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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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Foquet B, Rapkin J, Sharma MD, Sadd BM, Sakaluk SK, Hunt J. Transcriptomic responses of females to consumption of nuptial food gifts as a potential mediator of sexual conflict in decorated crickets. J Evol Biol 2023; 36:183-194. [PMID: 36357978 DOI: 10.1111/jeb.14114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/16/2022] [Accepted: 09/02/2022] [Indexed: 11/12/2022]
Abstract
Nuptial food gift provisioning by males to females at mating is a strategy in many insects that is thought to be shaped by sexual conflict or sexual selection, as it affords males access to a female's physiology. While males often attempt to use these gifts to influence female behaviour to their own advantage, females can evolve counter mechanisms. In decorated crickets, the male's nuptial gift comprises part of the spermatophore, the spermatophylax, the feeding on which deters the female from prematurely terminating sperm transfer. However, ingested compounds in the spermatophylax and attachment of the sperm-containing ampulla could further influence female physiology and behaviour. We investigated how mating per se and these two distinct routes of potential male-mediated manipulation influence the female transcriptomic response. We conducted an RNA sequencing experiment on gut and head tissues from females for whom nuptial food gift consumption and receipt of an ejaculation were independently manipulated. In the gut tissue, we found that females not permitted to feed during mating exhibited decreased overall gene expression, possibly caused by a reduced gut function, but this was countered by feeding on the spermatophylax or a sham gift. In the head tissue, we found only low numbers of differentially expressed genes, but a gene co-expression network analysis revealed that ampulla attachment and spermatophylax consumption independently induce distinct gene expression patterns. This study provides evidence that spermatophylax feeding alters the female post-mating transcriptomic response in decorated crickets, highlighting its potential to mediate sexual conflict in this system.
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Affiliation(s)
- Bert Foquet
- Behavior, Ecology, Evolution & Systematics Section, School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - James Rapkin
- Center for Ecology and Conservation, University of Exeter, Cornwall, UK
| | - Manmohan D Sharma
- Center for Ecology and Conservation, University of Exeter, Cornwall, UK
| | - Ben M Sadd
- Behavior, Ecology, Evolution & Systematics Section, School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - Scott K Sakaluk
- Behavior, Ecology, Evolution & Systematics Section, School of Biological Sciences, Illinois State University, Normal, Illinois, USA
| | - John Hunt
- Center for Ecology and Conservation, University of Exeter, Cornwall, UK.,School of Science, Western Sydney University, Richmond, New South Wales, Australia
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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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Pan YN, Zhao RN, Fu D, Yu C, Pan CN, Zhou W, Chen WL. Assessment of Suitable Reference Genes for qRT-PCR Normalization in Eocanthecona furcellata (Wolff). INSECTS 2022; 13:773. [PMID: 36135474 PMCID: PMC9505644 DOI: 10.3390/insects13090773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is a widely used tool for measuring gene expression; however, its accuracy relies on normalizing the data to one or more stable reference genes. Eocanthecona furcellata (Wolff) is a polyphagous predatory natural enemy insect that preferentially feeds on more than 40 types of agricultural and forestry pests, such as those belonging to the orders Lepidoptera, Coleoptera, and Hymenoptera. However, to our knowledge, the selection of stable reference genes has not been reported in detail thus far. In this study, nine E. furcellata candidate reference genes (β-1-TUB, RPL4, RPL32, RPS17, RPS25, SDHA, GAPDH2, EF2, and UBQ) were selected based on transcriptome sequencing results. The expression of these genes in various samples was examined at different developmental stages, in the tissues of male and female adults, and after temperature and starvation treatments. Five algorithms were used, including ΔCt, geNorm, NormFinder, BestKeeper, and RefFinder, to evaluate reference gene expression stability. The results revealed that the most stable reference genes were RPL32 and RPS25 at different developmental stages; RPS17, RPL4, and EF2 for female adult tissue samples; RPS17 and RPL32 for male adult tissue samples; RPS17 and RPL32 for various temperature treatments of nymphs; RPS17 and RPS25 for nymph samples under starvation stress; and RPS17 and RPL32 for all samples. Overall, we obtained a stable expression of reference genes under different conditions in E. furcellata, which provides a basis for future molecular studies on this organism.
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Li X, Li X, Yan W, Coates B, Zhou X, Wang C, Haifeng G, Zhang Y, Zhu X. Selection of Reference Genes for RT-qPCR Analysis of Wing Dimorphism in English Grain Aphid, Sitobion avenae (Hemiptera: Aphididae). JOURNAL OF ECONOMIC ENTOMOLOGY 2022; 115:313-324. [PMID: 34850027 DOI: 10.1093/jee/toab214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 06/13/2023]
Abstract
The English grain aphid, Sitobion avenae (Fabricius), exhibits classic and dramatic phenotypic plasticity in wing development. Both genetic and environmental inputs contribute to the wing polyphenism in aphids, an extreme form of phenotypic plasticity in which a single genotype produces discrete winged and wingless morphs. Validated reference genes are needed to accurately normalize temporal and spatial variation in gene expression estimates by RT-qPCR. In this research, the stability of 11 candidate reference genes selected from S. avenae transcriptomes was evaluated under an array of abiotic and biotic conditions relevant to wing development. RefFinder, a comprehensive software integrating rankings from delta Ct, BestKeeper, NormFinder, and geNorm, offered a series of reference genes for every experimental condition. Overall, helicase (HEL) and ubiquitin ribosomal protein S27A fusion protein (RpS27) are suited for most of the conditions examined in this study, although exceptions do exist. Specifically, NADH dehydrogenase (Ap-NADH) and 28S ribosomal RNA (28S) are recommended for insecticide and antibiotic treatments, while ribosomal RNA L14 (RPL14) and 18S ribosomal RNA (18S) are selected for density treatment, respectively. This study provides a suite of reference genes to investigate the wing polyphenism in S. avenae, and is important for application of RT-qPCR in future experiments of novel tactics to control aphids.
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Affiliation(s)
- Xiangrui Li
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinan Li
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Resource and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Weiwei Yan
- Research Institute of Pomology, Chinese Academy of Agricultural Science, Xingcheng, Liaoning, China
| | - Brad Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, Ames, IA, USA
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Chao Wang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gao Haifeng
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi, Xinjiang, China
| | - Yunhui Zhang
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Shen CH, Peng LJ, Zhang YX, Zeng HR, Yu HF, Jin L, Li GQ. Reference Genes for Expression Analyses by qRT-PCR in Phthorimaea operculella (Lepidoptera: Gelechiidae). INSECTS 2022; 13:insects13020140. [PMID: 35206714 PMCID: PMC8879603 DOI: 10.3390/insects13020140] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/04/2022]
Abstract
Due to a lack of effective internal references, studies on functional genes in Phthorimaea operculella, a serious Lepidopteran pest attacking potatoes worldwide, have been greatly limited. To select suitable endogenous controls, ten housekeeping genes of actin (ACT), α-tubulin (α-TUB), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1α (EF1α), 18S and 28S ribosomal RNA (18S, 28S), ribosomal protein genes RPL4, RPL13 and RPL27 and superoxide dismutase (SOD) were tested. Their expression levels were determined under three different experimental conditions (developmental stages, tissues/organs and temperatures) using qRT-PCR technology. The stability was evaluated with five methods (Ct value, geNorm, NormFinder, BestKeeper and RefFinder). The results clarified that RPL13, EF1α and RPL27 are ranked as the best reference gene combination for measuring gene expression levels among different developing stages and under various temperatures; EF1α and RPL13 are recommended to normalize the gene expression levels among diverse tissues. EF1α and RPL13 are the best reference genes in all the experimental conditions. To validate the utility of the selected reference pair, EF1α and RPL13, we estimated the tissue-biased expression level of chitin synthase A gene (PoChSA). As expected, PoChSA was abundantly expressed in ectodermally derived epidermal cells, and lowly transcribed in the midgut. These findings will lay the foundation for future research on the molecular physiology and biochemistry of P. operculella.
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Affiliation(s)
| | | | | | | | | | - Lin Jin
- Correspondence: ; Tel.: +86-25-84395248
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Guo YQ, Yang Y, Chai Y, Gao LL, Ma R. Identification and Evaluation of Reference Genes for Quantitative PCR Normalization in Alligator Weed Flea Beetle (Coleoptera: Chrysomelidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:6378301. [PMID: 34591086 PMCID: PMC8482964 DOI: 10.1093/jisesa/ieab067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Stably expressed reference genes are critical internal standards for the quantification of gene transcription levels using quantitative real-time PCR. Housekeeping genes are commonly used as reference genes but their expressions were variable depending on experimental conditions in many insect species studied. Here we report the identification and evaluation of 10 housekeeping genes in alligator weed flea beetle, Agasicles hygrophila Selman & Vogt (Coleoptera: Chrysomelidae), a biocontrol agent of alligator weed. The 10 housekeeping genes are: beta-actin (Actin), ribosomal protein L13A (PRL13a), succinate dehydrogenase complex subunit A (SDHA), ribosomal protein S20 (RPS20), ribosomal protein S13 (RPS13), glyceraldehyde phosphate dehydrogenase (GAPDH), TATA-box-binding protein (TBP), ribosomal protein L32 (RPL32), tubulin alpha-1 chain (TUBULIN), and elongation factor-1 alpha (ELF). Five programs, geNorm, NormFinder, BestKeeper, ΔCt method, and RefFinder, were used to evaluate the expression stability of the 10 genes among various A. hygrophila body parts and with different nutrient types (starvation, diet types). The expression stability analysis showed that RPS32 and RPL13a were reliable reference genes for the study of gene transcription in different body parts; Actin and RPL13a were optimal reference genes for different nutrient types. The selections of reference genes were validated using a CarE gene (GeneBank No: KX353552). The results of this study provide useful bases for studies of gene expression in various aspects relating to A. hygrophila.
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Affiliation(s)
- Yan-Qiong Guo
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Yongchang Yang
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Yanping Chai
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, China
| | - Ling-Ling Gao
- CSIRO Agriculture and Food, Wembley 6014, Western Australia, Australia
| | - Ruiyan Ma
- College of Plant Protection, Shanxi Agricultural University, Taigu, Shanxi 030801, China
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Bai Y, Lv YN, Zeng M, Jia PY, Lu HN, Zhu YB, Li S, Cui YY, Luan YX. Selection of Reference Genes for Normalization of Gene Expression in Thermobia domestica (Insecta: Zygentoma: Lepismatidae). Genes (Basel) 2020; 12:genes12010021. [PMID: 33375665 PMCID: PMC7823838 DOI: 10.3390/genes12010021] [Citation(s) in RCA: 12] [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: 11/24/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 02/06/2023] Open
Abstract
Zygentoma occupies a key evolutionary position for understanding the evolution of insect metamorphosis but has received little attention in terms of genetic analysis. To develop functional genomic studies in this insect, we evaluated five candidate internal reference genes for quantitative RT-PCR (qPCR) studies from Thermobia domestica, a representative species of Zygentoma, including Actin 5C (Actin5C), Elongation factor-1 alpha (EF1A), Ribosome protein S26 (RPS26), Ribosome protein L32 (RPL32), and Superoxide dismutase 2 (SOD2), at different developmental stages, in various body parts, and under dsRNA microinjection and starvation stresses, using four algorithms (delta Ct, geNorm, NormFinder and BestKeeper) and a comparative algorithm (RefFinder). Specific suitable reference genes were recommended across specific experimental conditions, and the combination of RPS26 and RPL32 was appropriate for all tested samples. Employing our selected reference gene combination, we investigated the gene expression pattern of Myoglianin (Myo), a crucial gene-regulating insect metamorphosis, in ametabolous T. domestica, and demonstrated the efficiency of RNA interference (RNAi) in firebrat nymphs. This study provides a basis for reliable quantitative studies of genes and greatly benefits evolutionary and functional genomics studies in Zygentoma.
