ashmead (Hymenoptera: Helicopteridae). Front Physiol 2022; 13:1046204. [PMID: 36338494 PMCID: PMC9626802 DOI: 10.3389/fphys.2022.1046204] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022] Open
Abstract
RT-qPCR remains a vital approach for molecular biology studies aimed at quantifying gene expression in a range of physiological or pathological settings. However, the use of appropriate reference genes is essential to attain meaningful RT-qPCR results. Anastatus japonicus Ashmead (Hymenoptera: Helicopteridae) is an important egg parasitoid wasp and natural enemy of fruit bugs and forest caterpillars. While recent transcriptomic studies have analyzed gene expression profiles in A. japonicus specimens, offering a robust foundation for functional research focused on this parasitoid, no validated A. japonicus reference genes have yet been established, hampering further research efforts. Accordingly, this study sought to address this issue by screening for the most stable internal reference genes in A. japonicus samples to permit reliable RT-qPCR analyses. The utility of eight candidate reference genes (ACTIN, TATA, GAPDH, TUB, RPL13, RPS6, EF1α, RPS3a) was assessed under four different conditions by comparing developmental stages (larvae, pupae, adults), tissues (abdomen, chest, head), sex (male or female adults), or diapause states (diapause induction for 25, 35, 45, or 55 days, or diapause termination). RefFinder was used to calculate gene stability based on the integration of four algorithms (BestKeeper, Normfinder, geNorm, and ΔCt method) to determine the optimal RT-qPCR reference gene. Based on this approach, RPS6 and RPL13 were found to be the most reliable reference genes when assessing different stages of development, while ACTIN and EF1α were optimal when comparing adults of different sexes, RPL13 and EF1α were optimal when analyzing different tissues, and TATA and ACTIN were optimal for different diapause states. These results provide a valuable foundation for future RT-qPCR analyses of A. japonicus gene expression and function under a range of experimental conditions.
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Affiliation(s)
- Zixin Liu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Junjiang Xiao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Yue Xia
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qifeng Wu
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Can Zhao
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Can Zhao, Dunsong Li,
| | - Dunsong Li
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Can Zhao, Dunsong Li,
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Fan R, Tao XY, Xia ZQ, Sim S, Hu LS, Wu BD, Wang QH, Hao CY. Comparative Transcriptome and Metabolome Analysis of Resistant and Susceptible Piper Species Upon Infection by the Oomycete Phytophthora Capsici. FRONTIERS IN PLANT SCIENCE 2022; 13:864927. [PMID: 35845707 PMCID: PMC9278165 DOI: 10.3389/fpls.2022.864927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/16/2022] [Indexed: 06/04/2023]
Abstract
Phytophthora capsici is a destructive oomycete pathogen that causes devastating disease in black pepper, resulting in a significant decline in yield and economic losses. Piper nigrum (black pepper) is documented as susceptible to P. capsici, whereas its close relative Piper flaviflorum is known to be resistant. However, the molecular mechanism underlying the resistance of P. flaviflorum remains obscure. In this study, we conducted a comparative transcriptome and metabolome analysis between P. flaviflorum and P. nigrum upon P. capsici infection and found substantial differences in their gene expression profiles, with altered genes being significantly enriched in terms relating to plant-pathogen interaction, phytohormone signal transduction, and secondary metabolic pathways, including phenylpropanoid biosynthesis. Further metabolome analysis revealed the resistant P. flaviflorum to have a high background endogenous ABA reservoir and time-course-dependent accumulation of ABA and SA upon P. capsici inoculation, while the susceptible P. nigrum had a high background endogenous IAA reservoir and time-course-dependent accumulation of JA-Ile, the active form of JA. Investigation of the phenylpropanoid biosynthesis metabolome further indicated the resistant P. flaviflorum to have more accumulation of lignin precursors than the susceptible P. nigrum, resulting in a higher accumulation after inoculation. This study provides an overall characterization of biologically important pathways underlying the resistance of P. flaviflorum, which theoretically explains the advantage of using this species as rootstock for the management of oomycete pathogen in black pepper production.
