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Xiao H, Ma C, Peng R, Xie M. Insights into the role of non-coding RNAs in the development of insecticide resistance in insects. Front Genet 2024; 15:1429411. [PMID: 39036703 PMCID: PMC11257933 DOI: 10.3389/fgene.2024.1429411] [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: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 07/23/2024] Open
Abstract
Pest control heavily relies on chemical pesticides has been going on for decades. However, the indiscriminate use of chemical pesticides often results in the development of resistance in pests. Almost all pests have developed some degree of resistance to pesticides. Research showed that the mechanisms of insecticide resistance in insects encompass metabolic resistance, behavioral resistance, penetration resistance and target-site resistance. Research on the these mechanisms has been mainly focused on the cis-regulatory or trans-regulatory for the insecticide resistance-related genes, with less attention paid to non-coding RNAs (ncRNAs), such as microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). There has been increased studies focus on understanding how these ncRNAs are involved in post-transcriptional regulation of insecticide resistance-related genes. Besides, the formatted endogenous RNA (ceRNA) regulatory networks (lncRNA/circRNA-miRNA-mRNA) has been identified as a key player in governing insect resistance formation. This review delves into the functions and underlying mechanisms of miRNA, lncRNA, and circRNA in regulating insect resistance. ncRNAs orchestrate insect resistance by modulating the expression of detoxification enzyme genes, insecticide target genes, as well as receptor genes, effectively regulating both target-site, metabolic and penetration resistance in insects. It also explores the regulatory mechanisms of ceRNA networks in the development of resistance. By enhancing our understanding of the mechanisms of ncRNAs in insecticide resistance, it will not only provide valuable insights into the new mechanisms of insecticide resistance but also help to enrich new directions in ncRNAs gene regulation research.
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Affiliation(s)
- Huamei Xiao
- Key Laboratory of Crop Growth and Development Regulation of Jiangxi Province, College of Life Sciences and Resource Environment, Yichun University, Yichun, China
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Kaplanoglu E, Scott IM, Vickruck J, Donly C. Role of CYP9E2 and a long non-coding RNA gene in resistance to a spinosad insecticide in the Colorado potato beetle, Leptinotarsa decemlineata. PLoS One 2024; 19:e0304037. [PMID: 38787856 PMCID: PMC11125468 DOI: 10.1371/journal.pone.0304037] [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: 01/05/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Spinosads are insecticides used to control insect pests, especially in organic farming where limited tools for pest management exist. However, resistance has developed to spinosads in economically important pests, including Colorado potato beetle (CPB), Leptinotarsa decemlineata. In this study, we used bioassays to determine spinosad sensitivity of two field populations of CPB, one from an organic farm exposed exclusively to spinosad and one from a conventional farm exposed to a variety of insecticides, and a reference insecticide naïve population. We found the field populations exhibited significant levels of resistance compared with the sensitive population. Then, we compared transcriptome profiles between the two field populations to identify genes associated primarily with spinosad resistance and found a cytochrome P450, CYP9E2, and a long non-coding RNA gene, lncRNA-2, were upregulated in the exclusively spinosad-exposed population. Knock-down of these two genes simultaneously in beetles of the spinosad-exposed population using RNA interference (RNAi) resulted in a significant increase in mortality when gene knock-down was followed by spinosad exposure, whereas single knock-downs of each gene produced smaller effects. In addition, knock-down of the lncRNA-2 gene individually resulted in significant reduction in CYP9E2 transcripts. Finally, in silico analysis using an RNA-RNA interaction tool revealed that CYP9E2 mRNA contains multiple binding sites for the lncRNA-2 transcript. Our results imply that CYP9E2 and lncRNA-2 jointly contribute to spinosad resistance in CPB, and lncRNA-2 is involved in regulation of CYP9E2 expression. These results provide evidence that metabolic resistance, driven by overexpression of CYP and lncRNA genes, contributes to spinosad resistance in CPB.