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Li X, Gong P, Wang B, Wang C, Li M, Zhang Y, Li X, Gao H, Ju J, Zhu X. Selection and validation of experimental condition-specific reference genes for qRT-PCR in Metopolophium dirhodum (Walker) (Hemiptera: Aphididae). Sci Rep 2020; 10:21951. [PMID: 33319828 PMCID: PMC7738536 DOI: 10.1038/s41598-020-78974-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 11/05/2020] [Indexed: 11/09/2022] Open
Abstract
Metopolophium dirhodum (Walker) (Hemiptera: Aphididae) is one of the most common aphid pests of winter cereals. To facilitate accurate gene expression analyses with qRT-PCR assays, the expression stability of candidate reference genes under specific experimental conditions must be verified before they can be used to normalize target gene expression levels. In this study, 10 candidate reference genes in M. dirhodum were analyzed by qRT-PCR under various experimental conditions. Their expression stability was evaluated with delta Ct, BestKeeper, geNorm, and NormFinder methods, and the final stability ranking was determined with RefFinder. The results indicate that the most appropriate sets of internal controls were SDHB and RPL8 across geographic population; RPL8, Actin, and GAPDH across developmental stage; SDHB and NADH across body part; RPL8 and Actin across wing dimorphism and temperature; RPL4 and EF1A across starvation stress; AK and RPL4 across insecticide treatments; RPL8 and NADH across antibiotic treatments; RPL8, RPL4, Actin, and NADH across all samples. The results of this study provide useful insights for establishing a standardized qRT-PCR procedure for M. dirhodum and may be relevant for identifying appropriate reference genes for molecular analyses of related insects.
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Affiliation(s)
- Xinan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No.2, Haidian District, Beijing, 100193, China.,School of Resource and Environmental Sciences, Henan Institute of Science and Technology, Eastern HuaLan Avenue, Xinxiang, 453003, Henan, China
| | - Peipan Gong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No.2, Haidian District, Beijing, 100193, China
| | - Bingting Wang
- College of Life Science, Hebei Normal University, Road Nan er huan dong No.20, Shijiazhuang, 050024, Hebei, China
| | - Chao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No.2, Haidian District, Beijing, 100193, China
| | - Mengyi Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No.2, Haidian District, Beijing, 100193, China
| | - Yunhui Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No.2, Haidian District, Beijing, 100193, China
| | - Xiangrui Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No.2, Haidian District, Beijing, 100193, China
| | - Haifeng Gao
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Ürümqi, 830091, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Road Nan er huan dong No.20, Shijiazhuang, 050024, Hebei, China.
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No.2, Haidian District, Beijing, 100193, China.
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Foquet B, Song H. There is no magic bullet: the importance of testing reference gene stability in RT-qPCR experiments across multiple closely related species. PeerJ 2020; 8:e9618. [PMID: 32832268 PMCID: PMC7409783 DOI: 10.7717/peerj.9618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/06/2020] [Indexed: 11/20/2022] Open
Abstract
Reverse Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR) is the current gold standard tool for the study of gene expression. This technique is highly dependent on the validation of reference genes, which exhibit stable expression levels among experimental conditions. Often, reference genes are assumed to be stable a priori without a rigorous test of gene stability. However, such an oversight can easily lead to misinterpreting expression levels of target genes if the references genes are in fact not stable across experimental conditions. Even though most gene expression studies focus on just one species, comparative studies of gene expression among closely related species can be very informative from an evolutionary perspective. In our study, we have attempted to find stable reference genes for four closely related species of grasshoppers (Orthoptera: Acrididae) that together exhibit a spectrum of density-dependent phenotypic plasticity. Gene stability was assessed for eight reference genes in two tissues, two experimental conditions and all four species. We observed clear differences in the stability ranking of these reference genes, both between tissues and between species. Additionally, the choice of reference genes clearly influenced the results of a gene expression experiment. We offer suggestions for the use of reference genes in further studies using these four species, which should be taken as a cautionary tale for future studies involving RT-qPCR in a comparative framework.
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Affiliation(s)
- Bert Foquet
- Department of Entomology, Texas A&M University, College Station, TX, United States of America
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, United States of America
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Wang X, Kong X, Liu S, Huang H, Chen Z, Xu Y. Selection of Reference Genes for Quantitative Real-Time PCR in Chrysoperla nipponensis (Neuroptera: Chrysopidae) Under Tissues in Reproduction and Diapause. JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5893937. [PMID: 32809020 PMCID: PMC7433768 DOI: 10.1093/jisesa/ieaa079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Indexed: 04/30/2023]
Abstract
Chrysoperla nipponensis (Okamoto), which has the unique diapause phenotype distinguishable from nondiapause adult, is an ideal model organism for studying the mechanism of reproductive diapause. However, there is no reliable and effective reference genes used for the reproductive diapause study of C. nipponensis. Therefore, in this study, we evaluated the expression stability of 10 candidate reference genes (Tub1, Arpc5, EF1a, 128up, RpS5, RpS26e, GAPDH, Arp3, Actin, α-Tub) in adults under diapause and nondiapause induction conditions using four statistical algorithms including GeNorm, NormFinder, Bestkeeper, and ∆CT method. Results showed that Arp3 and Tub1 were the most stable reference genes in all samples and in the adult tissues group. Arp3 and RpS5 were the most stable reference genes in the development degree group. α-Tub and EF1a were unstable reference genes under the conditions of this study. Meanwhile, to verify the reliability of the reference genes, we evaluated the relative expression levels of Vg and VgR in different treatments. Significant upregulation and downregulation in expression level of two genes in response to diapause termination and diapause fat body tissue was, respectively, observed when using Arp3 as the reference gene but not when using an unstable reference gene. The reference genes identified in this work provided not only the basis for future functional genomics research in diapause of C. nipponensis and will also identify reliable normalization factors for real-time quantitative real-time polymerase chain reaction data for other related insects.
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Affiliation(s)
- Xiao Wang
- Department of Entomology, Shandong Agricultural University, Taian, Shandong, P. R. China
| | - Xue Kong
- Department of Entomology, Shandong Agricultural University, Taian, Shandong, P. R. China
| | - Shaoye Liu
- Department of Entomology, Shandong Agricultural University, Taian, Shandong, P. R. China
| | - Haiyi Huang
- Department of Entomology, Shandong Agricultural University, Taian, Shandong, P. R. China
| | - Zhenzhen Chen
- Department of Entomology, Shandong Agricultural University, Taian, Shandong, P. R. China
| | - Yongyu Xu
- Department of Entomology, Shandong Agricultural University, Taian, Shandong, P. R. China
- Corresponding author, e-mail:
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12
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Sahoo PK, Parida S, Mohapatra A, Mohanty J. Selection of candidate reference genes for RT-qPCR analysis in Argulus siamensis and their validation through screening of drugs and drug targets. Sci Rep 2019; 9:18365. [PMID: 31798003 PMCID: PMC6892791 DOI: 10.1038/s41598-019-54881-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/18/2019] [Indexed: 01/01/2023] Open
Abstract
Argulus spp. are economically important fish ectoparasites. The development of antiparasitic drugs is thus important and real time PCR is an indispensable tool in drug development. The analytical potential of RT-PCR depends upon accurate normalisation by the use of stable reference genes. Here, we identified stable reference genes of Argulus siamensis for validation of efficacy of drugs and drug targets. Seven candidate genes were evaluated by evaluating their expression under different states of Argulus using the RefFinder tool. The four algorithms together generated a comprehensive ranking with elongation factor-1 alpha (EF-1α) being the most stable and 18S ribosomal protein (18S) the least stable gene. Taking EF-1α and 18S genes as references, the effectiveness of six anti-parasitic compounds against Argulus was evaluated by studying their effect on the expression pattern of few ion channel genes; this was to understand their mode of action, besides validating the reference genes. EF-1α was found to be the most stable gene in the validation. Collectively, this study is the first report to validate the optimal reference genes of A. siamensis for normalisation, and the potential of the ion channel genes for evaluating effective drug targets in parasite control.
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Affiliation(s)
- Pramoda Kumar Sahoo
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India.
| | - Sonali Parida
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India
| | - Amruta Mohapatra
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India
| | - Jyotirmaya Mohanty
- Fish Genetics & Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751 002, India
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13
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Identification of suitable reference genes for normalization of RT-qPCR data in eggplant fruit and shoot borer (Leucinodes orbonalis Guenée). Biologia (Bratisl) 2019. [DOI: 10.2478/s11756-019-00346-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Wang C, Yang J, Pan Q, Yu S, Luo R, Liu H, Li H, Cong L, Ran C. Screening of reference genes using real-time quantitative PCR for gene expression studies in Neoseiulus barkeri Hughes (Acari: Phytoseiidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2019; 109:443-452. [PMID: 30370873 DOI: 10.1017/s000748531800072x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A stable reference gene is a key prerequisite for accurate assessment of gene expression. At present, the real-time reverse transcriptase quantitative polymerase chain reaction has been widely used in the analysis of gene expression in a variety of organisms. Neoseiulus barkeri Hughes (Acari: Phytoseiidae) is a major predator of mites on many important economically crops. Until now, however, there are no reports evaluating the stability of reference genes in this species. In view of this, we used GeNorm, NormFinder, BestKeeper, and RefFinder software tools to evaluate the expression stability of 11 candidate reference genes in developmental stages and under various abiotic stresses. According to our results, β-ACT and Hsp40 were the top two stable reference genes in developmental stages. The Hsp60 and Hsp90 were the most stable reference genes in various acaricides stress. For alterations in temperature, Hsp40 and α-TUB were the most suitable reference genes. About UV stress, EF1α and α-TUB were the best choice, and for the different prey stress, β-ACT and α-TUB were best suited. In normal conditions, the β-ACT and α-TUB were the two of the highest stable reference genes to respond to all kinds of stresses. The current study provided a valuable foundation for the further analysis of gene expression in N. barkeri.