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Affiliation(s)
- Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
| | - Xiao-yuan Tao
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | | | - Soonliang Sim
- Academy of Sciences Malaysia, Kuala Lumpur, Malaysia
| | - Li-song Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, China
| | - Bao-duo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Wanning, China
| | - Qing-huang Wang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
| | - Chao-yun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences (CATAS), Wanning, China
- Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture and Rural Affairs, Wanning, China
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Reliable reference genes for qPCR normalization in females of the mirid predator, Cyrtorhinus lividipennis (Hemiptera: Miridae). Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01093-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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10
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Selection and Validation of Reliable Reference Genes for qRT-PCR Normalization of Bursaphelenchus xylophilus from Different Temperature Conditions and Developmental Stages. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a powerful technique for studying gene expression. The key to quantitative accuracy depends on the stability of the reference genes used for data normalization under different experimental conditions. Pine wood nematode (PWN; Bursaphelenchus xylophilus) is the causal agent of the devastating pine wilt disease (PWD). Extensive and prompt research is needed to understand the molecular mechanism of PWD, but identification of the reference PWN genes for standardized qRT-PCR has not been reported yet. We have analyzed eight candidate reference genes of PWN across different temperature conditions and developmental stages. Delta Ct method, GeNorm, NormFinder, BestKeeper, and RefFinder algorithms were used to evaluate the stability of expression of these genes. Finally, we use arginine kinase gene (AK) in different temperatures and heat shock protein 90 (HSP90) in different developmental stages to confirm the stability of these genes. UBCE and EF1γ were most stable across different temperature treatments, whereas EF1γ and Actin were most stable across different developmental stages. In general, these results indicate that EF1γ is the most stable gene for qRT-PCR under different conditions. The systematic analysis of qRT-PCR reference gene selection will be helpful for future functional analysis and exploration of B. xylophilus genetic resources.
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Díez-López C, Tajes Orduña M, Enjuanes Grau C, Moliner Borja P, González-Costello J, García-Romero E, Francesch Manzano J, Yun Viladomat S, Jiménez-Marrero S, Ramos-Polo R, Ras Jiménez MDM, Comín-Colet J. Blood Differential Gene Expression in Patients with Chronic Heart Failure and Systemic Iron Deficiency: Pathways Involved in Pathophysiology and Impact on Clinical Outcomes. J Clin Med 2021; 10:jcm10214937. [PMID: 34768457 PMCID: PMC8585093 DOI: 10.3390/jcm10214937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Iron deficiency is a common disorder in patients with heart failure and is related with adverse outcomes and poor quality of life. Previous experimental studies have shown biological connections between iron homeostasis, mitochondrial metabolism, and myocardial function. However, the mechanisms involved in this crosstalk are yet to be unfolded. Methods: The present research attempts to investigate the intrinsic biological mechanisms between heart failure and iron deficiency and to identify potential prognostic biomarkers by determining the gene expression pattern in the blood of heart failure patients, using whole transcriptome and targeted TaqMan® low-density array analyses. Results: We performed a stepwise cross-sectional longitudinal study in a cohort of chronic heart failure patients with and without systemic iron deficiency. First, the full transcriptome was performed in a nested case-control exploratory cohort of 7 paired patients and underscored 1128 differentially expressed transcripts according to iron status (cohort1#). Later, we analyzed the messenger RNA levels of 22 genes selected by their statistical significance and pathophysiological relevance, in a validation cohort of 71 patients (cohort 2#). Patients with systemic iron deficiency presented lower mRNA levels of mitochondrial ferritin, sirtuin-7, small integral membrane protein 20, adrenomedullin and endothelin converting enzyme-1. An intermediate mitochondrial ferritin gene expression and an intermediate or low sirtuin7 and small integral membrane protein 20 mRNA levels were associated with an increased risk of all-cause mortality and heart failure admission ((HR 2.40, 95% CI 1.04–5.50, p-value = 0.039), (HR 5.49, 95% CI 1.78–16.92, p-value = 0.003), (HR 9.51, 95% CI 2.69–33.53, p-value < 0.001), respectively). Conclusions: Patients with chronic heart failure present different patterns of blood gene expression depending on systemic iron status that affect pivotal genes involved in iron regulation, mitochondrial metabolism, endothelial function and cardiovascular physiology, and correlate with adverse clinical outcomes.
