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Shen CH, Tang M, Li XF, Zhu L, Li W, Deng P, Zhai Q, Wu G, Yan XH. Evaluation of reference genes for quantitative expression analysis in Mylabris sibirica (Coleoptera, Meloidae). Front Physiol 2024; 15:1345836. [PMID: 38651047 PMCID: PMC11033477 DOI: 10.3389/fphys.2024.1345836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Mylabris sibirica is a hypermetamorphic insect whose adults feed on oilseed rape. However, due to a shortage of effective and appropriate endogenous references, studies on molecular functional genes in Mylabris sibirica, have been tremendously limited. In this study, ten internal reference genes (ACT, ARF1, AK, EF1α, GAPDH, α-TUB, RPL6, RPL13, RPS3 and RPS18) were tested and assessed under four selected treatments including adult ages, adult tissues, temperatures, and sex by RT-qPCR based on five methods (Ct value, geNorm, NormFinder, BestKeeper and RefFinder). Our findings showed that RPL6 and RPL13 were the most optimal internal reference gene combination for gene expression during various adult ages and under diverse temperatures; The combination of RPL6 and RPS18 was recommended to test gene transcription levels under different adult tissues. AK and RPL6 were the best reference genes in male and female adults. RPL6 and RPL13 were the most appropriate reference gene pair to estimate gene expression levels under four different tested backgrounds. The relative transcript levels of a uridine diphosphate (UDP)-N-acetylglucosamine-pyrophosphorylase (MsUAP), varied greatly according to normalization with the two most- and least-suited reference genes. This study will lay the basis for further molecular physiology and biochemistry studies in M. sibirica, such as development, reproduction, sex differentiation, cold and heat resistance.
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Affiliation(s)
- Chen-Hui Shen
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Min Tang
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiao-Fei Li
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Li Zhu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wei Li
- Northern Propagation Experiment Station, Center for Science and Technology Dissemination and Industrial Development, Oil Crops Research Institute of Chinese Academy of Agricultural Science, Wuhan, China
| | - Pan Deng
- Institute of Leisure Agriculture, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qing Zhai
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Gang Wu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiao-Hong Yan
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Science/Supervision and Test Center (Wuhan) for Plant Ecological Environment Safety, Ministry of Agriculture and Rural Affairs, Wuhan, China
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Huo Y, Li X, Sun C, Pan Z, Li Q, Du X. From stability to reliability: Unveiling the un-biased reference genes in porcine ovarian granulosa cells under different conditions. Gene 2024; 897:148089. [PMID: 38123003 DOI: 10.1016/j.gene.2023.148089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/02/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Selection of optimal reference genes (RGs) is fundamental for functional genomics studies and gene expression analysis, which are two main approaches to identify functional genes and their expression patterns. However, no systematic study has identified the suitable RGs in porcine ovarian granulosa cells (GCs) which are essential for follicle fate and sow fertility. In this study, the expression profiles of 12 widely-used RGs (GAPDH, RPLP0, ACTB, TUBA1B, EIF3K, PPIA, ATP5F1, B2M, HPRT1, UBC, RPS3, and EEF1A1) in porcine GCs during follicular development and under different abiotic stresses were systematically investigated. Expression stability of the candidate RGs were comprehensively accessed by five statistical algorithms including ΔCt, NormFinder, BestKeeper, geNorm, and RefFinder, indicating that RPS3 and PPIA are the optimal RGs during follicular development, EEF1A1 and RPLP0 are most stable under oxidative stress and inflammation, while ATP5F1, B2M, and RPS3 have higher stability under starvation and heat stress. Notably, the most commonly used RGs (ACTB, GAPDH, and TUBA1B) exhibited low stability in GCs. Reliability of stable RGs was verified by RT-qPCR and showed that selection of the stable RGs significantly improved the detection accuracy of qPCR, which confirms once again that the stability of RGs should not be taken for granted. Our findings identified optimal RG sets in porcine GCs under different conditions, which is helpful in future studies to accurately identify the key regulators and their expression patterns during follicular development in sows.