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Affiliation(s)
- C Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - J Yang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - Q Pan
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - S Yu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - R Luo
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - H Liu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - H Li
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - L Cong
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
| | - C Ran
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400712, China
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15
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Lü J, Yang C, Zhang Y, Pan H. Selection of Reference Genes for the Normalization of RT-qPCR Data in Gene Expression Studies in Insects: A Systematic Review. Front Physiol 2018; 9:1560. [PMID: 30459641 PMCID: PMC6232608 DOI: 10.3389/fphys.2018.01560] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/18/2018] [Indexed: 02/03/2023] Open
Abstract
Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for quantifying expression levels of targeted genes during various biological processes in numerous areas of clinical and biological research. Selection of appropriate reference genes for RT-qPCR normalization is an elementary prerequisite for reliable measurements of gene expression levels. Here, by analyzing datasets published between 2008 and 2017, we summarized the current trends in reference gene selection for insect gene expression studies that employed the most widely used SYBR Green method for RT-qPCR normalization. We curated 90 representative papers, mainly published in 2013–2017, in which a total of 78 insect species were investigated in 100 experiments. Furthermore, top five journals, top 10 frequently used reference genes, and top 10 experimental factors have been determined. The relationships between the numbers of the reference genes, experimental factors, analysis tools on the one hand and publication date (year) on the other hand was investigated by linear regression. We found that the more recently the paper was published, the more experimental factors it tended to explore, and more analysis tools it used. However, linear regression analysis did not reveal a significant correlation between the number of reference genes and the study publication date. Taken together, this meta-analysis will be of great help to researchers that plan gene expression studies in insects, especially the non-model ones, as it provides a summary of appropriate reference genes for expression studies, considers the optimal number of reference genes, and reviews the average number of experimental factors and analysis tools per study.
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Affiliation(s)
- Jing Lü
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Department of Entomology, South China Agricultural University, Guangzhou, China
| | - Chunxiao Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huipeng Pan
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Department of Entomology, South China Agricultural University, Guangzhou, China
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Identification and Validation of Reference Genes for RT-qPCR Normalization in Mythimna separata (Lepidoptera: Noctuidae). BIOMED RESEARCH INTERNATIONAL 2018; 2018:1828253. [PMID: 30151374 PMCID: PMC6091413 DOI: 10.1155/2018/1828253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/28/2018] [Accepted: 06/21/2018] [Indexed: 11/18/2022]
Abstract
Mythimna separata is a major agricultural pest with seasonal migrating trait in China. Formation and regulation mechanism of migration behavior has resulted in a large number of fundamental researches involving quantitative studies of gene expression in this species. Using appropriate reference gene is critical in RT-qPCR data normalization. A comprehensive study on the reference genes in M. separata is lacking. In this paper, expression stabilities of ten candidate reference genes were evaluated in M. separata under various biotic and abiotic conditions by employing four different software geNorm, NormFinder, BestKeeper, and the comparative ΔCT method. The comprehensive stabilities ranking of these genes were suggested by RefFinder. PKG as a target gene was employed to justify the number of reference genes in four larval tissues and two photoperiod treatments. Results demonstrate that the first three most stable genes were as follows: EF, CypA, and β-TUB for developmental stages; EF, CypA, and RPL12 for larval tissues; EF, TBP, and β-TUB for adult tissues. RPL12, β-TUB, and EF for densities; EF, RPL12, and GAPDH for photoperiod treatments; β-TUB, EF, and ATPase for temperature treatments. Stable reference gene combinations may reduce bias in normalization. This work provides for the first time a comprehensive list of appropriate reference genes and facilitates future studies on gene function of M. separata.
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Li HB, Dai CG, Zhang CR, He YF, Ran HY, Chen SH. Screening potential reference genes for quantitative real-time PCR analysis in the oriental armyworm, Mythimna separata. PLoS One 2018; 13:e0195096. [PMID: 29617430 PMCID: PMC5884543 DOI: 10.1371/journal.pone.0195096] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/18/2018] [Indexed: 11/19/2022] Open
Abstract
The oriental armyworm, Mythimna separata, is a major insect pest in China and other Asian countries. Unfortunately, suitable reference genes for quantitative real-time PCR (qRT-PCR) have not been previously identified in M. separata for normalizing target gene expression. In this study, we evaluated the expression stability of eight candidate genes (18S, ACT, EF1-α, GAPDH, RPS7, RPS13, RPL32 and TUB) in M. separata using the comparative ΔCt method, BestKeeper, Normfinder geNorm and ReFinder, a comprehensive software platform. The results indicated that the appropriate reference gene varied depending on the experimental conditions. We found that ACTIN, EF1-α and TUB were optimal for different developmental stages; TUB, RPS13 and EF1-α showed the most stable expresssion in different tissues; RPS13 and 18S were the best reference genes for monitoring expression under high temperature conditions; TUB, RPS13 and RPS7 exhibited the most stable expression under larval-crowding conditions; RPS7, EF1-α, RPL32 and GAPDH were the best for pesticide exposure experiments. This study provides tools for reliable normalization of qRT-PCR data and forms a foundation for functional studies of target gene expression in M. separata.
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Affiliation(s)
- Hong-Bo Li
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
- * E-mail: (HBL); (YFH)
| | - Chang-Geng Dai
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
| | - Chang-Rong Zhang
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
| | - Yong-Fu He
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
- * E-mail: (HBL); (YFH)
| | - Hai-Yan Ran
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
| | - Shi-Hong Chen
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
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18
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Sanders R, Bustin S, Huggett J, Mason D. Improving the standardization of mRNA measurement by RT-qPCR. BIOMOLECULAR DETECTION AND QUANTIFICATION 2018; 15:13-17. [PMID: 29922589 PMCID: PMC6006386 DOI: 10.1016/j.bdq.2018.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 02/09/2018] [Accepted: 03/06/2018] [Indexed: 12/31/2022]
Abstract
Human health and safety depend on reliable measurements in medical diagnosis and on tests that support the selection and evaluation of therapeutic intervention and newly discovered molecular biomarkers must pass a rigorous evaluation process if they are to be of benefit to patients. Measurement standardization helps to maximize data quality and confidence and ultimately improves the reproducibility of published research. Failure to consider how a given experiment may be standardized can be costly, both financially as well as in time and failure to perform and report pre-clinical research in an appropriately rigorous manner will hinder the development of diagnostic methods. Hence standardization is a crucial step in maintaining the integrity of scientific studies and is a key feature of robust investigation.
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Affiliation(s)
- Rebecca Sanders
- Molecular and Cell Biology, Science and Innovation, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK
| | - Stephen Bustin
- Faculty of Medical Science, Anglia Ruskin University, Michael Salmon Building, Chelmsford, Essex CM1 1SQ, UK
| | - Jim Huggett
- Molecular and Cell Biology, Science and Innovation, LGC, Queens Road, Teddington, Middlesex TW11 0LY, UK
| | - Deborah Mason
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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19
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Gao XK, Zhang S, Luo JY, Wang CY, Lü LM, Zhang LJ, Zhu XZ, Wang L, Lu H, Cui JJ. Comprehensive evaluation of candidate reference genes for gene expression studies in Lysiphlebia japonica (Hymenoptera: Aphidiidae) using RT-qPCR. Gene 2017; 637:211-218. [PMID: 28964897 DOI: 10.1016/j.gene.2017.09.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 09/13/2017] [Accepted: 09/26/2017] [Indexed: 10/18/2022]
Abstract
Lysiphlebia japonica (Ashmead) is a predominant parasitoid of cotton-melon aphids in the fields of northern China with a proven ability to effectively control cotton aphid populations in early summer. For accurate normalization of gene expression in L. japonica using quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR), reference genes with stable gene expression patterns are essential. However, no appropriate reference genes is L. japonica have been investigated to date. In the present study, 12 selected housekeeping genes from L. japonica were cloned. We evaluated the stability of these genes under various experimental treatments by RT-qPCR using four independent (geNorm, NormFinder, BestKeeper and Delta Ct) and one comparative (RefFinder) algorithm. We identified genes showing the most stable levels of expression: DIMT, 18S rRNA, and RPL13 during different stages; AK, RPL13, and TBP among sexes; EF1A, PPI, and RPL27 in different tissues, and EF1A, RPL13, and PPI in adults fed on different diets. Moreover, the expression profile of a target gene (odorant receptor 1, OR1) studied during the developmental stages confirms the reliability of the chosen selected reference genes. This study provides for the first time a comprehensive list of suitable reference genes for gene expression studies in L. japonica and will benefit subsequent genomics and functional genomics research on this natural enemy.
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Affiliation(s)
- Xue-Ke Gao
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Shuai Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Jun-Yu Luo
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Chun-Yi Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Li-Min Lü
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Li-Juan Zhang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Xiang-Zhen Zhu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Li Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Hui Lu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Jin-Jie Cui
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China.
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20
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Xu J, Lu MX, Cui YD, Du YZ. Selection and Evaluation of Reference Genes for Expression Analysis Using qRT-PCR in Chilo suppressalis (Lepidoptera: Pyralidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:683-691. [PMID: 28115499 DOI: 10.1093/jee/tow297] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Indexed: 06/06/2023]
Abstract
Quantitative real-time polymerase chain reaction (qRT-PCR) is a valuable tool for estimating gene expression; however, the validity is largely dependent on the selection of stable reference genes. The suitability of various reference genes for qRT-PCR analysis was evaluated in, Chilo suppressalis (Walker). The ΔCt method, geNorm, NormFinder, and BestKeeper were used to evaluate the suitability of nine candidate reference genes for normalizing gene expression in larval tissues and organs and during high and low temperature stress. The ΔCt method, geNorm, and NormFinder produced similar stability rankings; H3, UBI, and EF1 were the most stable reference genes for monitoring gene expression in larval tissue and organs, and EF1, TUB, and AK were the optimal genes for thermal stress. However, for thermal stress, RPS11 was the most stable gene based on BestKeeper. To validate these recommendations, the expression profile of the gene encoding heat shock protein 60 (Hsp60) was investigated. Hsp60 transcript levels showed significant differences when normalized to the most versus least stable reference genes. These results further confirm the importance of testing reference genes using the selected experimental parameters. The reference genes identified in the present study will improve the quality of gene expression data obtained for C. suppressalis and will facilitate future studies aimed at understanding the biology of this important insect pest.