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Affiliation(s)
- Carles Díez-López
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Advanced Heart Failure and Heart Transplant Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Barcelona, Spain
| | - Marta Tajes Orduña
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
| | - Cristina Enjuanes Grau
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Pedro Moliner Borja
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - José González-Costello
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Advanced Heart Failure and Heart Transplant Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Barcelona, Spain
| | - Elena García-Romero
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Advanced Heart Failure and Heart Transplant Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Josep Francesch Manzano
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
| | - Sergi Yun Viladomat
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Internal Medicine, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Santiago Jiménez-Marrero
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Raul Ramos-Polo
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Maria del Mar Ras Jiménez
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Internal Medicine, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
| | - Josep Comín-Colet
- Bio-Heart Cardiovascular Diseases Research Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, 08907 Barcelona, Spain; (C.D.-L.); (M.T.O.); (C.E.G.); (P.M.B.); (J.G.-C.); (E.G.-R.); (J.F.M.); (S.Y.V.); (S.J.-M.); (R.R.-P.); (M.d.M.R.J.)
- Community Heart Failure Unit, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Department of Clinical Sciences, School of Medicine, University of Barcelona, 08907 Barcelona, Spain
- Community Heart Failure Program, Cardiology Department, Bellvitge University Hospital, L’Hospitalet de Llobregat, 08907 Barcelona, Spain
- Correspondence: ; Tel.: +34-932-607-078
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Selection and Evaluation of Reference Genes for qRT-PCR in Spodoptera frugiperda (Lepidoptera: Noctuidae). INSECTS 2021; 12:insects12100902. [PMID: 34680671 PMCID: PMC8538597 DOI: 10.3390/insects12100902] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/20/2022]
Abstract
Simple Summary The fall armyworm Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) is an extremely important omnivorous agricultural pest, it poses a severe threat to food security and agricultural production. Quantitative real-time PCR (qRT-PCR) is an important molecular technology widely used for expression profile analyses of various target genes. It is essential to use reference genes as the benchmark to eliminate various errors and normalize the qRT-PCR analysis. In our study, 10 reference genes were evaluated under six experimental conditions, including developmental stages, tissues, mating status, hormones, diets, and temperatures. Finally, the expression profile of the target gene SfrOBP1 in various tissues of S. frugiperda was evaluated to verify the accuracy of the results. This study will provide a preliminary evaluation of reference genes of S. frugiperda, which can be beneficial to the further research of functional gene expression. Abstract As an accurate and convenient technique, the qRT-PCR is always used in the quantitative expression analysis of functional genes. Normalization of the data relies on stable reference genes. The fall armyworm Spodoptera frugiperda (J. E. Smith) is an important invasive and migratory pest that seriously threatens corn production around the world. In this paper, we selected 10 candidate reference genes (18S, AK, RPL10, RPS24, 28S, SOD, ATP, GAPDH, ACT, and a-TUB) and determined their expression levels under different conditions (different developmental stages, various tissues, mating status, hormones, diets, and temperatures). Subsequently, the stability of reference genes was evaluated by four algorithms (Delta Ct method, geNorm, NormFinder, BestKeeper). The optimal combination of reference genes for each treatment was obtained by geNorm. Finally, the comprehensive ranks were determined by the online tool RefFinder. Results showed that the most stable reference genes were SOD, RPL10, and RPS24 for developmental stages, α-TUB, RPL10, and ATP for different tissues, AK, RPL10, and 18S for mating status, 18S and AK under hormone treatment, 18S, RPL10, and SOD under diet treatment, RPL10, 18S, and RPS24 under temperature treatment. This study confirmed recent data on a few reference genes and provided an evaluation of a number of additional reference genes of S. frugiperda under various conditions.
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Yuan XQ, Zhang XM. Melatonin reduces inflammation in intestinal cells, organoids and intestinal explants. Inflammopharmacology 2021; 29:1555-1564. [PMID: 34431007 DOI: 10.1007/s10787-021-00869-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/14/2021] [Indexed: 01/08/2023]
Abstract
Inflammatory bowel diseases (IBDs) are chronic and recurrent diseases that often occur in young people and place a heavy burden on public health in both developed and developing countries. Melatonin has been confirmed to be useful in various diseases, including Alzheimer's disease, liver injuries and diseases, and cancers, while its role in IBDs remains unclear. To uncover the function of melatonin in IBDs, three intestinal models, including Caco-2 cells, 3D intestinal organoids and intestinal explants, were used. It was found that different concentrations of melatonin could significantly inhibit the expression levels of NFκB and its downstream cytokines, including IL6 and IL8 in Caco-2 cells (*P < 0.05, **P < 0.01), 3D intestinal organoids (*P < 0.05, **P < 0.01) and intestinal explants (*P < 0.05, **P < 0.01). Melatonin abolished the activation of LPS on the expression levels of NFκB, IL6, and IL8 in three intestinal models (*P < 0.05, **P < 0.01, ***P < 0.001). Importantly, the roles of melatonin in the regulation of inflammation was dependent on its receptor (i.e., MTNR1), since it was found that silencing of the melatonin receptor (MTNR1A) abolished the reduction in inflammation induced by melatonin in Caco-2 cells (***P < 0.001) and 3D intestinal organoids (***P < 0.01, ****P < 0.0001). Herein, the findings in this study might provide useful information for understanding the pathogenesis of IBDs and developing novel drugs to treat the diseases.
