1
|
Reliable reference genes for qPCR normalization in females of the mirid predator, Cyrtorhinus lividipennis (Hemiptera: Miridae). Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01093-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
|
2
|
Selection and Evaluation of Reference Genes for qRT-PCR in Spodoptera frugiperda (Lepidoptera: Noctuidae). INSECTS 2021; 12:insects12100902. [PMID: 34680671 PMCID: PMC8538597 DOI: 10.3390/insects12100902] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/20/2022]
Abstract
Simple Summary The fall armyworm Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae) is an extremely important omnivorous agricultural pest, it poses a severe threat to food security and agricultural production. Quantitative real-time PCR (qRT-PCR) is an important molecular technology widely used for expression profile analyses of various target genes. It is essential to use reference genes as the benchmark to eliminate various errors and normalize the qRT-PCR analysis. In our study, 10 reference genes were evaluated under six experimental conditions, including developmental stages, tissues, mating status, hormones, diets, and temperatures. Finally, the expression profile of the target gene SfrOBP1 in various tissues of S. frugiperda was evaluated to verify the accuracy of the results. This study will provide a preliminary evaluation of reference genes of S. frugiperda, which can be beneficial to the further research of functional gene expression. Abstract As an accurate and convenient technique, the qRT-PCR is always used in the quantitative expression analysis of functional genes. Normalization of the data relies on stable reference genes. The fall armyworm Spodoptera frugiperda (J. E. Smith) is an important invasive and migratory pest that seriously threatens corn production around the world. In this paper, we selected 10 candidate reference genes (18S, AK, RPL10, RPS24, 28S, SOD, ATP, GAPDH, ACT, and a-TUB) and determined their expression levels under different conditions (different developmental stages, various tissues, mating status, hormones, diets, and temperatures). Subsequently, the stability of reference genes was evaluated by four algorithms (Delta Ct method, geNorm, NormFinder, BestKeeper). The optimal combination of reference genes for each treatment was obtained by geNorm. Finally, the comprehensive ranks were determined by the online tool RefFinder. Results showed that the most stable reference genes were SOD, RPL10, and RPS24 for developmental stages, α-TUB, RPL10, and ATP for different tissues, AK, RPL10, and 18S for mating status, 18S and AK under hormone treatment, 18S, RPL10, and SOD under diet treatment, RPL10, 18S, and RPS24 under temperature treatment. This study confirmed recent data on a few reference genes and provided an evaluation of a number of additional reference genes of S. frugiperda under various conditions.
Collapse
|
3
|
Livraghi L, Hanly JJ, Van Bellghem SM, Montejo-Kovacevich G, van der Heijden ESM, Loh LS, Ren A, Warren IA, Lewis JJ, Concha C, Hebberecht L, Wright CJ, Walker JM, Foley J, Goldberg ZH, Arenas-Castro H, Salazar C, Perry MW, Papa R, Martin A, McMillan WO, Jiggins CD. Cortex cis-regulatory switches establish scale colour identity and pattern diversity in Heliconius. eLife 2021; 10:e68549. [PMID: 34280087 PMCID: PMC8289415 DOI: 10.7554/elife.68549] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
In Heliconius butterflies, wing colour pattern diversity and scale types are controlled by a few genes of large effect that regulate colour pattern switches between morphs and species across a large mimetic radiation. One of these genes, cortex, has been repeatedly associated with colour pattern evolution in butterflies. Here we carried out CRISPR knockouts in multiple Heliconius species and show that cortex is a major determinant of scale cell identity. Chromatin accessibility profiling and introgression scans identified cis-regulatory regions associated with discrete phenotypic switches. CRISPR perturbation of these regions in black hindwing genotypes recreated a yellow bar, revealing their spatially limited activity. In the H. melpomene/timareta lineage, the candidate CRE from yellow-barred phenotype morphs is interrupted by a transposable element, suggesting that cis-regulatory structural variation underlies these mimetic adaptations. Our work shows that cortex functionally controls scale colour fate and that its cis-regulatory regions control a phenotypic switch in a modular and pattern-specific fashion.