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Affiliation(s)
- Jing Xu
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China ( ; ; )
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Ming-Xing Lu
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China ( ; ; )
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Ya-Dong Cui
- Department of Life Science, Fuyang Normal College, Fuyang 236032, China
| | - Yu-Zhou Du
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou 225009, China ( ; ; )
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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21
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Kang ZW, Liu FH, Tian HG, Zhang M, Guo SS, Liu TX. Evaluation of the reference genes for expression analysis using quantitative real-time polymerase chain reaction in the green peach aphid, Myzus persicae. INSECT SCIENCE 2017; 24:222-234. [PMID: 26749166 DOI: 10.1111/1744-7917.12310] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/20/2015] [Indexed: 05/10/2023]
Abstract
The green peach aphid, Myzus persicae Sulzer (Hemiptera, Aphididae), is an important cosmopolitan pest. Real time qRT-PCR has been used for target gene expression analysis on M. persicae. Using real time qRT-PCR, the expression levels are normalized on the basis of the reliable reference genes. However, to date, the stability of available reference genes has been insufficient. In this study, we evaluated nine candidate reference genes from M. persicae under diverse experimental conditions. The tested candidate genes were comprehensively ranked based on five alternative methods (RefFinder, geNorm, Normfinder, BestKeeper and the comparative ΔCt method). 18s, Actin and ribosomal protein L27 (L27) were recommended as the most stable reference genes for M. persicae, whereas ribosomal protein L27 (L27) was found to be the least stable reference genes for abiotic studies (photoperiod, temperature and insecticide susceptibility). Our finding not only sheds light on establishing an accurate and reliable normalization of real time qRT-PCR data in M. persicae but also lays a solid foundation for further studies of M. persicae involving RNA interference and functional gene research.
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Affiliation(s)
- Zhi-Wei Kang
- State Key Laboratory of Crop Stress Biology for the Arid Areas, and Key Laboratory of Northwest Loess Plateau Crop Pest Management of Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fang-Hua Liu
- State Key Laboratory of Crop Stress Biology for the Arid Areas, and Key Laboratory of Northwest Loess Plateau Crop Pest Management of Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Hong-Gang Tian
- State Key Laboratory of Crop Stress Biology for the Arid Areas, and Key Laboratory of Northwest Loess Plateau Crop Pest Management of Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Meng Zhang
- State Key Laboratory of Crop Stress Biology for the Arid Areas, and Key Laboratory of Northwest Loess Plateau Crop Pest Management of Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Shan-Shan Guo
- State Key Laboratory of Crop Stress Biology for the Arid Areas, and Key Laboratory of Northwest Loess Plateau Crop Pest Management of Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Tong-Xian Liu
- State Key Laboratory of Crop Stress Biology for the Arid Areas, and Key Laboratory of Northwest Loess Plateau Crop Pest Management of Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
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22
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Xu L, Li L, Yang P, Ma Z. Calmodulin as a downstream gene of octopamine-OAR α1 signalling mediates olfactory attraction in gregarious locusts. INSECT MOLECULAR BIOLOGY 2017; 26:1-12. [PMID: 27717101 DOI: 10.1111/imb.12266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The migratory locust (Locusta migratoria) shows aggregative traits in nymph marching bands and swarm formations through mutual olfactory attraction of conspecifics. However, olfactory preference in different nymph stages in gregarious locusts is not sufficiently explored. In this study, we found that the nymph olfactory preference for gregarious volatiles exhibited obvious variations at different developmental stages. The gregarious locusts show attractive response to conspecific volatiles from the third stadium. Transcriptome comparison between third- and fourth-stadium nymphs showed that the G protein-coupled receptor (GPCR) pathways are significantly enriched. Amongst the genes present in GPCR pathways, the expression level of calmodulin in locust brains significantly increased from the third- to the fourth-stadium nymphs. Amongst the four octopamine receptors (OARs) belonging to the GPCR family, only OAR α1 showed similar expression patterns to those of calmodulin, and knockdown of OAR α1 reduced the expression level of calmodulin. RNA interference of calmodulin decreased locomotion and induced the loss of olfactory attraction in gregarious locusts. Moreover, the activation of OAR α1 in calmodulin-knockdown locusts did not induce olfactory attraction of the nymphs to gregarious volatiles. Thus, calmodulin as a downstream gene of octopamine-OAR α1 (OA-OAR α1) signalling mediates olfactory attraction in gregarious locusts. Overall, this study provides novel insights into the mechanism of OA-OAR α1 signalling involved in olfactory attraction of gregarious locusts.
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Affiliation(s)
- L Xu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - L Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - P Yang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Z Ma
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
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23
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B-chromosome effects on Hsp70 gene expression does not occur at transcriptional level in the grasshopper Eyprepocnemis plorans. Mol Genet Genomics 2016; 291:1909-17. [PMID: 27334602 DOI: 10.1007/s00438-016-1228-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/17/2016] [Indexed: 01/01/2023]
Abstract
As intragenomic parasites, B chromosomes can elicit stress in the host genome, thus inducing a response for host adaptation to this kind of continuous parasitism. In the grasshopper Eyprepocnemis plorans, B-chromosome presence has been previously associated with a decrease in the amount of the heat-shock protein 70 (HSP70). To investigate whether this effect is already apparent at transcriptional level, we analyze the expression levels of the Hsp70 gene in gonads and somatic tissues of males and females with and without B chromosomes from two populations, where the predominant B chromosome variants (B2 and B24) exhibit different levels of parasitism, by means of quantitative real-time PCR (qPCR) on complementary DNA (cDNA). The results revealed the absence of significant differences for Hsp70 transcripts associated with B-chromosome presence in virtually all samples. This indicates that the decrease in HSP70 protein levels, formerly reported in this species, may not be a consequence of transcriptional down-regulation of Hsp70 genes, but the result of post-transcriptional regulation. These results will help to design future studies oriented to identifying factors modulating Hsp70 expression, and will also contribute to uncover the biological role of B chromosomes in eukaryotic genomes.
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Yu SH, Yang P, Sun T, Qi Q, Wang XQ, Xu DL, Chen XM. Identification and evaluation of reference genes in the Chinese white wax scale insect Ericerus pela. SPRINGERPLUS 2016; 5:791. [PMID: 27390632 PMCID: PMC4916112 DOI: 10.1186/s40064-016-2548-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/08/2016] [Indexed: 01/08/2023]
Abstract
BACKGROUND The Chinese white wax scale insect, Ericerus pela, is a well-known resource insect. The females and males are dramatically distinct at each developmental stage. We sought to identify suitable reference genes to use as internal controls in molecular research on E. plea. RESULTS geNorm, RefFinder and Normfinder analyses showed that ßTub-2 was the best reference gene throughout different developmental stages; SdhA-1 was the most stable reference gene in different tissues, and ßTub-1 was the most reliable reference gene under treatment with different temperatures. The results also showed that the optimal number of reference genes for analyzing target gene expression levels in the three experimental conditions was two. CONCLUSIONS The identified reference genes are suitable reference genes for normalization in RT-qPCR of E. pela samples.
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Affiliation(s)
- Shu-Hui Yu
- Research Institute of Resources Insects, Chinese Academy of Forestry, Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming, 650224 China
| | - Pu Yang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming, 650224 China
| | - Tao Sun
- Research Institute of Resources Insects, Chinese Academy of Forestry, Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming, 650224 China
| | - Qian Qi
- Research Institute of Resources Insects, Chinese Academy of Forestry, Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming, 650224 China
| | - Xue-Qing Wang
- Research Institute of Resources Insects, Chinese Academy of Forestry, Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming, 650224 China
| | - Dong-Li Xu
- Research Institute of Resources Insects, Chinese Academy of Forestry, Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming, 650224 China
| | - Xiao-Ming Chen
- Research Institute of Resources Insects, Chinese Academy of Forestry, Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming, 650224 China
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Ibanez F, Tamborindeguy C. Selection of reference genes for expression analysis in the potato psyllid, Bactericera cockerelli. INSECT MOLECULAR BIOLOGY 2016; 25:227-238. [PMID: 26936438 DOI: 10.1111/imb.12219] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The selection of reference genes is a crucial step for quantitative real-time PCR analyses and increasingly the use of more than one reference gene for accurate and reliable normalization is being recommended. In this study, a set of six genes was selected and their stability was assessed in different life stages and female organs of Bactericera cockerelli harbouring or not the bacterial pathogen 'Candidatus Liberibacter solanacearum' (Lso) haplotype B. The stability of each gene was determined using the BestKeeper, NormFinder and GeNorm programs. These analyses identified elongation factor-1a, ribosomal protein subunit L5 and ribosomal protein subunit 18 as the most stable genes to analyse gene expression during the insect life stages irrespective of Lso presence; Lso haplotype B only affected their respective ranking. By contrast, a common set of normalizers could not be found amongst the different female organs tested (bacteriomes, alimentary canals and reproductive organs).
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Affiliation(s)
- F Ibanez
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - C Tamborindeguy
- Department of Entomology, Texas A&M University, College Station, TX, USA
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Robinson KL, Tohidi-Esfahani D, Ponton F, Simpson SJ, Sword GA, Lo N. Alternative migratory locust phenotypes are associated with differences in the expression of genes encoding the methylation machinery. INSECT MOLECULAR BIOLOGY 2016; 25:105-115. [PMID: 26612460 DOI: 10.1111/imb.12203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Despite the importance of locust density-dependent polyphenism as a model system for understanding phenotypic plasticity, there is still much to be learnt about its underlying molecular control. Here we describe the first investigation into the expression of genes encoding the DNA methylation machinery in the migratory locust (Locusta migratoria). We show that the alternative solitarious and gregarious phenotypic states induced by different locust rearing densities are associated with significant differences in the expression of the target genes DNA methyltransferase 1, DNA methyltransferase 2 and methyl-CpG-binding domain protein 2/3. This variation was most pronounced in the embryos of solitarious vs. gregarious mothers. We mapped the embryonic methylation profiles of several intragenic regions and a Long Interspersed Nuclear Element (LINE), each of which is known to be differentially expressed between alternative locust phenotypes or has been directly implicated in phase change. LmI and three genes, adenyl cyclase-associated binding protein 2, choline kinase alpha-like and henna, were methylated. Our results set the stage for future studies investigating the specific role of DNA methylation in the maternal transfer of migratory locust phase polyphenism.
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Affiliation(s)
- K L Robinson
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
| | - D Tohidi-Esfahani
- ANU College of Medicine, Biology and Environment, Australian National University, Canberra, ACT, Australia
| | - F Ponton
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, NSW, Australia
- Department of Biological Sciences, Macquarie University, North Ryde NSW, Australia
| | - S J Simpson
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, NSW, Australia
| | - G A Sword
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - N Lo
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
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Ma KS, Li F, Liang PZ, Chen XW, Liu Y, Gao XW. Identification and Validation of Reference Genes for the Normalization of Gene Expression Data in qRT-PCR Analysis in Aphis gossypii (Hemiptera: Aphididae). JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew003. [PMID: 28076279 PMCID: PMC5778981 DOI: 10.1093/jisesa/iew003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/10/2016] [Indexed: 05/13/2023]
Abstract
To obtain accurate and reliable results from quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) analysis, it is necessary to select suitable reference genes as standards for normalizing target gene expression data. QRT-PCR is a popular analytical methodology for studying gene expression and it has been used widely in studies of Aphis gossypii Glover in recent years. However, there is absence of study on the stability of the expression of reference genes in A. gossypii. In this study, eight commonly used candidate reference genes, including 18S, 28S, β-ACT, GAPDH, EF1α, RPL7, α-TUB, and TBP, were evaluated under various experimental conditions to assess their suitability for use in the normalization of qRT-PCR data. The optimal number of reference genes was determined using the geNorm program, and the suitability of particular reference genes was empirically validated by performing normalizations of expression data for the HSP70 gene. The results showed the most suitable combinations of reference genes for the different experimental conditions. For experiments based on divergent developmental stages, EF1α, β-ACT, and RPL7 are the optimal reference gene combination, both EF1α and β-ACT are the optimal combination used in the experiments of different geographical populations, whereas for experiments of the temperature changes, the combination of GAPDH and RPL7 is optimal, both 18S and β-ACT are an optimal combination for feeding assay experiments. These research results should be useful for the selection of the suitable reference genes to obtain reliable qRT-PCR data in the gene expression study of A. gossypii.