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Affiliation(s)
- Xiao-Qiang Yuan
- Department of Trauma, Tangshan Gongren Hospital, No. 27, Wenhua Road, Lubei District, Tangshan, 063000, Hebei, China
| | - Xu-Ming Zhang
- Anorectal Surgery, Tangshan Gongren Hospital, Tangshan, 063000, Hebei, China.
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14
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Torres S, Lama C, Mantecón L, Flemetakis E, Infante C. Selection and validation of reference genes for quantitative real-time PCR in the green microalgae Tetraselmis chui. PLoS One 2021; 16:e0245495. [PMID: 33444403 PMCID: PMC7808622 DOI: 10.1371/journal.pone.0245495] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/30/2020] [Indexed: 01/08/2023] Open
Abstract
Quantitative real-time reverse transcription PCR (RT-qPCR) is a highly sensitive technique that can be applied to analyze how genes are modulated by culture conditions, but identification of appropriate reference genes for normalization is a critical factor to be considered. For this reason, the expression stability of 18 candidate reference genes was evaluated for the green microalgae Tetraselmis chui using the widely employed algorithms geNorm, NormFinder, BestKeeper, the comparative ΔCT method, and RefFinder. Microalgae samples were collected from large scale outdoor photobioreactors during the growing phase (OUT_GP), and during the semi-continuous phase at different times of the day (OUT_DC). Samples from standard indoor cultures under highly controlled conditions (IND) were also collected to complement the other data. Different rankings for the candidate reference genes were obtained depending on the culture conditions and the algorithm employed. After comparison of the achieved ranks with the different methods, the references genes selected for samples from specific culture conditions were ALD and EFL in OUT_GP, RPL32 and UBCE in OUT_DC, and cdkA and UBCE in IND. Moreover, the genes EFL and cdkA or EFL and UBCE appeared as appropriate combinations for pools generated from all samples (ALL). Examination in the OUT_DC cultures of genes encoding the large and small subunits of ADP-glucose pyrophosphorylase (AGPL and AGPS, respectively) confirmed the reliability of the identified reference genes, RPL32 and UBCE. The present study represents a useful contribution for studies of gene expression in T. chui, and also represents the first step to set-up an RT-qPCR platform for quality control of T. chui biomass production in industrial facilities.
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Affiliation(s)
- Sonia Torres
- Fitoplancton Marino, S.L., El Puerto de Santa María, Cádiz, Spain
| | - Carmen Lama
- Fitoplancton Marino, S.L., El Puerto de Santa María, Cádiz, Spain
| | - Lalia Mantecón
- Fitoplancton Marino, S.L., El Puerto de Santa María, Cádiz, Spain
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, Agricultural University of Athens, Athens, Greece
| | - Carlos Infante
- Fitoplancton Marino, S.L., El Puerto de Santa María, Cádiz, Spain
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15
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Jeon JH, Moon K, Kim Y, Kim YH. Reference gene selection for qRT-PCR analysis of season- and tissue-specific gene expression profiles in the honey bee Apis mellifera. Sci Rep 2020; 10:13935. [PMID: 32811887 PMCID: PMC7435199 DOI: 10.1038/s41598-020-70965-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/07/2020] [Indexed: 01/10/2023] Open
Abstract
Honey bees are both important pollinators and model insects due to their highly developed sociality and colony management. To better understand the molecular mechanisms underlying honey bee colony management, it is important to investigate the expression of genes putatively involved in colony physiology. Although quantitative real-time PCR (qRT-PCR) can be used to quantify the relative expression of target genes, internal reference genes (which are stably expressed across different conditions) must first be identified to ensure accurate normalisation of target genes. To identify reliable reference genes in honey bee (Apis mellifera) colonies, therefore, we evaluated seven candidate genes (ACT, EIF, EF1, RPN2, RPS5, RPS18 and GAPDH) in samples collected from three honey bee tissue types (head, thorax and abdomen) across all four seasons using three analysis programmes (NormFinder, BestKeeper and geNorm). Subsequently, we validated various normalisation methods using each of the seven reference genes and a combination of multiple genes by calculating the expression of catalase (CAT). Although the genes ranked as the most stable gene were slightly different on conditions and analysis methods, our results suggest that RPS5, RPS18 and GAPDH represent optimal honey bee reference genes for target gene normalisation in qRT-PCR analysis of various honey bee tissue samples collected across seasons.