Collapse
Affiliation(s)
- Luca Livraghi
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Joseph J Hanly
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Steven M Van Bellghem
- Department of Biology, Centre for Applied Tropical Ecology and Conservation, University of Puerto RicoRio PiedrasPuerto Rico
| | | | - Eva SM van der Heijden
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Ling Sheng Loh
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Anna Ren
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | - Ian A Warren
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell UniversityIthacaUnited States
| | | | - Laura Hebberecht
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| | - Charlotte J Wright
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | - Jonah M Walker
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
| | | | - Zachary H Goldberg
- Cell & Developmental Biology, Division of Biological Sciences, UC San DiegoLa JollaUnited States
| | | | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences, Universidad del RosarioBogotáColombia
| | - Michael W Perry
- Cell & Developmental Biology, Division of Biological Sciences, UC San DiegoLa JollaUnited States
| | - Riccardo Papa
- Department of Biology, Centre for Applied Tropical Ecology and Conservation, University of Puerto RicoRio PiedrasPuerto Rico
| | - Arnaud Martin
- The George Washington University Department of Biological Sciences, Science and Engineering HallWashingtonUnited States
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Downing St.CambridgeUnited Kingdom
- Smithsonian Tropical Research InstituteGamboaPanama
| |
Collapse
|
4
|
Wang Z, Meng Q, Zhu X, Sun S, Liu A, Gao S, Gou Y. Identification and Evaluation of Reference Genes for Normalization of Gene Expression in Developmental Stages, Sexes, and Tissues of Diaphania caesalis (Lepidoptera, Pyralidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:5700579. [PMID: 31925425 PMCID: PMC6954454 DOI: 10.1093/jisesa/iez130] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Indexed: 05/04/2023]
Abstract
Diaphania caesalis (Walker) is an important boring insect mainly distributed in subtropical and tropical areas and attacked tropical woody grain crops, such as starchy plants of Artocarpus. Quantitative real-time polymerase chain reaction (qRT-PCR) is a powerful approach for investigating target genes expression profiles at the transcriptional level. However, the identification and selection of internal reference genes, which is often overlooked, is the most vital step before the analysis of target gene expression by qRT-PCR. So far, the reliable internal reference genes under a certain condition of D. caesalis have not been investigated. Therefore, this study evaluated the expression stability of eight candidate reference genes including ACT, β-TUB, GAPDH, G6PDH, RPS3a, RPL13a, EF1α, and EIF4A in different developmental stages, tissues and sexes using geNorm, NormFinder and BestKeeper algorithms. To verify the stability of the recommended internal reference genes, the expression levels of DcaeOBP5 were analyzed under different treatment conditions. The results indicated that ACT, RPL13a, β-TUB, RPS3a, and EF1α were identified as the most stable reference genes for further studies on target gene expression involving different developmental stages of D. caesalis. And ACT and EIF4A were recommended as stable reference genes for different tissues. Furthermore, ACT, EF1α, and RPS3a were ranked as the best reference genes in different sexes based on three algorithms. Our research represents the critical first step to normalize qRT-PCR data and ensure the accuracy of expression of target genes involved in phylogenetic and physiological mechanism at the transcriptional level in D. caesalia.
Collapse
Affiliation(s)
- Zheng Wang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Qianqian Meng
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Corresponding author, e-mail:
| | - Xi Zhu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shiwei Sun
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Aiqin Liu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Shengfeng Gao
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Yafeng Gou
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| |
Collapse
|
5
|
Wang Z, Meng Q, Zhu X, Sun S, Gao S, Gou Y, Liu A. Evaluation and Validation of Reference Genes for Quantitative Real-Time PCR in Helopeltis theivora Waterhouse (Hemiptera: Miridae). Sci Rep 2019; 9:13291. [PMID: 31527603 PMCID: PMC6746731 DOI: 10.1038/s41598-019-49479-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/23/2019] [Indexed: 02/06/2023] Open
Abstract
Helopeltis theivora Waterhouse is a predominant sucking pest in many tropic economic crops, such as tea, cocoa and coffee. Quantitative real-time PCR (qRT-PCR) is one of the most powerful tools to analyze the gene expression level and investigate the mechanism of insect physiology at transcriptional level. Gene expression studies utilizing qRT-PCR have been applied to numerous insects so far. However, no universal reference genes could be used for H. theivora. To obtain accurate and reliable normalized data in H. theivora, twelve candidate reference genes were examined under different tissues, developmental stages and sexes by using geNorm, NormFinder, BestKeeper, Delta Ct and RefFinder algorithms, respectively. The results revealed that the ideal reference genes differed across the treatments, and the consensus rankings generated from stability values provided by these programs suggested a combination of two genes for normalization. To be specific, RPS3A and Actin were the best suitable reference genes for tissues, RPL13A and GAPDH were suitable for developmental stages, EF1α and RPL13A were suitable for sexes, and RPL13A and RPS3A were suitable for all samples. This study represents the first systematic analysis of reference genes for qRT-PCR experiments in H. theivora, and the results can provide a credible normalization for qRT-PCR data, facilitating transcript profiling studies of functional genes in this insect.