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Affiliation(s)
- Yangan Huo
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaoxue Li
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chen Sun
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zengxiang Pan
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qifa Li
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xing Du
- Laboratory of Statistical Genetics and Epigenetics, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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He L, Wang JY, Su QJ, Chen ZH, Xie F. Selection and validation of reference genes for RT-qPCR in ophiocordyceps sinensis under different experimental conditions. PLoS One 2024; 19:e0287882. [PMID: 38319940 PMCID: PMC10846742 DOI: 10.1371/journal.pone.0287882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/14/2023] [Indexed: 02/08/2024] Open
Abstract
The Chinese caterpillar mushroom, Ophiocordyceps sinensis (O. sinensis), is a rarely medicinal fungus in traditional chinese herbal medicine due to its unique medicinal values, and the expression stability of reference genes is essential to normalize its gene expression analysis. In this study, BestKeeper, NormFinder and geNorm, three authoritative statistical arithmetics, were applied to evaluate the expression stability of sixteen candidate reference genes (CRGs) in O. sinensis under different stress [low temperature (4°C), light treatment (300 lx), NaCl (3.8%)] and different development stages (mycelia, primordia and fruit bodies) and formation of morphologic mycelium (aeriasubstrate, hyphae knot mycelium). The paired variation values indicated that two genes could be enough to accurate standardization exposed to different conditions of O.sinensis. Among these sixteen CRGs, 18S ribosomal RNA (18S rRNA) and beta-Tubulin (β-TUB) showed the topmost expression stability in O.sinensis exposed to all conditions, while glutathione hydrolase proenzym (GGT) and Phosphoglucose isomerase (PGI) showed the least expression stability. The optimal reference gene in different conditions was various. β-TUB and Ubiquitin (UBQ) were identified as the two most stable genes in different primordia developmental stage, while phosphoglucomutase (PGM) with elongation factor 1-alpha (EF1-α) and 18S rRNA with UBQ were the most stably expressed for differentially morphologic mycelium stages and different stresses, respectively. These results will contribute to more accurate evaluation of the gene relative expression levels in O.sinensis under different conditions using the optimal reference gene in real-time quantitative PCR (RT-qPCR) analysis.
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Affiliation(s)
- Li He
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Jin Yi Wang
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Qiang Jun Su
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Zhao He Chen
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
| | - Fang Xie
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, GanSu, P. R. China
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Sellamuthu G, Naseer A, Hradecký J, Chakraborty A, Synek J, Modlinger R, Roy A. Gene expression plasticity facilitates different host feeding in Ips sexdentatus (Coleoptera: Curculionidae: Scolytinae). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024; 165:104061. [PMID: 38151136 DOI: 10.1016/j.ibmb.2023.104061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 12/29/2023]
Abstract
Host shift is ecologically advantageous and a crucial driver for herbivore insect speciation. Insects on the non-native host obtain enemy-free space and confront reduced competition, but they must adapt to survive. Such signatures of adaptations can often be detected at the gene expression level. It is astonishing how bark beetles cope with distinct chemical environments while feeding on various conifers. Hence, we aim to disentangle the six-toothed bark beetle (Ips sexdentatus) response against two different conifer defences upon host shift (Scots pine to Norway spruce). We conducted bioassay and metabolomic analysis followed by RNA-seq experiments to comprehend the beetle's ability to surpass two different terpene-based conifer defence systems. Beetle growth rate and fecundity were increased when reared exclusively on spruce logs (alternative host) compared to pine logs (native host). Comparative gene expression analysis identified differentially expressed genes (DEGs) related to digestion, detoxification, transporter activity, growth, signalling, and stress response in the spruce-feeding beetle gut. Transporter genes were highly abundant during spruce feeding, suggesting they could play a role in pumping a wide variety of endogenous and xenobiotic compounds or allelochemicals out. Trehalose transporter (TRET) is also up-regulated in the spruce-fed beetle gut to maintain homeostasis and stress tolerance. RT-qPCR and enzymatic assays further corroborated some of our findings. Taken together, the transcriptional plasticity of key physiological genes plays a crucial role after the host shift and provides vital clues for the adaptive potential of bark beetles on different conifer hosts.