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Affiliation(s)
- Ji Hyang Jeon
- Department of Applied Biology, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
| | - KyungHwan Moon
- Department of Ecological Science, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
| | - YeongHo Kim
- Department of Ecological Science, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
| | - Young Ho Kim
- Department of Applied Biology, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea. .,Department of Ecological Science, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea.
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16
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Deng Y, Zhao H, Yang S, Zhang L, Zhang L, Hou C. Screening and Validation of Reference Genes for RT-qPCR Under Different Honey Bee Viral Infections and dsRNA Treatment. Front Microbiol 2020; 11:1715. [PMID: 32849362 PMCID: PMC7406718 DOI: 10.3389/fmicb.2020.01715] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 06/30/2020] [Indexed: 01/22/2023] Open
Abstract
Honey bee viruses are one of the most important pathogens that have contributed to the decrease in honey bee colony health. To analyze the infection dynamics of honey bee viruses, quantification of viral gene expression by RT-qPCR is necessary. However, suitable reference genes have not been reported from viral and RNAi studies of honey bee. Here, we evaluated the expression of 11 common reference genes (ache2, rps18, β-actin, tbp, tif, rpl32, gadph, ubc, α-tubulin, rpl14, and rpsa) from Apis mellifera (Am) and Apis cerana (Ac) under Israeli acute paralysis virus (IAPV), chronic bee paralysis virus (CBPV), and Chinese sacbrood virus (CSBV) infection as well as dsRNA-PGRP-SA treatment, and we confirmed their validation by evaluating the levels of the defensin 1 and prophenoloxidase (ppo) genes during viral infection. Our results showed that the expression of selected genes varied under different viral infections. ache2, rps18, β-actin, tbp, and tif can be used to normalize expression levels in Apis mellifera under IAPV infection, while the combination of actin and tif is suitable for CBPV-infected experiments. The combination of rpl14, tif, rpsa, ubc, and ache2 as well as more reference genes is suitable for CSBV treatment in Apis cerana. Rpl14, tif, rps18, ubc, and α-tubulin were the most stable reference genes under dsRNA treatment in Apis mellifera. Furthermore, the geNorm and NormFinder algorithms showed that tif was the best suitable reference gene for these four treatments. This study screened and validated suitable reference genes for the quantification of viral levels in honey bee, as well as for RNAi experiments.
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Affiliation(s)
- Yanchun Deng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing, China.,Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongxia Zhao
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangdong Academy of Science, Guangzhou, China
| | - Sa Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Li Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Lina Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China.,Key laboratory of Pollinating Insect Biology, Ministry of Agriculture and Rural Affairs, Beijing, China
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Pinheiro DH, Moreira RO, Leite NA, Redoan AC, Xavier ADS, Barros BDA, Carneiro NP. Suitable reference genes for RT-qPCR analysis in Dichelops melacanthus (Hemiptera: Pentatomidae). Mol Biol Rep 2020; 47:4989-5000. [PMID: 32594344 DOI: 10.1007/s11033-020-05550-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 05/23/2020] [Indexed: 10/24/2022]
Abstract
The relative quantification of gene expression is mainly realized through reverse transcription-quantitative PCR (RT-qPCR). However, the accuracy of this technique is deeply influenced by the expression stability of the reference genes used for data normalization. Therefore, the selection of suitable reference genes for a given experimental condition is a prerequisite in gene expression studies. Dichelops melacanthus (Hemiptera: Pentatomidae) is an important phloem sap-sucking insect pest of soybean, wheat, and maize in Brazil. Most of the genetic and molecular biology studies require gene expression analysis. Nevertheless, there are no reports about reference genes for RT-qPCR data normalization in D. melacanthus. In this study, we evaluated the expression stability of nine candidate reference genes (nadh, sdhb, gapdh, fau, ef1a, rpl9, ube4a, gus and rps23) in different developmental stages, body parts, sex, starvation-induced stress and dsRNA exposure by RefFinder software that integrates the statistical algorithms geNorm, NormFinder, BestKeeper, and ΔCt method. Our results showed that ef1a and nadh are the most stable reference genes for developmental stages, fau and rps23 for sex, ube4a and rps23 for body parts, rpl9 and fau for starvation stress, and nadh and sdhb for dsRNA exposure treatment. The reference genes selected in this work will be useful for further RT-qPCR analyses on D. melacanthus, facilitating future gene expression studies that can provide a better understanding of the developmental, physiological, and molecular processes of this important insect pest. Moreover, the knowledge gained from these studies can be helpful to design effective and sustainable pest management strategies.