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Affiliation(s)
- Emine Kaplanoglu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ian M. Scott
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Jessica Vickruck
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Cam Donly
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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3
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Han Y, Pu Q, Fan T, Wei T, Xu Y, Zhao L, Liu S. Long non-coding RNAs as promising targets for controlling disease vector mosquitoes. INSECT SCIENCE 2024. [PMID: 38783627 DOI: 10.1111/1744-7917.13383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Hematophagous female mosquitoes are important vectors of numerous devastating human diseases, posing a major public health threat. Effective prevention and control of mosquito-borne diseases rely considerably on progress in understanding the molecular mechanisms of various life activities, and accordingly, the molecules that regulate the various life activities of mosquitoes are potential targets for implementing future vector control strategies. Many long non-coding RNAs (lncRNAs) have been identified in mosquitoes and significant progress has been made in determining their functions. Here, we present a comprehensive overview of the research advances on mosquito lncRNAs, including their molecular identification, function, and interaction with other non-coding RNAs, as well as their synergistic regulatory roles in mosquito life activities. We also highlight the potential roles of competitive endogenous RNAs in mosquito growth and development, as well as in insecticide resistance and virus-host interactions. Insights into the biological functions and mechanisms of lncRNAs in mosquito life activities, viral replication, pathogenesis, and transmission will contribute to the development of novel drugs and safe vaccines.
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Affiliation(s)
- Yujiao Han
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Qian Pu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Ting Fan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Tianqi Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Yankun Xu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Lu Zhao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Shiping Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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Li Y, Wu S, Xu Y, Li Y, Liu Y, Wang J. Transcriptomic Identification and Characterization of Trehalose-6-Phosphate Synthase in Fat Body of the Oriental Fruit Fly, Bactrocera dorsalis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5725-5733. [PMID: 38452362 DOI: 10.1021/acs.jafc.3c06197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The destructive agricultural pest oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), has been causing huge damage to the fruits and vegetable industry. Although many pertinent studies have been conducted on B. dorsalis, the functions of fat body still remain largely unknown. To this end, the comparative transcriptome analysis between fat body and carcass was performed in an attempt to provide insights into functions of fat body of B. dorsalis in the present study. A total of 1431 upregulated and 2511 downregulated unigenes were discovered in the fat body vs carcass comparison, respectively. The enrichment analysis of differentially expressed genes (DEG) revealed that most of the enriched pathways were related to metabolism. The reliability of DEG analysis was validated by qRT-PCR measurements of 12 genes in starch and sucrose metabolism pathway, including the trehalose-6-phosphate synthase (BdTPS) which was highly expressed in eggs, 5 d-old adults, and fat body. The RNAi of BdTPS significantly affected trehalose and chitin metabolism, larval growth, and larva-pupa metamorphosis. Collectively, the findings in this study enriched our understanding of fat body functions in metabolism and demonstrated the indispensable roles of BdTPS in trehalose-related physiological pathways.
