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Baril T, Pym A, Bass C, Hayward A. Transposon accumulation at xenobiotic gene family loci in aphids. Genome Res 2023; 33:1718-1733. [PMID: 37852781 PMCID: PMC10691553 DOI: 10.1101/gr.277820.123] [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: 02/20/2023] [Accepted: 08/29/2023] [Indexed: 10/20/2023]
Abstract
The evolution of resistance is a major challenge for the sustainable control of pests and pathogens. Thus, a deeper understanding of the evolutionary and genomic mechanisms underpinning resistance evolution is required to safeguard health and food production. Several studies have implicated transposable elements (TEs) in xenobiotic-resistance evolution in insects. However, analyses are generally restricted to one insect species and/or one or a few xenobiotic gene families (XGFs). We examine evidence for TE accumulation at XGFs by performing a comparative genomic analysis across 20 aphid genomes, considering major subsets of XGFs involved in metabolic resistance to insecticides: cytochrome P450s, glutathione S-transferases, esterases, UDP-glucuronosyltransferases, and ABC transporters. We find that TEs are significantly enriched at XGFs compared with other genes. XGFs show similar levels of TE enrichment to those of housekeeping genes. But unlike housekeeping genes, XGFs are not constitutively expressed in germline cells, supporting the selective enrichment of TEs at XGFs rather than enrichment owing to chromatin availability. Hotspots of extreme TE enrichment occur around certain XGFs. We find, in aphids of agricultural importance, particular enrichment of TEs around cytochrome P450 genes with known functions in the detoxification of synthetic insecticides. Our results provide evidence supporting a general role for TEs as a source of genomic variation at host XGFs and highlight the existence of considerable variability in TE content across XGFs and host species. These findings show the need for detailed functional verification analyses to clarify the significance of individual TE insertions and elucidate underlying mechanisms at TE-XGF hotspots.
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Affiliation(s)
- Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Adam Pym
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
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2
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Li YJ, Ma CS, Yan Y, Renault D, Colinet H. The interspecific variations in molecular responses to various doses of heat and cold stress: the case of cereal aphids. JOURNAL OF INSECT PHYSIOLOGY 2023; 147:104520. [PMID: 37148996 DOI: 10.1016/j.jinsphys.2023.104520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/17/2023] [Accepted: 05/02/2023] [Indexed: 05/08/2023]
Abstract
Insects are currently subjected to unprecedented thermal stress due to recent increases in the frequency and amplitude of temperature extremes. Understanding molecular responses to thermal stress is critically important to appreciate how species react to thermal stress. Three co-occurring cosmopolitan species are found within the guild of cereal aphids: Sitobion avenae, Ropalosiphum padi and Metopolophium dirhodum. Earlier reports have shown that increasing frequency of temperature extremes causes a shift in dominant species within guilds of cereal aphids by differently altering the population's growth. We hypothesize that a differential molecular response to stress among species may partially explain these changes. Heat shock proteins (HSPs) are molecular chaperones well known to play an important role in protecting against the adverse effects of thermal stress. However, few studies on molecular chaperones have been conducted in cereal aphids. In this study, we compared the heat and cold tolerance between three aphid species by measuring the median lethal time (Lt50) and examined the expression profiles of seven hsp genes after exposures to comparable thermal injury levels and also after same exposure durations. Results showed that R. padi survived comparatively better at high temperatures than the two other species but was more cold-sensitive. Hsp genes were induced more strongly by heat than cold stress. Hsp70A was the most strongly up-regulated gene in response to both heat and cold stress. R. padi had more heat inducible genes and significantly higher mRNA levels of hsp70A, hsp10, hsp60 and hsp90 than the other two species. Hsps ceased to be expressed at 37°C in M. dirhodum and S. avenae while expression was maintained in R. padi. In contrast, M. dirhodum was more cold tolerant and had more cold inducible genes than the others. These results confirm species-specific differences in molecular stress responses and suggest that differences in induced expression of hsps may be related to species' thermal tolerance, thus causing the changes in the relative abundance.
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Affiliation(s)
- Yuan-Jie Li
- Université de Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)] - UMR 6553, 35000 Rennes, France; School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Climate Change Biology Research Group, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Chun-Sen Ma
- School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China; Climate Change Biology Research Group, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - Yi Yan
- Climate Change Biology Research Group, State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No 2, Yuanmingyuan West Road, Haidian District, Beijing 100193, China
| | - David Renault
- Université de Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)] - UMR 6553, 35000 Rennes, France
| | - Hervé Colinet
- Université de Rennes, CNRS, ECOBIO [(Ecosystèmes, biodiversité, évolution)] - UMR 6553, 35000 Rennes, France.