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Affiliation(s)
- Kang-Sheng Ma
- Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China (; ; ; ; ; )
| | - Fen Li
- Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China (; ; ; ; ; )
| | - Ping-Zhuo Liang
- Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China (; ; ; ; ; )
| | - Xue-Wei Chen
- Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China (; ; ; ; ; )
| | - Ying Liu
- Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China (; ; ; ; ; )
| | - Xi-Wu Gao
- Department of Entomology, China Agricultural University, Beijing 100193, People's Republic of China (; ; ; ; ; )
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Sugahara R, Saeki S, Jouraku A, Shiotsuki T, Tanaka S. Knockdown of the corazonin gene reveals its critical role in the control of gregarious characteristics in the desert locust. JOURNAL OF INSECT PHYSIOLOGY 2015; 79:80-87. [PMID: 26092175 DOI: 10.1016/j.jinsphys.2015.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/13/2015] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
The two plague locusts, Schistocerca gregaria and Locusta migratoria, exhibit density-dependent phase polyphenism. Nymphs occurring at low population densities (solitarious forms) are uniformly colored and match their body color to the background color of their habitat, whereas those occurring at high population densities (gregarious) develop black patterns. An injection of the neuropeptide, corazonin (Crz) has been shown to induce black patterns in locusts and affect the classical morphometric ratio, F/C (F, hind femur length; C, maximum head width). We herein identified and cloned the CRZ genes from S. gregaria (SgCRZ) and L. migratoria. A comparative analysis of prepro-Crz sequences among insects showed that the functional peptide was well conserved; its conservation was limited to the peptide region. Silencing of the identified SgCRZ gene in gregarious S. gregaria nymphs markedly lightened their body color and shifted the adult F/C ratio toward the value typical of solitarious forms. In addition, knockdown of the gene in solitarious nymphs strongly inhibited darkening even after a transfer to crowded conditions; however, these individuals developed black patterns after being injected with the Crz as a rescue treatment. SgCRZ was constitutively expressed in the brains of S. gregaria during nymphal development in both phases. This gene was highly expressed not only in the brain in both phases, but also in the corpora allata in the gregarious phase. This conspicuous phase-dependent difference in SgCRZ gene expression may indicate a functional role in the control of phase polyphenism in this locust.
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Affiliation(s)
- Ryohei Sugahara
- Insect Growth Regulation Research Unit, National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Shinjiro Saeki
- Locust Research Laboratory, National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan; Graduate School of Agricultural Science, Kobe University, 657-8501, Japan
| | - Akiya Jouraku
- Insect Genome Research Unit, National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Takahiro Shiotsuki
- Insect Growth Regulation Research Unit, National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan.
| | - Seiji Tanaka
- Locust Research Laboratory, National Institute of Agrobiological Sciences, 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan.
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Shang F, Wei DD, Jiang XZ, Wei D, Shen GM, Feng YC, Li T, Wang JJ. Reference Gene Validation for Quantitative PCR Under Various Biotic and Abiotic Stress Conditions in Toxoptera citricida (Hemiptera, Aphidiae). JOURNAL OF ECONOMIC ENTOMOLOGY 2015; 108:2040-2047. [PMID: 26470351 DOI: 10.1093/jee/tov184] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/09/2015] [Indexed: 06/05/2023]
Abstract
The regulation of mRNA expression level is critical for gene expression studies. Currently, quantitative reverse transcription polymerase chain reaction (qRT-PCR) is commonly used to investigate mRNA expression level of genes under various experimental conditions. An important factor that determines the optimal quantification of qRT-PCR data is the choice of the reference gene for normalization. To advance gene expression studies in Toxoptera citricida (Kirkaldy), an important citrus pest and a main vector of the Citrus tristeza virus, we used five tools (GeNorm, NormFinder, BestKeeper, ΔCt methods, and RefFinder) to evaluate seven candidate reference genes (elongation factor-1 alpha [EF1α], beta tubulin [β-TUB], 18S ribosomal RNA [18S], RNA polymerase II large subunit (RNAP II), beta actin (β-ACT), alpha tubulin, and glyceraldhyde-3-phosphate dehydrogenase) under different biotic (developmental stages and wing dimorphism) and abiotic stress (thermal, starvation, and UV irradiation) conditions. The results showed that EF1α and 18S were the most stable genes under various biotic states, β-ACT and β-TUB during thermal stress, EF1α and RNAP II under starvation stress, and RNAP II, β-ACT, and EF1α under UV irradiation stress conditions. This study provides useful resources for the transcriptional profiling of genes in T. citricida and closely related aphid species.
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Affiliation(s)
- Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, P. R. China
| | - Dan-Dan Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, P. R. China
| | - Xuan-Zhao Jiang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, P. R. China
| | - Dong Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, P. R. China
| | - Guang-Mao Shen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, P. R. China
| | - Ying-Cai Feng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, P. R. China
| | - Ting Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, P. R. China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, P. R. China.
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Ridgeway JA, Timm AE. Reference gene selection for quantitative real-time PCR normalization in larvae of three species of Grapholitini (Lepidoptera: Tortricidae). PLoS One 2015; 10:e0129026. [PMID: 26030743 PMCID: PMC4450875 DOI: 10.1371/journal.pone.0129026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/04/2015] [Indexed: 12/02/2022] Open
Abstract
Despite the agricultural importance of species in the Grapholitini (Lepidoptera: Tortricidae), and the value of gene expression analysis for improved population management, few gene expression studies based on quantitative real-time PCR (qPCR) have been conducted for this tribe. Part of the reason for this lack of information is that suitable reference genes, which are fundamental for accurate normalization of qPCR studies, have not been identified for the tribe. Thus, the expression stability of six potential reference genes (ACT, AK, COI, EF1, ENO and TUB) was assessed in three different tissues (whole body, midgut and cuticle) of Cryptophlebia peltastica (Meyrick), Cydia pomonella (L.) and Thaumatotibia leucotreta (Meyrick). Additionally, these reference genes were tested using T. leucotreta at different temperatures (15°C, 25°C and 35°C) with and without baculovirus infection. Suitable reference genes were identified for the whole body and midgut tissue of all three species, and for cuticle tissue of Cy. pomonella and T. leucotreta. When T. leucotreta was infected with the virus at all temperature conditions ACT, AK and EF1 were found to be the most suitable reference genes for experimental normalization. In general, for all tissue types, species and stress conditions, AK and EF1 were the best-performing reference genes. However, even though the three species analysed were closely related and within the same tribe, each species required varying gene combinations for suitable normalization. This study provides the first reference gene evaluation for the Tortricidae, and paves the way for future qPCR analysis in Tortricidae.
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Affiliation(s)
- Jaryd A. Ridgeway
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Alicia E. Timm
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
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Pulpitel T, Pernice M, Simpson SJ, Ponton F. Tissue-Specific Immune Gene Expression in the Migratory Locust, Locusta Migratoria. INSECTS 2015; 6:368-80. [PMID: 26463191 PMCID: PMC4553485 DOI: 10.3390/insects6020368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 11/16/2022]
Abstract
The ability of hosts to respond to infection involves several complex immune recognition pathways. Broadly conserved pathogen-associated molecular patterns (PAMPs) allow individuals to target a range of invading microbes. Recently, studies on insect innate immunity have found evidence that a single pathogen can activate different immune pathways across species. In this study, expression changes in immune genes encoding peptidoglycan-recognition protein SA (PGRP-SA), gram-negative binding protein 1 (GNBP1) and prophenoloxidase (ProPO) were investigated in Locusta migratoria, following an immune challenge using injected lipopolysaccharide (LPS) solution from Escherichia coli. Since immune activation might also be tissue-specific, gene expression levels were followed across a range of tissue types. For PGRP-SA, expression increased in response to LPS within all seven of the tissue-types assayed and differed significantly between tissues. Expression of GNBP1 similarly varied across tissue types, yet showed no clear expression difference between LPS-injected and uninfected locusts. Increases in ProPO expression in response to LPS, however, could only be detected in the gut sections. This study has revealed tissue-specific immune response to add a new level of complexity to insect immune studies. In addition to variation in recognition pathways identified in previous works, tissue-specificity should be carefully considered in similar works.
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Affiliation(s)
- Tamara Pulpitel
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia.
| | - Mathieu Pernice
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, New South Wales 2007, Australia.
| | - Stephen J Simpson
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia.
- The Charles Perkins Centre, The University of Sydney, NSW 2006, Australia.
| | - Fleur Ponton
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia.
- The Charles Perkins Centre, The University of Sydney, NSW 2006, Australia.
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Tan QQ, Zhu L, Li Y, Liu W, Ma WH, Lei CL, Wang XP. A de novo transcriptome and valid reference genes for quantitative real-time PCR in Colaphellus bowringi. PLoS One 2015; 10:e0118693. [PMID: 25692689 PMCID: PMC4334893 DOI: 10.1371/journal.pone.0118693] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 01/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background The cabbage beetle Colaphellus bowringi Baly is a serious insect pest of crucifers and undergoes reproductive diapause in soil. An understanding of the molecular mechanisms of diapause regulation, insecticide resistance, and other physiological processes is helpful for developing new management strategies for this beetle. However, the lack of genomic information and valid reference genes limits knowledge on the molecular bases of these physiological processes in this species. Results Using Illumina sequencing, we obtained more than 57 million sequence reads derived from C. bowringi, which were assembled into 39,390 unique sequences. A Clusters of Orthologous Groups classification was obtained for 9,048 of these sequences, covering 25 categories, and 16,951 were assigned to 255 Kyoto Encyclopedia of Genes and Genomes pathways. Eleven candidate reference gene sequences from the transcriptome were then identified through reverse transcriptase polymerase chain reaction. Among these candidate genes, EF1α, ACT1, and RPL19 proved to be the most stable reference genes for different reverse transcriptase quantitative polymerase chain reaction experiments in C. bowringi. Conversely, aTUB and GAPDH were the least stable reference genes. Conclusion The abundant putative C. bowringi transcript sequences reported enrich the genomic resources of this beetle. Importantly, the larger number of gene sequences and valid reference genes provide a valuable platform for future gene expression studies, especially with regard to exploring the molecular mechanisms of different physiological processes in this species.