Collapse
Affiliation(s)
- Zheng Wang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
| | - Qianqian Meng
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
| | - Xi Zhu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China.,Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Shiwei Sun
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
| | - Shengfeng Gao
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
| | - Yafeng Gou
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China
| | - Aiqin Liu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, 571533, China. .,Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
| |
Collapse
|
6
|
Zhao Z, Wang L, Yue D, Ye B, Li P, Zhang B, Fan Q. Evaluation of Reference Genes for Normalization of RT-qPCR Gene Expression Data for Trichoplusia ni Cells During Antheraea pernyi (Lepidoptera: Saturniidae) Multicapsid Nucleopolyhedrovirus (AnpeNPV) Infection. JOURNAL OF INSECT SCIENCE (ONLINE) 2019; 19:5280859. [PMID: 30624703 PMCID: PMC6324657 DOI: 10.1093/jisesa/iey133] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Indexed: 06/01/2023]
Abstract
Baculovirus infection impacts global gene expression in the host cell, including the expression of housekeeping genes. Evaluation of candidate reference genes during a viral infection will inform the selection of appropriate reference gene(s) for the normalization of expression data generated by Reverse Transcription Quantitative Real-timePolymerase Chain Reaction (RT-qPCR). Antheraea pernyi multicapsid nucleopolyhedrovirus (AnpeNPV) is able to infect the High Five cells (Tn-Hi5). In the present study, 10 candidate reference genes were evaluated in AnpeNPV-infected Tn-Hi5 cells. Gene expression data were analyzed using geNorm, NormFinder, BestKeeper, and RefFinder. The candidate genes were further validated as reliable reference genes for RT-qPCR by analyzing the expression of three target genes. The results of data analysis using four statistical methods showed that RPS18 was the least stable among the candidate reference genes tested. 18S rRNA and 28S rRNA were not suitable as reference genes for RT-qPCR analysis in AnpeNPV-infected Tn-Hi5 cells. Comprehensive ranking of the 10 candidate reference genes by RefFinder analysis indicated that Ann B, c45128_g1, and ACT were the top three genes. Normalization of the expression of three target genes using the candidate reference genes indicated the same expression pattern when Ann B and c45128_g1 were used as reference genes, with slight differences in the relative expression at each infection time point. Overall, Ann B and c45128_g1 were recommended to be more suitable than the most commonly used reference genes, such as ACT, GAPDH, and TUB, for RT-qPCR data normalization in AnpeNPV-infected Tn-Hi5 cells up to 48 hpi.
Collapse
Affiliation(s)
- Zhenjun Zhao
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, P. R. China
| | - Linmei Wang
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, P. R. China
| | - Dongmei Yue
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, P. R. China
| | - Bo Ye
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, P. R. China
| | - Peipei Li
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, P. R. China
| | - Bo Zhang
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, P. R. China
| | - Qi Fan
- Dalian Institute of Biotechnology, Liaoning Academy of Agricultural Sciences, Dalian, P. R. China
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Selection and validation of reference genes for reverse transcription quantitative real-time PCR (RT-qPCR) in silkworm infected with Bombyx mori bidensovirus. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0086-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
9
|
Wang B, Du H, Yao Z, Ren C, Ma L, Wang J, Zhang H, Ma H. Validation of reference genes for accurate normalization of gene expression with quantitative real-time PCR in Haloxylon ammodendron under different abiotic stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:455-463. [PMID: 29692553 PMCID: PMC5911265 DOI: 10.1007/s12298-018-0520-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/20/2017] [Accepted: 02/08/2018] [Indexed: 05/27/2023]
Abstract
Haloxylon ammodendron plays an important role in maintaining the structure and function of the entire ecosystem where it grows. No suitable reference genes have been reported in H. ammodendron plants to date. In this study, a total of 8 reference genes (18S, ACT1, ACT7, UBC18, TUA5, GAPDH, EF-1α and UBQ10) were selected from the available trancriptome database, and the expression stability of these 8 candidate genes was validated under different abiotic stress with three different statistical algorithms (geNorm, NormFinder and BestKeeper). The results produced from different models were in agreement with each other essentially: 18S and TUA5 were the most stable genes under drought stress, 18S, the most stable gene under heat stress and mechanical damage, ACT7 and UBC18, stable under salt stress while TUA5 and GAPDH expressed constantly under mechanical damage, and ACT1 expressed steadily under cold conditions. Expression profiles of several stress response genes, including FT-5, FT-9, DREB2A and DREB2C, were further confirmed with various candidate reference genes. None of the candidate genes showed a constant expression among all tested samples. Hence, it's essential to use more than one reference gene in order to guarantee the accuracy of quantitative real-time PCR. The results of this study will contribute to the accuracy and reliability in transcripts quantification, which is of significance to transcription-based studies and applications in this important shrub H. ammodendron.