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Gandrabur E, Terentev A, Fedotov A, Emelyanov D, Vereshchagina A. The Peculiarities of Metopolophium dirhodum (Walk.) Population Formation Depending on Its Clonal and Morphotypic Organization during the Summer Period. INSECTS 2023; 14:271. [PMID: 36975956 PMCID: PMC10051124 DOI: 10.3390/insects14030271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
The ecological plasticity of aphid populations is determined by their clonal and morphotypic diversity. Clones will be successful when the development of their component morphotypes is optimized. The purpose of this work was to reveal the peculiarities of clonal composition and the developmental characteristics of different summer morphotypes for the rose-grass aphid, Metopolophium dirhodum (Walk.), which is an important host-alternating cereal pest and a useful model species. During the experiments, aphids were kept under ambient conditions on wheat seedlings at natural temperatures and humidity levels. An analysis of the reproduction of summer morphotypes and the resulting composition of offspring found that variation among the clones and morphotypes, as well as generational effects and an influence of sexual reproduction (and interactions between all factors) influenced the population structure of M. dirhodum. The reproduction of emigrants was less among the clones than that of the apterous or alate exules. The number of offspring produced by apterous exules differed throughout the growing season (generational effects) and between years, with different clones exhibiting different responses. There were dispersing aphids only among the offspring of apterous exules. These results can contribute to future advances in the forecasting and monitoring of aphid populations.
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Affiliation(s)
- Elena Gandrabur
- All-Russian Institute of Plant Protection, 196608 Saint Petersburg, Russia; (A.T.)
| | - Anton Terentev
- All-Russian Institute of Plant Protection, 196608 Saint Petersburg, Russia; (A.T.)
- Advanced Digital Technologies, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia;
| | - Alexander Fedotov
- Advanced Digital Technologies, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia;
| | - Dmitriy Emelyanov
- All-Russian Institute of Plant Protection, 196608 Saint Petersburg, Russia; (A.T.)
- Advanced Digital Technologies, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia;
| | - Alla Vereshchagina
- All-Russian Institute of Plant Protection, 196608 Saint Petersburg, Russia; (A.T.)
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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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Kong D, Shi D, Wang C, Zhai R, Lyu L, He Y, Wang D. Identification and Validation of Reference Genes for Expression Analysis Using qRT-PCR in Cimex hemipterus (Hemiptera: Cimicidae). INSECTS 2022; 13:784. [PMID: 36135485 PMCID: PMC9502763 DOI: 10.3390/insects13090784] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The tropical bed bug, Cimex hemipterus (F.) (Hemiptera: Cimicidae) is an important public-health pest that feeds on the blood of humans and some other animals. To explore the function of the target genes of C. hemipterus, it is essential to select suitable reference genes for the accurate quantification of gene expression. Here, we selected 10 frequently used reference genes in insects and evaluated their stability in C. hemipterus under various biotic (developmental stage, sex, and tissue) and abiotic (gas stimulation and temperature) conditions through RefFinder (which integrates four computational programs: geNorm, NormFinder, BestKeeper, and ∆Ct). Results indicate that the optimal combination of reference genes for each experimental condition was as follows: RPL8 and EF1α for the developmental stage (eggs, early instar nymphs, late instar nymphs, and adults), RPL8 and RPS16 for adult sex, RPL8 and RPL11 for adult tissue (head, thorax, abdomen, and legs), RPL8 and β-tubulin for gas stimulation (air and carbon dioxide), and RPL8 and NADH for temperature (0, 5, 17, 30, and 37 °C). Finally, the expression pattern of the HSP70 and GR21 genes were analyzed, and the results highlight the importance of appropriate reference-gene selection. Our results provide a comprehensive list of optimal reference genes from C. hemipterus for the first time, which will contribute to accurately analyzing the expression of target genes.