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Affiliation(s)
- Ying Li
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Shunjiao Wu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yonghong Xu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yaying Li
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Yinghong Liu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
- College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Jia Wang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Southwest University, Chongqing 400715, China
- College of Plant Protection, Southwest University, Chongqing 400715, China
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Muthu Lakshmi Bavithra C, Murugan M, Pavithran S, Naveena K. Enthralling genetic regulatory mechanisms meddling insecticide resistance development in insects: role of transcriptional and post-transcriptional events. Front Mol Biosci 2023; 10:1257859. [PMID: 37745689 PMCID: PMC10511911 DOI: 10.3389/fmolb.2023.1257859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023] Open
Abstract
Insecticide resistance in insects severely threatens both human health and agriculture, making insecticides less compelling and valuable, leading to frequent pest management failures, rising input costs, lowering crop yields, and disastrous public health. Insecticide resistance results from multiple factors, mainly indiscriminate insecticide usage and mounted selection pressure on insect populations. Insects respond to insecticide stress at the cellular level by modest yet significant genetic propagations. Transcriptional, co-transcriptional, and post-transcriptional regulatory signals of cells in organisms regulate the intricate processes in gene expressions churning the genetic information in transcriptional units into proteins and non-coding transcripts. Upregulation of detoxification enzymes, notably cytochrome P450s (CYPs), glutathione S-transferases (GSTs), esterases [carboxyl choline esterase (CCE), carboxyl esterase (CarE)] and ATP Binding Cassettes (ABC) at the transcriptional level, modification of target sites, decreased penetration, or higher excretion of insecticides are the noted insect physiological responses. The transcriptional regulatory pathways such as AhR/ARNT, Nuclear receptors, CncC/Keap1, MAPK/CREB, and GPCR/cAMP/PKA were found to regulate the detoxification genes at the transcriptional level. Post-transcriptional changes of non-coding RNAs (ncRNAs) such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and epitranscriptomics, including RNA methylation, are reported in resistant insects. Additionally, genetic modifications such as mutations in the target sites and copy number variations (CNV) are also influencing insecticide resistance. Therefore, these cellular intricacies may decrease insecticide sensitivity, altering the concentrations or activities of proteins involved in insecticide interactions or detoxification. The cellular episodes at the transcriptional and post-transcriptional levels pertinent to insecticide resistance responses in insects are extensively covered in this review. An overview of molecular mechanisms underlying these biological rhythms allows for developing alternative pest control methods to focus on insect vulnerabilities, employing reverse genetics approaches like RNA interference (RNAi) technology to silence particular resistance-related genes for sustained insect management.
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Affiliation(s)
| | - Marimuthu Murugan
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Kathirvel Naveena
- Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India
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Meng LW, Yuan GR, Chen ML, Zheng LS, Dou W, Peng Y, Bai WJ, Li ZY, Vontas J, Wang JJ. Cuticular competing endogenous RNAs regulate insecticide penetration and resistance in a major agricultural pest. BMC Biol 2023; 21:187. [PMID: 37667263 PMCID: PMC10478477 DOI: 10.1186/s12915-023-01694-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/29/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND The continuously developing pesticide resistance is a great threat to agriculture and human health. Understanding the mechanisms of insecticide resistance is a key step in dealing with the phenomenon. Insect cuticle is recently documented to delay xenobiotic penetration which breaks the previous stereotype that cuticle is useless in insecticide resistance, while the underlying mechanism remains scarce. RESULTS Here, we find the integument contributes over 40.0% to insecticide resistance via different insecticide delivery strategies in oriental fruit fly. A negative relationship exists between cuticle thickening and insecticide penetration in resistant/susceptible, also in field strains of oriental fruit fly which is a reason for integument-mediated resistance. Our investigations uncover a regulator of insecticide penetration that miR-994 mimic treatment causes cuticle thinning and increases susceptibility to malathion, whereas miR-994 inhibitor results in opposite phenotypes. The target of miR-994 is a most abundant cuticle protein (CPCFC) in resistant/susceptible integument expression profile, which possesses capability of chitin-binding and influences the cuticle thickness-mediated insecticide penetration. Our analyses find an upstream transcriptional regulatory signal of miR-994 cascade, long noncoding RNA (lnc19419), that indirectly upregulates CPCFC in cuticle of the resistant strain by sponging miR-994. Thus, we elucidate the mechanism of cuticular competing endogenous RNAs for regulating insecticide penetration and demonstrate it also exists in field strain of oriental fruit fly. CONCLUSIONS We unveil a regulatory axis of lnc19419 ~ miR-994 ~ CPCFC on the cuticle thickness that leads to insecticide penetration resistance. These findings indicate that competing endogenous RNAs regulate insecticide resistance by modulating the cuticle thickness and provide insight into the resistance mechanism in insects.