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Affiliation(s)
- Gothandapani Sellamuthu
- Czech University of Life Sciences Prague, Forest Molecular Entomology Lab, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Aisha Naseer
- Czech University of Life Sciences Prague, Forest Molecular Entomology Lab, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Jaromír Hradecký
- Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Amrita Chakraborty
- Czech University of Life Sciences Prague, Forest Molecular Entomology Lab, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Forest Microbiome Team, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Jiří Synek
- Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Roman Modlinger
- Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic
| | - Amit Roy
- Czech University of Life Sciences Prague, Forest Molecular Entomology Lab, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Excellent Team for Mitigation (ETM), Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic; Czech University of Life Sciences Prague, Forest Microbiome Team, Faculty of Forestry & Wood Sciences, Kamýcká 129, Prague, 16500, Czech Republic.
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Zhao X, Guo J, Lu Y, Sun T, Tian J, Huang J, Xu H, Wang Z, Lu Z. Reference Genes for Expression Analysis Using RT-qPCR in Cnaphalocrocis medinalis (Lepidoptera: Pyralidae). INSECTS 2022; 13:insects13111046. [PMID: 36421949 PMCID: PMC9697642 DOI: 10.3390/insects13111046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 05/31/2023]
Abstract
Cnaphalocrocis medinalis is a destructive migratory rice pest. Although many studies have investigated its behavioral and physiological responses to environmental changes and migration-inducing factors, little is known about its molecular mechanisms. This study was conducted to select suitable RT-qPCR reference genes to facilitate future gene expression studies. Here, thirteen candidate housekeeping genes (EF1α, AK, EF1β, GAPDH, PGK, RPL13, RPL18, RPS3, 18S rRNA, TBP1, TBP2, ACT, and UCCR) were selected to evaluate their stabilities under different conditions using the ∆CT method; the geNorm, NormFinder, BestKeeper algorithms; and the online tool RefFinder. The results showed that the most stable reference genes were EF1β, PGK, and RPL18, related to developmental stages; RPS3 and RPL18 in larval tissues; EF1β and PGK in larvae feeding on different rice varieties; EF1α, EF1β, and PGK in larvae temperature treatments; PGK and RPL13, related to different adult ages; PGK, EF1α, and ACT, related to adult nutritional conditions; RPL18 and PGK, related to adult mating status; and, RPS3 and PGK, related to different adult take-off characteristics. Our results reveal reference genes that apply to various experimental conditions and will greatly improve the reliability of RT-qPCR analysis for the further study of gene function in this pest.
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Affiliation(s)
- Xiaoyu Zhao
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiawen Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yanhui Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Tianyi Sun
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Junce Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianlei Huang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou 075000, China
| | - Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhengliang Wang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongxian Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Zhao ZQ, Zheng KY, Ou Q, Xu PZ, Qin S, Sun X, Li MW, Wu YC, Wang XY. Identification of optimal reference genes in Bombyx mori (Lepidoptera) for normalization of stress-responsive genes after challenge with pesticides. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21896. [PMID: 35355317 DOI: 10.1002/arch.21896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Pesticides are frequently used to control pests in agriculture due to their ease of use and effectiveness, but their use causes serious economic losses to sericulture when their production overlaps with agriculture. However, no suitable internal reference genes (RGs) have been reported in the study of silkworms in response to pesticides. In this study, a standard curve was established to detect the expression levels of seven RGs in different tissues of different silkworm strains after feeding with pesticides using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), including BmGAPDH, BmActin3, BmTBP, BmRPL3, Bm28sRNA, Bmα-tubulin, and BmUBC, and the stability of them was evaluated by using NormFinder, geNorm, Delta CT, BestKeeper, and RefFinder. The results showed that BmGAPDH and Bmα-tubulin were relatively stable in the midgut after feeding with fenvalerate, BmGAPDH and Bmactin3 were relatively stable in the fat body, and Bmα-tubulin and Bmactin3 were relatively stable in the hemolymph, indicating that Bmactin3 was the most suitable RG when evaluating fenvalerate, followed by BmGAPDH and Bmα-tubulin. Besides, BmGAPDH and Bmactin3 were relatively stable in the midgut after treatment with DDVP, BmGAPDH and Bmα-tubulin were relatively stable in the fat body, and BmGAPDH and Bmα-tubulin were relatively stable in the hemolymph, indicating that Bmα-tubulin was the most stable RG when evaluating DDVP, followed by BmGAPDH and Bmactin3. Of note, BmGAPDH was shared by the two pesticides. The results will be valuable for RG selection in studying the pesticide response mechanism of silkworms and other lepidopteran insects.