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Affiliation(s)
- Daniele Heloísa Pinheiro
- Nucleus of Applied Biology, Embrapa Maize and Sorghum, Sete Lagoas, MG, 35701-970, Brazil.,Laboratory of Plant-Pest Molecular Interaction, Embrapa Genetic Resources and Biotechnology, Brasília, DF, 70770-917, Brazil
| | - Raquel Oliveira Moreira
- Nucleus of Applied Biology, Embrapa Maize and Sorghum, Sete Lagoas, MG, 35701-970, Brazil.,School of Agrarian and Veterinary Sciences, São Paulo State University-UNESP, Jaboticabal, SP, 14884-900, Brazil
| | - Natália Alves Leite
- Nucleus of Applied Biology, Embrapa Maize and Sorghum, Sete Lagoas, MG, 35701-970, Brazil.,Department of Crop Protection, Federal University of Rio Grande Do Sul, Porto Alegre, RS, 91540-00, Brazil
| | - Ana Carolina Redoan
- Nucleus of Applied Biology, Embrapa Maize and Sorghum, Sete Lagoas, MG, 35701-970, Brazil
| | - André da Silva Xavier
- Nucleus of Applied Biology, Embrapa Maize and Sorghum, Sete Lagoas, MG, 35701-970, Brazil.,Department of Agronomy, Federal University of Espírito Santo, Alegre, ES, 29500-000, Brazil
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18
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Wang Z, Meng Q, Zhu X, Sun S, Liu A, Gao S, Gou Y. Identification and Evaluation of Reference Genes for Normalization of Gene Expression in Developmental Stages, Sexes, and Tissues of Diaphania caesalis (Lepidoptera, Pyralidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5700579. [PMID: 31925425 PMCID: PMC6954454 DOI: 10.1093/jisesa/iez130] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Indexed: 05/04/2023]
Abstract
Diaphania caesalis (Walker) is an important boring insect mainly distributed in subtropical and tropical areas and attacked tropical woody grain crops, such as starchy plants of Artocarpus. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful approach for investigating target genes expression profiles at the transcriptional level. However, the identification and selection of internal reference genes, which is often overlooked, is the most vital step before the analysis of target gene expression by qRT-PCR. So far, the reliable internal reference genes under a certain condition of D. caesalis have not been investigated. Therefore, this study evaluated the expression stability of eight candidate reference genes including ACT, β-TUB, GAPDH, G6PDH, RPS3a, RPL13a, EF1α, and EIF4A in different developmental stages, tissues and sexes using geNorm, NormFinder and BestKeeper algorithms. To verify the stability of the recommended internal reference genes, the expression levels of DcaeOBP5 were analyzed under different treatment conditions. The results indicated that ACT, RPL13a, β-TUB, RPS3a, and EF1α were identified as the most stable reference genes for further studies on target gene expression involving different developmental stages of D. caesalis. And ACT and EIF4A were recommended as stable reference genes for different tissues. Furthermore, ACT, EF1α, and RPS3a were ranked as the best reference genes in different sexes based on three algorithms. Our research represents the critical first step to normalize qRT-PCR data and ensure the accuracy of expression of target genes involved in phylogenetic and physiological mechanism at the transcriptional level in D. caesalia.
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Affiliation(s)
- Zheng Wang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Qianqian Meng
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Corresponding author, e-mail:
| | - Xi Zhu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shiwei Sun
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Aiqin Liu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shengfeng Gao
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Yafeng Gou
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
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