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Affiliation(s)
- Li-Wei Meng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Meng-Ling Chen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - Li-Sha Zheng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yu Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - Wen-Jie Bai
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - Zhen-Yu Li
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China
| | - John Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013, Heraklion, Greece
- Pesticide Science Laboratory, Department of Crop Science, Agricultural University of Athens, Athens, 11855, Greece
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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Wang QN, Xiao WQ, Yao Y, Kong XD, Sun Y. Response patterns of lncRNAs of the Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae under 23 pesticide treatments. JOURNAL OF INSECT SCIENCE (ONLINE) 2023; 23:8. [PMID: 37471132 DOI: 10.1093/jisesa/iead059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/13/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
The response of Spodoptera frugiperda genes toward insecticides is crucial for guiding insecticide use. The regulation of the S. frugiperda genes via long noncoding RNAs (lncRNAs) under insecticide treatment should be investigated. In this study, 452 differentially expressed lncRNAs were identified by analyzing RNA-sequencing data of S. frugiperda under 23 pesticide treatments. We found 59 and 43 differentially expressed lncRNAs that could regulate detoxification-related cytochrome P450 and UDP-glucuronosyltransferase genes, respectively. Furthermore, the target genes of differentially expressed lncRNAs were enriched in Pfam, including chitin bind 4 and gene ontology terms such as structural constituent of the cuticle, revealing their potential mechanism of action on the growth inhibition of S. frugiperda larvae. Insecticide-specific expression of lncRNAs highlights the properties and commonalities of different insecticide-induced lncRNA regulatory mechanisms. To conclude, the results of this study provide new insights and perspectives on the use of 23 insecticides via lncRNA regulation of mRNAs.
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Affiliation(s)
- Qing-Nan Wang
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Wen-Qing Xiao
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Yu Yao
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Xiang-Dong Kong
- Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yang Sun
- Key Laboratory for Conservation and Use of Important Biological Resources of Anhui Province, Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Shang Y, Feng Y, Ren L, Zhang X, Yang F, Zhang C, Guo Y. Genome-wide analysis of long noncoding RNAs and their association in regulating the metamorphosis of the Sarcophaga peregrina (Diptera: Sarcophagidae). PLoS Negl Trop Dis 2023; 17:e0011411. [PMID: 37363930 DOI: 10.1371/journal.pntd.0011411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The flesh fly, Sarcophaga peregrina (Diptera: Sarcophagidae), is an important hygiene pest, that causes myiasis in humans and other mammals, typically livestock, and as a vector for various parasitic agents, including bacteria, viruses, and parasites. The role of long non-coding RNAs (lncRNAs) in regulating gene expression during metamorphosis of the flesh fly has not been well established. METHODOLOGY/PRINCIPAL FINDINGS In this study, we performed genome-wide identification and characterization of lncRNAs from the early pupal stage (1-days pupae), mid-term pupal stage (5-days pupae), and late pupal stage (9-days pupae) of S. peregrina by RNA-seq, and a total of 6921 lncRNAs transcripts were identified. RT-qPCR and enrichment analyses revealed the differentially expressed lncRNAs (DE lncRNAs) that might be associated with insect metamorphosis development. Furthermore, functional analysis revealed that the DE lncRNA (SP_lnc5000) could potentially be involved in regulating the metamorphosis of S. peregrina. RNA interference of SP_lnc5000 caused reduced expression of metamorphosis-related genes in 20-hydroxyecdysone (20E) signaling (Br-c, Ftz-F1), cuticle tanning pathway (TH, DOPA), and chitin related pathway (Cht5). Injection of dsSP_lnc5000 in 3rd instar larvae of S. peregrina resulted in deformed pupae, stagnation of pupal-adult metamorphosis, and a decrease in development time of pupal, pupariation rates and eclosion rates. Hematoxylin-eosin staining (H&E), scanning electron microscope (SEM) observation and cuticle hydrocarbons (CHCs) analysis indicated that SP_lnc5000 had crucial roles in the metamorphosis developmental by modulating pupal cuticular development. CONCLUSIONS/SIGNIFICANCE We established that the lncRNA SP_lnc5000 potentially regulates the metamorphosis of S. peregrina by putatively affecting the structure and composition of the pupal cuticle. This study enhances our understanding of lncRNAs as regulators of metamorphosis in S. peregrina, and provide valuable insights into the identification of potential targets for vector control and the development of effective strategies for controlling the spread of myiasis and parasitic diseases.