Collapse
Affiliation(s)
- Bo Wang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Huihui Du
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Zhengpei Yao
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Cai Ren
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Li Ma
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Jiao Wang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Hua Zhang
- College of Agriculture, Xinjiang Agricultural University, Urumqi, 830052 China
- Institute of Desert in the Arid Areas, College of Grassland and Environment Sciences, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Hao Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
10
|
Shu B, Zhang J, Cui G, Sun R, Sethuraman V, Yi X, Zhong G. Evaluation of Reference Genes for Real-Time Quantitative PCR Analysis in Larvae of Spodoptera litura Exposed to Azadirachtin Stress Conditions. Front Physiol 2018; 9:372. [PMID: 29695976 PMCID: PMC5904281 DOI: 10.3389/fphys.2018.00372] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/27/2018] [Indexed: 12/03/2022] Open
Abstract
Azadirachtin is an efficient and broad-spectrum botanical insecticide against more than 150 kinds of agricultural pests with the effects of mortality, antifeedant and growth regulation. Real-time quantitative polymerase chain reaction (RT-qPCR) could be one of the powerful tools to analyze the gene expression level and investigate the mechanism of azadirachtin at transcriptional level, however, the ideal reference genes are needed to normalize the expression profiling of target genes. In this present study, the fragments of eight candidate reference genes were cloned and identified from the pest Spodoptera litura. In addition, the expression stability of these genes in different samples from larvae of control and azadirachtin treatments were evaluated by the computational methods of NormFinder, BestKeeper, Delta CT, geNorm, and RefFinder. According to our results, two of the reference genes should be the optimal number for RT-qPCR analysis. Furthermore, the best reference genes for different samples were showed as followed: EF-1α and EF2 for cuticle, β-Tubulin and RPL7A for fat body, EF2 and Actin for midgut, EF2 and RPL13A for larva and RPL13A and RPL7A for all the samples. Our results established a reliable normalization for RT-qPCR experiments in S. litura and ensure the data more accurate for the mechanism analysis of azadirachtin.
Collapse
Affiliation(s)
- Benshui Shu
- Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Jingjing Zhang
- Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Gaofeng Cui
- Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Ranran Sun
- Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Veeran Sethuraman
- Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Xin Yi
- Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| | - Guohua Zhong
- Key Laboratory of Crop Integrated Pest Management in South China, Ministry of Agriculture, Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, South China Agricultural University, Guangzhou, China
| |
Collapse
|
11
|
Bradley D, Xu P, Mohorianu II, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. Evolution of flower color pattern through selection on regulatory small RNAs. Science 2017; 358:925-928. [DOI: 10.1126/science.aao3526] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/06/2017] [Indexed: 12/19/2022]
Abstract
Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.
Collapse
Affiliation(s)
- Desmond Bradley
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Irina-Ioana Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Annabel Whibley
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - David Field
- Department of Botany and Biodiversity Research, University of Vienna, Faculty of Life Sciences, Rennweg 14, A-1030 Vienna, Austria
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Hugo Tavares
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Matthew Couchman
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Lucy Copsey
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Rosemary Carpenter
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Miaomiao Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qun Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
| | - Yongbiao Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100190, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Enrico Coen
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| |
Collapse
|