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Affiliation(s)
- Zi-Qin Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Kai-Yi Zheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Qi Ou
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Ping-Zhen Xu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Mu-Wang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Yang-Chun Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Xue-Yang Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
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Li J, Fu N, Ren L, Luo Y. Identification and Validation of Reference Genes for Gene Expression Analysis in Monochamus saltuarius Under Bursaphelenchus xylophilus Treatment. Front Physiol 2022; 13:882792. [PMID: 35547586 PMCID: PMC9082747 DOI: 10.3389/fphys.2022.882792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
A special mutual relationship exists between the pine wood nematode (PWN) Bursaphelenchus xylophilus and its vector beetles of genus Monochamus, which enables PWN to spread, at the same time provides longhorned beetles with more weak hosts. PWN are attracted to the pupal chambers and then carried inside the trachea of beetle adults, which is a necessary part to complete the B. xylophilus infection cycle. The growth and immune responses of the vector beetle will affect this carrying process, however, they were rarely studied in Monochamus saltuarius. Real-time quantitative polymerase chain reaction (RT-qPCR), one of the most common methods for quantitative gene expression analysis, was performed to explore the key genes and pathways involved in the growth, development and immune responses of M. saltuarius at different developmental stages associated with infection of PWN and PWN treatment conditions. To enhance the accuracy of RT-qPCR data, the expression of target genes needs to be normalized with reference genes, which are stably expressed under varied experimental conditions. In our study, the stability of 14 candidate reference genes in M. saltuarius samples at different developmental stages associated with infection of PWN or PWN treatment conditions was evaluated using delta Ct, geNorm, NormFinder, BestKeeper and RefFinder algorithms. Moreover, KLF gene was used to validate the stability of the selected reference genes. Under experimental conditions of this study, RPL7 and TER were suitable reference genes at different developmental stages associated with infection of PWN. RPL7 and RPS5 were considered the most stable reference genes in the pupae treated with PWN. RPS5 and SNX6 could be used as reference genes in the adults treated with PWN. RPL7, EF1-γ, and RPS5 could be used as stable reference genes in all the samples. This work is the first to evaluate reference genes in M. saltuarius, laying a foundation for further gene expression experimental procedures and understanding the phoretic relationship between M. saltuarius and B. xylophilus.
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Affiliation(s)
- Jiaxing Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ningning Fu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
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Sellamuthu G, Bílý J, Joga MR, Synek J, Roy A. Identifying optimal reference genes for gene expression studies in Eurasian spruce bark beetle, Ips typographus (Coleoptera: Curculionidae: Scolytinae). Sci Rep 2022; 12:4671. [PMID: 35304502 PMCID: PMC8933438 DOI: 10.1038/s41598-022-08434-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/07/2022] [Indexed: 11/09/2022] Open
Abstract
Eurasian spruce bark beetle (Ips typographus [L.]) causes substantial damage to spruce forests worldwide. Undoubtedly, more aggressive measures are necessary to restrict the enduring loss. Finishing genome sequencing is a landmark achievement for deploying molecular techniques (i.e., RNA interference) to manage this pest. Gene expression studies assist in understanding insect physiology and deployment of molecular approaches for pest management. RT-qPCR is a valuable technique for such studies. However, accuracy and reliability depend on suitable reference genes. With the genome sequence available and the growing requirement of molecular tools for aggressive forest pest management, it is crucial to find suitable reference genes in Ips typographus under different experimental conditions. Hence, we evaluated the stability of twelve candidate reference genes under diverse experimental conditions such as biotic (developmental, sex and tissues) and abiotic factors (i.e., temperature and juvenile hormone treatment) to identify the reference genes. Our results revealed that ribosomal protein 3a (RPS3-a) was the best reference gene across all the experimental conditions, with minor exceptions. However, the stability of the reference gene can differ based on experiments. Nevertheless, present study provides a comprehensive list of reference genes under different experimental conditions for Ips typographus and contributes to "future genomic and functional genomic research".
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Affiliation(s)
- Gothandapani Sellamuthu
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jan Bílý
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Mallikarjuna Reddy Joga
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jiří Synek
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic. .,EVA 4.0 Unit, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czech Republic.
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