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Affiliation(s)
- Delong Kong
- Department of Entomology, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, China
| | - Daxia Shi
- Department of Entomology, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, China
| | - Changlu Wang
- Department of Entomology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ruyue Zhai
- Department of Entomology, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, China
| | - Lingling Lyu
- Ningbo Dayang Technology Co., Ltd., Ningbo 315000, China
| | - Yurong He
- Department of Entomology, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, China
| | - Desen Wang
- Department of Entomology, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou 510642, China
- Engineering Research Center of Biological Control, Ministry of Education, Guangzhou 510642, China
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6
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Su RR, Huang ZY, Qin CW, Zheng XL, Lu W, Wang XY. Evaluation of Reference Genes in Glenea cantor (Fabricius) by Using qRT-PCR. Genes (Basel) 2021; 12:1984. [PMID: 34946935 PMCID: PMC8701190 DOI: 10.3390/genes12121984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 12/04/2022] Open
Abstract
Kapok is the main host of Glenea cantor (Fabricius), which causes serious damage and is difficult to control. In severe cases, it often causes the kapok trees to die continuously, which seriously affects the results of urban landscaping. To provide reference for the functional research on related genes in G. cantor, we screened the stable expression of candidate reference genes at different developmental stages (i.e., eggs, larvae, pupae, and adults), in various adult tissues (i.e., head, thorax, abdomen, feet, antennae, and wings), and sexes (i.e., male pupae, female pupae, male adults, and female adults). In this study, 12 candidate reference genes (i.e., ACTINLIKE, ACTININ, TUB, RPL36, RPL32, RPS20, TBP, GAPDH, 18S rRNA, EF1A1, EF1A2, and UBQ) were evaluated using different adult tissues, developmental stages, and sexes. RefFinder, geNorm, NormFinder, and BestKeeper were used to evaluate and comprehensively analyze the stability of the expression of the candidate reference genes. The results show that RPL32 and EF1A1 were the most suitable reference genes in the different adult tissues, and RPL36 and EF1A1 were best at the different developmental stages. RPL36 and EF1A2 were the best fit for the qRT-PCR reference genes in the different sexes, while RPL36 and EF1A1 were the most appropriate qRT-PCR reference genes in all samples. Results from geNorm showed that the optimal number of reference genes was two. We also surveyed the expression of cellulase at the different developmental stages and in the different adult tissues. Results further verified the reliability of the reference genes, and confirmed the best reference genes under the different experimental conditions. This study provides a useful tool for molecular biological studies on G. cantor.
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Affiliation(s)
| | | | | | | | | | - Xiao-Yun Wang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China; (R.-R.S.); (Z.-Y.H.); (C.-W.Q.); (X.-L.Z.); (W.L.)
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7
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Li M, Li X, Wang C, Li Q, Zhu S, Zhang Y, Li X, Yang F, Zhu X. Selection and Validation of Reference Genes For qRT-PCR Analysis of Rhopalosiphum padi (Hemiptera: Aphididae). Front Physiol 2021; 12:663338. [PMID: 33935809 PMCID: PMC8079785 DOI: 10.3389/fphys.2021.663338] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/22/2021] [Indexed: 11/23/2022] Open
Abstract
Rhopalosiphum padi (L.) (Hemiptera: Aphididae) is an important cosmopolitan pest in cereal crops. Reference genes can significantly affect qRT-PCR results. Therefore, selecting appropriate reference genes is a key prerequisite for qRT-PCR analyses. This study was conducted to identify suitable qRT-PCR reference genes in R. padi. We systematically analyzed the expression profiles of 11 commonly used reference genes. The ΔCt method, the BestKeeper, NormFinder, geNorm algorithms, and the RefFinder online tool were used to evaluate the suitability of these genes under diverse experimental conditions. The data indicated that the most appropriate sets of reference genes were β-actin and GAPDH (for developmental stages), AK and TATA (for populations), RPS18 and RPL13 (for tissues), TATA and GAPDH (for wing dimorphism), EF-1α and RPS6 (for antibiotic treatments), GAPDH and β-actin (for insecticide treatments), GAPDH, TATA, RPS18 (for starvation-induced stress), TATA, RPS6, and AK (for temperatures), and TATA and GAPDH (for all conditions). Our study findings, which revealed the reference genes suitable for various experimental conditions, will facilitate the standardization of qRT-PCR programs, while also improving the accuracy of qRT-PCR analyses, with implications for future research on R. padi gene functions.
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Affiliation(s)
- Mengyi Li
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China.,Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
| | - Xinan Li
- School of Resource and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, China
| | - Chao Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
| | - Qiuchi Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
| | - Saige Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
| | - Yunhui Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
| | - Xiangrui Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
| | - Fengshan Yang
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Xun Zhu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China
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