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Affiliation(s)
- Qian-Qian Tan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, P. R. China
| | - Li Zhu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yi Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Wen Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Wei-Hua Ma
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, P. R. China
- * E-mail: (WHM); (XPW)
| | - Chao-Liang Lei
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiao-Ping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
- * E-mail: (WHM); (XPW)
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Zheng YT, Li HB, Lu MX, Du YZ. Evaluation and validation of reference genes for qRT-PCR normalization in Frankliniella occidentalis (Thysanoptera: Thripidae). PLoS One 2014; 9:e111369. [PMID: 25356721 PMCID: PMC4214748 DOI: 10.1371/journal.pone.0111369] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 09/30/2014] [Indexed: 11/19/2022] Open
Abstract
Quantitative real time PCR (qRT-PCR) has emerged as a reliable and reproducible technique for studying gene expression analysis. For accurate results, the normalization of data with reference genes is particularly essential. Once the transcriptome sequencing of Frankliniella occidentalis was completed, numerous unigenes were identified and annotated. Unfortunately, there are no studies on the stability of reference genes used in F. occidentalis. In this work, seven candidate reference genes, including actin, 18S rRNA, H3, tubulin, GAPDH, EF-1 and RPL32, were evaluated for their suitability as normalization genes under different experimental conditions using the statistical software programs BestKeeper, geNorm, Normfinder and the comparative ΔCt method. Because the rankings of the reference genes provided by each of the four programs were different, we chose a user-friendly web-based comprehensive tool RefFinder to get the final ranking. The result demonstrated that EF-1 and RPL32 displayed the most stable expression in different developmental stages; RPL32 and GAPDH showed the most stable expression at high temperatures, while 18S and EF-1 exhibited the most stable expression at low temperatures. In this study, we validated the suitable reference genes in F. occidentalis for gene expression profiling under different experimental conditions. The choice of internal standard is very important in the normalization of the target gene expression levels, thus validating and selecting the best genes will help improve the quality of gene expression data of F. occidentalis. What is more, these validated reference genes could serve as the basis for the selection of candidate reference genes in other insects.
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Affiliation(s)
- Yu-Tao Zheng
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Hong-Bo Li
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
- Guizhou Institute of Plant Protection, Guiyang, China
| | - Ming-Xing Lu
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
| | - Yu-Zhou Du
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University, Yangzhou, China
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Validation of reference housekeeping genes for gene expression studies in western corn rootworm (Diabrotica virgifera virgifera). PLoS One 2014; 9:e109825. [PMID: 25356627 PMCID: PMC4214676 DOI: 10.1371/journal.pone.0109825] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 09/10/2014] [Indexed: 11/19/2022] Open
Abstract
Quantitative Real-time PCR (qRT-PCR) is a powerful technique to investigate comparative gene expression. In general, normalization of results using a highly stable housekeeping gene (HKG) as an internal control is recommended and necessary. However, there are several reports suggesting that regulation of some HKGs is affected by different conditions. The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is a serious pest of corn in the United States and Europe. The expression profile of target genes related to insecticide exposure, resistance, and RNA interference has become an important experimental technique for study of western corn rootworms; however, lack of information on reliable HKGs under different conditions makes the interpretation of qRT-PCR results difficult. In this study, four distinct algorithms (Genorm, NormFinder, BestKeeper and delta-CT) and five candidate HKGs to genes of reference (β-actin; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; β-tubulin; RPS9, ribosomal protein S9; EF1a, elongation factor-1α) were evaluated to determine the most reliable HKG under different experimental conditions including exposure to dsRNA and Bt toxins and among different tissues and developmental stages. Although all the HKGs tested exhibited relatively stable expression among the different treatments, some differences were noted. Among the five candidate reference genes evaluated, β-actin exhibited highly stable expression among different life stages. RPS9 exhibited the most similar pattern of expression among dsRNA treatments, and both experiments indicated that EF1a was the second most stable gene. EF1a was also the most stable for Bt exposure and among different tissues. These results will enable researchers to use more accurate and reliable normalization of qRT-PCR data in WCR experiments.
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Ruiz-Estévez M, Badisco L, Broeck JV, Perfectti F, López-León MD, Cabrero J, Camacho JPM. B chromosomes showing active ribosomal RNA genes contribute insignificant amounts of rRNA in the grasshopper Eyprepocnemis plorans. Mol Genet Genomics 2014; 289:1209-16. [PMID: 24997085 DOI: 10.1007/s00438-014-0880-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 06/14/2014] [Indexed: 11/25/2022]
Abstract
The genetic inertness of supernumerary (B) chromosomes has recently been called into question after finding several cases of gene activity on them. The grasshopper Eyprepocnemis plorans harbors B chromosomes containing large amounts of ribosomal DNA (rDNA) units, some of which are eventually active, but the amount of rRNA transcripts contributed by B chromosomes, compared to those of the standard (A) chromosomes, is unknown. Here, we address this question by means of quantitative PCR (qPCR) for two different ITS2 amplicons, one coming from rDNA units located in both A and B chromosomes (ITS2(A+B)) and the other being specific to B chromosomes (ITS2(B)). We analyzed six body parts in nine males showing rDNA expression in their B chromosomes in the testis. Amplification of the ITS2(B) amplicon was successful in RNA extracted from all six body parts analyzed, but showed relative quantification (RQ) values four orders of magnitude lower than those obtained for the ITS(A+B) amplicon. RQ values differed significantly between body parts for the two amplicons, with testis, accessory gland and wing muscle showing threefold higher values than head, gastric cecum and hind leg. We conclude that the level of B-specific rDNA expression is extremely low even in individuals where B chromosome rDNA is not completely silenced. Bearing in mind that B chromosomes carry the largest rDNA cluster in the E. plorans genome, we also infer that the relative contribution of B chromosome rRNA genes to ribosome biogenesis is insignificant, at least in the body parts analyzed.
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Affiliation(s)
- Mercedes Ruiz-Estévez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
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Yang Q, Li Z, Cao J, Zhang S, Zhang H, Wu X, Zhang Q, Liu X. Selection and assessment of reference genes for quantitative PCR normalization in migratory locust Locusta migratoria (Orthoptera: Acrididae). PLoS One 2014; 9:e98164. [PMID: 24887329 PMCID: PMC4041718 DOI: 10.1371/journal.pone.0098164] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 04/29/2014] [Indexed: 11/18/2022] Open
Abstract
Locusta migratoria is a classic hemimetamorphosis insect and has caused widespread economic damage to crops as a migratory pest. Researches on the expression pattern of functional genes in L. migratoria have drawn focus in recent years, especially with the release of genome information. Real-time quantitative PCR is the most reproducible and sensitive approach for detecting transcript expression levels of target genes, but optimal internal standards are key factors for its accuracy and reliability. Therefore, it's necessary to provide a systematic stability assessment of internal control for well-performed tests of target gene expression profile. In this study, twelve candidate genes (Ach, Act, Cht2, EF1α, RPL32, Hsp70, Tub, RP49, SDH, GAPDH, 18S, and His) were analyzed with four statistical methods: the delta Ct approach, geNorm, Bestkeeper and NormFinder. The results from these analyses aimed to choose the best suitable reference gene across different experimental situations for gene profile study in L. migratoria. The result demonstrated that for different developmental stages, EF1α, Hsp70 and RPL32 exhibited the most stable expression status for all samples; EF1α and RPL32 were selected as the best reference genes for studies involving embryo and larvae stages, while SDH and RP49 were identified for adult stage. The best-ranked reference genes across different tissues are RPL32, Hsp70 and RP49. For abiotic treatments, the most appropriate genes we identified were as follows: Act and SDH for larvae subjected to different insecticides; RPL32 and Ach for larvae exposed to different temperature treatments; and Act and Ach for larvae suffering from starvation. The present report should facilitate future researches on gene expression in L. migratoria with accessibly optimal reference genes under different experimental contexts.
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Affiliation(s)
- Qingpo Yang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Zhen Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Jinjun Cao
- Department of Entomology, China Agricultural University, Beijing, China
| | - Songdou Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Huaijiang Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xiaoyun Wu
- Department of Entomology, China Agricultural University, Beijing, China; Department of Horticulture, Beijing Vocational College of Agriculture, Beijing, China
| | - Qingwen Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology, China Agricultural University, Beijing, China
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Xie G, Zou J, Zhao L, Wu M, Wang S, Zhang F, Tang B. Inhibitional effects of metal Zn²⁺ on the reproduction of Aphis medicaginis and its predation by Harmonia axyridis. PLoS One 2014; 9:e87639. [PMID: 24533059 PMCID: PMC3922717 DOI: 10.1371/journal.pone.0087639] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 12/29/2013] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Contamination, including metals, can disturb the reproductive processes of many organisms, including both prey and predatory insects. However, there is virtually no information on the effects of high level Zinc (Zn) pollution on aphids and ladybirds. The high concentrations of Zn²⁺ or Zn pollution inhibit reproduction in the phytophagous aphid, Aphis medicaginis, and the predatory ladybird Harmonia axyridis could provide important information. RESULTS It was observed in this study that Zn concentrations in Vicia faba (broad bean) seeds and seedlings in all Zn²⁺ treatments were significantly higher than that in the control group, and increased with increasing Zn²⁺ concentrations in the solution. The rate of reproduction in A. medicaginis declined significantly (p<0.05) over time in the five groups fed on broad bean seedlings treated with different concentrations of Zn²⁺ solution compared with the control group. These results showed that higher concentrations of Zn²⁺ significantly inhibited the reproductive capacity of A. medicaginis. We also cloned and identified a gene encoding vitellogenin (Vg) from A. medicaginis, which has an important role in vitellogenesis, and therefore, reproduction was affected by exposure to Zn²⁺. Expression of AmVg was reduced with increasing exposure to Zn²⁺ and also in the F1-F3 generations of aphids exposed to different Zn²⁺ concentrations. Predation by H. axyridis was also reduced in aphids exposed to high-levels of Zn²⁺. Similarly, ovipositioning by H. axyridis was also reduced. CONCLUSIONS Our results suggest that Zn²⁺ can significantly affect the reproductive capacity of both A. medicaginis and its predator H. axyridis, the former through effects on the expression of AmVg and the latter through avoidance of aphids containing high levels of Zn²⁺.
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Affiliation(s)
- Guoqiang Xie
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jiaping Zou
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lina Zhao
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Mengjing Wu
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Shigui Wang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Fan Zhang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Bin Tang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Yuan M, Lu Y, Zhu X, Wan H, Shakeel M, Zhan S, Jin BR, Li J. Selection and evaluation of potential reference genes for gene expression analysis in the brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae) using reverse-transcription quantitative PCR. PLoS One 2014; 9:e86503. [PMID: 24466124 PMCID: PMC3900570 DOI: 10.1371/journal.pone.0086503] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 12/10/2013] [Indexed: 01/24/2023] Open
Abstract
The brown planthopper (BPH), Nilaparvata lugens (Hemiptera, Delphacidae), is one of the most important rice pests. Abundant genetic studies on BPH have been conducted using reverse-transcription quantitative real-time PCR (qRT-PCR). Using qRT-PCR, the expression levels of target genes are calculated on the basis of endogenous controls. These genes need to be appropriately selected by experimentally assessing whether they are stably expressed under different conditions. However, such studies on potential reference genes in N. lugens are lacking. In this paper, we presented a systematic exploration of eight candidate reference genes in N. lugens, namely, actin 1 (ACT), muscle actin (MACT), ribosomal protein S11 (RPS11), ribosomal protein S15e (RPS15), alpha 2-tubulin (TUB), elongation factor 1 delta (EF), 18S ribosomal RNA (18S), and arginine kinase (AK) and used four alternative methods (BestKeeper, geNorm, NormFinder, and the delta Ct method) to evaluate the suitability of these genes as endogenous controls. We examined their expression levels among different experimental factors (developmental stage, body part, geographic population, temperature variation, pesticide exposure, diet change, and starvation) following the MIQE (Minimum Information for publication of Quantitative real time PCR Experiments) guidelines. Based on the results of RefFinder, which integrates four currently available major software programs to compare and rank the tested candidate reference genes, RPS15, RPS11, and TUB were found to be the most suitable reference genes in different developmental stages, body parts, and geographic populations, respectively. RPS15 was the most suitable gene under different temperature and diet conditions, while RPS11 was the most suitable gene under different pesticide exposure and starvation conditions. This work sheds light on establishing a standardized qRT-PCR procedure in N. lugens, and serves as a starting point for screening for reference genes for expression studies of related insects.
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Affiliation(s)
- Miao Yuan
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanhui Lu
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Xun Zhu
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Hu Wan
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Shakeel
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Sha Zhan
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Byung-Rae Jin
- Laboratory of Insect Molecular Biology and Biotechnology, Department of Applied Biology, College of Natural Resources and Life Science, Dong-A University, Busan, Korea
| | - Jianhong Li
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
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Zhu X, Yuan M, Shakeel M, Zhang Y, Wang S, Wang X, Zhan S, Kang T, Li J. Selection and evaluation of reference genes for expression analysis using qRT-PCR in the beet armyworm Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae). PLoS One 2014; 9:e84730. [PMID: 24454743 PMCID: PMC3893131 DOI: 10.1371/journal.pone.0084730] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/18/2013] [Indexed: 11/19/2022] Open
Abstract
Quantitative real-time PCR (qRT-PCR) is a reliable and reproducible technique for measuring and evaluating changes in gene expression. The most common method for analyzing qRT-PCR data is to normalize mRNA levels of target genes to internal reference genes. Evaluating and selecting stable reference genes on a case-by-case basis is critical. The present study aimed to facilitate gene expression studies by identifying the most suitable reference genes for normalization of mRNA expression in qRT-PCR analysis of the beet armyworm Spodoptera exigua (Lepidoptera: Noctuidae). For this purpose, three software tools (geNorm, NormFinder and BestKeeper) were used to investigate 10 candidate reference genes in nine developmental stages and five different tissues (epidermis, head, midgut, fat body and hemolymph) in three larval physiological stages (molting, feeding and wandering stages) of, S. exigua. With the exception of 18S ribosomal RNA (18S), all other candidate genes evaluated, β-actin1(ACT1), β-actin2 (ACT2), elongation factor1(EF1), elongation factor 2 (EF2), Glyceralde hyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein L10 (L10), ribosomal protein L17A (L17A), superoxide dismutase (SOD), α-tubulin (TUB),proved to be acceptable reference genes. However, their suitability partly differed between physiological stages and different tissues. L10, EF2 and L17A ranked highest in all tissue sample sets. SOD, ACT2, GAPDH, EF1 and ACT1 were stably expressed in all developmental stage sample sets; ACT2, ACT1 and L10 for larvae sample sets; GAPDH, ACT1 and ACT2 for pupae and adults; SOD and L17A for males; and EF2 and SOD for females. The expression stability of genes varied in different conditions. The findings provided here demonstrated, with a few exceptions, the suitability of most of the 10 reference genes tested in tissues and life developmental stages. Overall, this study emphasizes the importance of validating reference genes for qRT-PCR analysis in S. exigua.
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Affiliation(s)
- Xun Zhu
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Miao Yuan
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Shakeel
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Wang
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Sha Zhan
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Tinghao Kang
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianhong Li
- Laboratory of Pesticide, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
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HP1 knockdown is associated with abnormal condensation of almost all chromatin types in a grasshopper (Eyprepocnemis plorans). Chromosome Res 2014; 22:253-66. [PMID: 24398928 DOI: 10.1007/s10577-013-9399-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/11/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
Abstract
Heterochromatin protein 1 (HP1) is a highly conserved family of eukaryotic proteins required for heterochromatic gene silencing and euchromatic gene transcription regulation. In addition, HP1 is involved in chromatin organization and protection of chromosome integrity during cell division. Here, we present a cytological and molecular analysis of the effects of HP1 knockdown in Eyprepocnemis plorans, a grasshopper species polymorphic for supernumerary heterochromatic chromosomes. Our results revealed contrasting effects of HP1 knockdown on gene activity. While the Bub1 gene decreased in expression level in HP1 knockdown animals, NOR activity, rRNA and, contrarily to previous reports in Drosophila, Hsp70 gene expression remained unchanged. Furthermore, HP1 knockdown resulted in abnormal chromatin condensation, chromosomal bridges, higher frequency of macrospermatids, loss of muscle mass and hemolymph amount as well as a low number of dividing cells and survival reduction. All these phenotypes are very likely due to the chromatin condensation disruption observed for almost all kinds of chromatin.
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Wang Y, Wang ZK, Huang Y, Liao YF, Yin YP. Identification of suitable reference genes for gene expression studies by qRT-PCR in the blister beetle Mylabris cichorii. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:94. [PMID: 25368050 PMCID: PMC4212844 DOI: 10.1093/jis/14.1.94] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 06/28/2013] [Indexed: 06/04/2023]
Abstract
The blister beetle Mylabris cichorii L. (Coleoptera: Meloidae) is a traditional medicinal insect recorded in the Chinese Pharmacopoeia. It synthesizes cantharidin, which kills cancer cells efficiently. Only males produce large amounts of cantharidin. Reference genes are required as endogenous controls for the analysis of differential gene expression in M. cichorii. Our study chose 10 genes as candidate reference genes. The stability of expression of these genes was analyzed by quantitative PCR and determined with two algorithms, geNorm and Normfinder. We recommend UBE3A and RPL22e as suitable reference genes in females and UBE3A, TAF5, and RPL22e in males.
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Affiliation(s)
- Yu Wang
- Bio-Engineering College of Chongqing University, Key Lab of Genetic Function and Regulation in Chongqing, Chongqing, China Panzhihua University, Panzhihua, China
| | - Zhong-Kang Wang
- Bio-Engineering College of Chongqing University, Key Lab of Genetic Function and Regulation in Chongqing, Chongqing, China
| | - Yi Huang
- Bio-Engineering College of Chongqing University, Key Lab of Genetic Function and Regulation in Chongqing, Chongqing, China
| | - Yu-Feng Liao
- Bio-Engineering College of Chongqing University, Key Lab of Genetic Function and Regulation in Chongqing, Chongqing, China
| | - You-Ping Yin
- Bio-Engineering College of Chongqing University, Key Lab of Genetic Function and Regulation in Chongqing, Chongqing, China
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Fu W, Xie W, Zhang Z, Wang S, Wu Q, Liu Y, Zhou X, Zhou X, Zhang Y. Exploring valid reference genes for quantitative real-time PCR analysis in Plutella xylostella (Lepidoptera: Plutellidae). Int J Biol Sci 2013; 9:792-802. [PMID: 23983612 PMCID: PMC3753443 DOI: 10.7150/ijbs.5862] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 06/15/2013] [Indexed: 12/17/2022] Open
Abstract
Abstract: Quantitative real-time PCR (qRT-PCR), a primary tool in gene expression analysis, requires an appropriate normalization strategy to control for variation among samples. The best option is to compare the mRNA level of a target gene with that of reference gene(s) whose expression level is stable across various experimental conditions. In this study, expression profiles of eight candidate reference genes from the diamondback moth, Plutella xylostella, were evaluated under diverse experimental conditions. RefFinder, a web-based analysis tool, integrates four major computational programs including geNorm, Normfinder, BestKeeper, and the comparative ΔCt method to comprehensively rank the tested candidate genes. Elongation factor 1 (EF1) was the most suited reference gene for the biotic factors (development stage, tissue, and strain). In contrast, although appropriate reference gene(s) do exist for several abiotic factors (temperature, photoperiod, insecticide, and mechanical injury), we were not able to identify a single universal reference gene. Nevertheless, a suite of candidate reference genes were specifically recommended for selected experimental conditions. Our finding is the first step toward establishing a standardized qRT-PCR analysis of this agriculturally important insect pest.
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Affiliation(s)
- Wei Fu
- Institute of Pesticide Science, Hunan Agricultural University, Changsha 410128, China
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Identification and validation of reference genes for gene expression analysis using quantitative PCR in Spodoptera litura (Lepidoptera: Noctuidae). PLoS One 2013; 8:e68059. [PMID: 23874494 PMCID: PMC3706614 DOI: 10.1371/journal.pone.0068059] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/24/2013] [Indexed: 12/04/2022] Open
Abstract
Reverse transcription quantitative polymerase chain reaction (qRT-PCR) has rapidly become the most sensitive and accurate method for the quantification of gene expression. To facilitate gene expression studies and obtain more accurate qRT-PCR data, normalization relative to stable housekeeping genes is required. These housekeeping genes need to show stable expression under the given experimental conditions for the qRT-PCR results to be accurate. Unfortunately, there are no studies on the stability of housekeeping genes used in Spodoptera litura. In this study, eight candidate reference genes, elongation factor 1 alpha (EF1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein L10 (RPL10), ribosomal protein S3 (RPS3), beta actin (ACTB), beta FTZ-F1 (FTZF1), ubiquinol-cytochrome c reductase (UCCR), and arginine kinase (AK), were evaluated for their suitability as normalization genes under different experimental conditions using the statistical software programs, BestKeeper, geNorm and Normfinder, and the comparative ΔCt method. We determined the expression levels of the candidate reference genes for three biotic factors (developmental stage, tissue and population), and four abiotic treatments (temperature, insecticide, food and starvation). The results indicated that the best sets of candidates as reference genes were as follows: GAPDH and UCCR for developmental stages; RPL10, AK and EF1 for different tissues; RPL10 and EF1 for different populations in China; GAPDH and EF1 for temperature-stressed larvae; AK and ACTB for larvae treated with different insecticides; RPL10, GAPDH and UCCR for larvae fed different diets; RPS3 and ACTB for starved larvae. We believe that these results make an important contribution to gene analysis studies in S. litura and form the basis of further research on stable reference genes in S. litura and other organisms.
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Marchal E, Hult EF, Huang J, Tobe SS. Sequencing and validation of housekeeping genes for quantitative real-time PCR during the gonadotrophic cycle of Diploptera punctata. BMC Res Notes 2013; 6:237. [PMID: 23777660 PMCID: PMC3750588 DOI: 10.1186/1756-0500-6-237] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 06/11/2013] [Indexed: 11/16/2022] Open
Abstract
Background Quantitative RT-PCR (q-RT-PCR) is a powerful tool that allows for the large scale analysis of small changes in gene expression. Accurate and reliable results depend on the use of stable reference genes for normalization. However, the expression of some widely used housekeeping genes can vary under different experimental setups. To our knowledge, no validation studies have been reported for reference genes in cockroaches. The aim of the current study is the identification and validation of a set of eight housekeeping genes during the first gonadotrophic cycle of the cockroach, Diploptera punctata. This study made use of two different algorithms (geNorm and Normfinder) to evaluate the stability of gene expression. Results Candidate housekeeping genes were sequenced: β-actin (Actin), elongation factor 1 alpha (EF1a), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), armadillo (Arm), ribosomal protein L32 (RpL32), succinate dehydrogenase (SDHa), annexin IX (AnnIX) and α-tubulin (Tub). The expression of these eight genes was analyzed in corpora allata (CA) and ovaries of adult female D. punctata. Both geNorm, as well as Normfinder characterized SDHa, EF1a and Arm as being the most stably expressed in the corpora allata. In the ovary, the geNorm calculation showed Tub, EF1a and RpL32 to be most stable, whereas Normfinder identified Tub, EF1a and Arm as the best. In ovary, the least stable gene was Actin, challenging its usefulness in normalization. As a proof of principle, the expression of follicle cell protein 3c and CYP15A1 was monitored during the first gonadotrophic cycle. Conclusion Arm and EF1a form the most stably expressed combination of two reference genes out of the eight candidates that were tested in the corpora allata. Our results show that the combined use of Tub, EF1a and RpL32 ensures an accurate normalization of gene expression levels in ovary of D. punctata. Our study has indicated that neither Actin nor AnnIX should be used for normalization of transcript levels when studying the first gonadotrophic cycle in CA or ovary of D. punctata. The results stress the necessity for validation of reference genes in q-RT-PCR studies in cockroaches.
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Affiliation(s)
- Elisabeth Marchal
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Canada
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Shi XQ, Guo WC, Wan PJ, Zhou LT, Ren XL, Ahmat T, Fu KY, Li GQ. Validation of reference genes for expression analysis by quantitative real-time PCR in Leptinotarsa decemlineata (Say). BMC Res Notes 2013; 6:93. [PMID: 23497596 PMCID: PMC3600673 DOI: 10.1186/1756-0500-6-93] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/07/2013] [Indexed: 11/25/2022] Open
Abstract
Background L. decemlineata is an exotic invasive insect pest, and invaded in Xinjiang Uygur autonomous region in China in the 1990s from Kazakhstan. It is a notorious defoliator of potato throughout most of the northern Xinjiang in current, and often causes extremely large yield losses of potato. Results The expression stability of nine L. decemlineata house-keeping genes (Actin, ACT1 and ACT2; ADP-ribosylation factor, ARF1 and ARF4; TATA box binding protein, TBP1 and TBP2; ribosomal protein RP4 and RP18; translation elongation factor 1α EF1α) was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) in seven developmental stages, three larval tissues and two insecticide treatments. The results were analyzed using three software programs: geNorm, NormFinder and BestKeeper. Although there was no consistent ranking observed among the house-keeping genes across the samples, the overall analysis revealed that RP18, RP4, ARF1, and ARF4 were the four most stable house-keeping genes. In contrast, ACT1 and ACT2, two of the most widely used reference genes, had the least stability. Our results suggest that the combined use of the four most stably expressed genes may produce optimal normalization for qRT-PCR. Conclusions The expression stability of the house-keeping genes varies among different developing stages, in different tissues and under different experimental conditions. Our results will enable a more accurate and reliable normalization of qRT-PCR data in L. decemlineata.
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Affiliation(s)
- Xiao-Qin Shi
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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Li R, Xie W, Wang S, Wu Q, Yang N, Yang X, Pan H, Zhou X, Bai L, Xu B, Zhou X, Zhang Y. Reference gene selection for qRT-PCR analysis in the sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae). PLoS One 2013; 8:e53006. [PMID: 23308130 PMCID: PMC3540095 DOI: 10.1371/journal.pone.0053006] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 11/19/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Accurate evaluation of gene expression requires normalization relative to the expression of reliable reference genes. Expression levels of "classical" reference genes can differ, however, across experimental conditions. Although quantitative real-time PCR (qRT-PCR) has been used extensively to decipher gene function in the sweetpotato whitefly Bemisia tabaci, a world-wide pest in many agricultural systems, the stability of its reference genes has rarely been validated. RESULTS In this study, 15 candidate reference genes from B. tabaci were evaluated using two Excel-based algorithms geNorm and Normfinder under a diverse set of biotic and abiotic conditions. At least two reference genes were selected to normalize gene expressions in B. tabaci under experimental conditions. Specifically, for biotic conditions including host plant, acquisition of a plant virus, developmental stage, tissue (body region of the adult), and whitefly biotype, ribosomal protein L29 was the most stable reference gene. In contrast, the expression of elongation factor 1 alpha, peptidylprolyl isomerase A, NADH dehydrogenase, succinate dehydrogenase complex subunit A and heat shock protein 40 were consistently stable across various abiotic conditions including photoperiod, temperature, and insecticide susceptibility. CONCLUSION Our finding is the first step toward establishing a standardized quantitative real-time PCR procedure following the MIQE (Minimum Information for publication of Quantitative real time PCR Experiments) guideline in an agriculturally important insect pest, and provides a solid foundation for future RNA interference based functional study in B. tabaci.
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Affiliation(s)
- Rumei Li
- Institute of Pesticide, Hunan Agricultural University, Changsha, P. R. China
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Nina Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xin Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huipeng Pan
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Xiaomao Zhou
- Institute of Pesticide, Hunan Agricultural University, Changsha, P. R. China
| | - Lianyang Bai
- Institute of Pesticide, Hunan Agricultural University, Changsha, P. R. China
| | - Baoyun Xu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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Majerowicz D, Alves-Bezerra M, Logullo R, Fonseca-de-Souza AL, Meyer-Fernandes JR, Braz GRC, Gondim KC. Looking for reference genes for real-time quantitative PCR experiments in Rhodnius prolixus (Hemiptera: Reduviidae). INSECT MOLECULAR BIOLOGY 2011; 20:713-722. [PMID: 21929722 DOI: 10.1111/j.1365-2583.2011.01101.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Quantitative real-time PCR (qPCR) has become one of the most used techniques to measure gene expression. However, normalization of gene expression data against reference genes is essential, although these are usually used without any kind of validation. The expression of seven genes was compared in organs of Rhodnius prolixus under diverse conditions, using published software to test gene expression stability. Rp18S and elongation factor 1 (RpEF -1) were the most reliable genes for normalization in qPCR when gene expression in different organs was compared. Moreover, both genes were found to be the best references when transcript levels were compared in the posterior midgut of insects infected with Trypanosoma cruzi. Rp18S was also the best reference gene in the fat bodies of unfed and fed insects. By contrast, RpEF-1 was found to be the best reference gene for comparison between posterior midguts, and RpMIP or RpActin should be used to compare gene expression in the ovaries. Although Rp18S is indicated here as the best reference in most cases, reports from the literature show that it is difficult to find an optimum reference gene. Nevertheless, validation of candidate genes to be taken as references is important when new experimental conditions are tested to avoid incorrect data interpretation.
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Affiliation(s)
- D Majerowicz
- Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho 373, Ilha do Fundão, Rio de Janeiro, RJ, Brazil.
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Chapuis MP, Simpson SJ, Blondin L, Sword GA. Taxa-specific heat shock proteins are over-expressed with crowding in the Australian plague locust. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:1562-1567. [PMID: 21867709 DOI: 10.1016/j.jinsphys.2011.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 08/08/2011] [Accepted: 08/09/2011] [Indexed: 05/31/2023]
Abstract
Most heat shock proteins (Hsps) function as molecular chaperones that help organisms to cope with stress. Although the best empirical evidence is related to heat shock, there is evidence that Hsps and their encoding genes are involved in resistance to other ecologically relevant types of stresses such as those imposed by high population density. We quantified density-dependent gene expression of large (i.e. Hsp40, Hsc70 and Hsp90) and small (Hsp20.5, Hsp20.6 and Hsp20.7) heat shock genes in neural tissue of fifth-instar nymphs of the Australian plague locust, Chortoicetes terminifera, using reverse transcription-quantitative PCR. Locusts are of particular interest when studying the influence of stress induced by high population density since they show an extreme form of phenotypic plasticity changing from a cryptic solitarious phase to a swarming gregarious phase. Crowding led to a synchronous and sustained 2-3 fold increase in the expression of only two Hsp genes, Hsp20.5 and Hsp20.7, which do not BLAST with any known animal sequences and therefore are likely to be unique to members of the Orthoptera. This study opens a range of experiments to investigate the possibility of specific roles for these two small Hsps in the resistance to stressful conditions imposed by crowded environments and/or the expression of gregarious behavior as well as their evolutionary significance to locusts whose populations are regularly exposed to high density conditions in the field.
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Ponton F, Chapuis MP, Pernice M, Sword GA, Simpson SJ. Evaluation of potential reference genes for reverse transcription-qPCR studies of physiological responses in Drosophila melanogaster. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:840-50. [PMID: 21435341 DOI: 10.1016/j.jinsphys.2011.03.014] [Citation(s) in RCA: 223] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 03/15/2011] [Accepted: 03/15/2011] [Indexed: 05/12/2023]
Abstract
Drosophila melanogaster is one of the most important genetic models and techniques such as reverse transcription quantitative real-time PCR (RT-qPCR) are being employed extensively for deciphering the genetics basis of physiological functions. In RT-qPCR, the expression levels of target genes are estimated on the basis of endogenous controls. The purpose of these reference genes is to control for variations in RNA quantity and quality. Although determination of suitable reference genes is essential to RT-qPCR studies, reports on the evaluation of reference genes in D. melanogaster studies are lacking. We analyzed the expression levels of seven candidate reference genes (Actin, EF1, Mnf, Rps20, Rpl32, Tubulin and 18S) in flies that were injured, heat-stressed, or fed different diets. Statistical analyses of variation were determined using three established software programs for reference gene selection, geNorm, NormFinder and BestKeeper. Best-ranked references genes differed across the treatments. Normalization candidacy of the selected candidate reference genes was supported by an analysis of gene expression values obtained from microarray datasets available online. The differences between the experimental treatments suggest that assessing the stability of reference gene expression patterns, determining candidates and testing their suitability is required for each experimental investigation.
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Affiliation(s)
- Fleur Ponton
- School of Biological Sciences, Heydon-Laurence building-A08, The University of Sydney, NSW 2006, Australia.
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