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Affiliation(s)
- Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yakai Feng
- Department of Forensic Science, School of Basic Medical Sciences, Xinjiang Medical University Ürümqi, China
| | - Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Fengqin Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Changquan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
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10
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Liu M, Xiao F, Zhu J, Fu D, Wang Z, Xiao R. Combined PacBio Iso-Seq and Illumina RNA-Seq Analysis of the Tuta absoluta (Meyrick) Transcriptome and Cytochrome P450 Genes. INSECTS 2023; 14:363. [PMID: 37103178 PMCID: PMC10146655 DOI: 10.3390/insects14040363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 03/29/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Tuta absoluta (Meyrick) is a devastating invasive pest worldwide. The abamectin and chlorantraniliprole complex have become an alternative option for chemical control because they can enhance insecticidal activity and delay increased drug resistance. Notably, pests are inevitably resistant to various types of insecticides, and compound insecticides are no exception. To identify potential genes involved in the detoxification of abamectin and chlorantraniliprole complex in T. absoluta, PacBio SMRT-seq transcriptome sequencing and Illumina RNA-seq analysis of abamectin and chlorantraniliprole complex-treated T. absoluta were performed. We obtained 80,492 non-redundant transcripts, 62,762 (77.97%) transcripts that were successfully annotated, and 15,524 differentially expressed transcripts (DETs). GO annotation results showed that most of these DETs were involved in the biological processes of life-sustaining activities, such as cellular, metabolic, and single-organism processes. The KEGG pathway enrichment results showed that the pathways related to glutathione metabolism, fatty acid and amino acid synthesis, and metabolism were related to the response to abamectin and chlorantraniliprole complex in T. absoluta. Among these, 21 P450s were differentially expressed (11 upregulated and 10 downregulated). The qRT-PCR results for the eight upregulated P450 genes after abamectin and chlorantraniliprole complex treatment were consistent with the RNA-Seq data. Our findings provide new full-length transcriptional data and information for further studies on detoxification-related genes in T. absoluta.
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Chen P, Cai M, Feng YJ, Li C, Dong ZQ, Xiao WF, Tang L, Zhu Y, Tian T, Deng BY, Pan MH, Lu C. Apoptosis-related long non-coding RNA LINC5438 of Bombyx mori promotes the proliferation of BmNPV. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105380. [PMID: 36963947 DOI: 10.1016/j.pestbp.2023.105380] [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: 12/25/2022] [Revised: 02/12/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Apoptosis, as an important part of the immune response, is one of the core events in the host-virus interaction. Studies have shown that long non-coding RNAs (lncRNAs) play important roles in the process of cell apoptosis and pathophysiology. To investigate the apoptosis-related lncRNAs involved in Bombyx mori nucleopolyhedrovirus (BmNPV) infecting silkworms, transcriptome sequencing was conducted based on silkworm cells infected with BmNPV before and after B. mori inhibitor of apoptosis (Bmiap) gene knockout. A total of 23 differentially expressed lncRNAs were identified as being associated with the mitochondrial apoptosis pathway. Moreover, we demonstrated that B. mori LINC5438 has the function of inhibiting apoptosis in silkworm cells. Overexpression of LINC5438 promoted the proliferation of BmNPV, while interference with LINC5438 inhibited its proliferation, indicating that LINC5438 plays an important role in BmNPV infection. Our results also showed that LINC5438 can regulate the expression of Bmiap, BmDronc, BmICE, and its predicted target gene BmAIF, suggesting that LINC5438 may function through the mitochondrial pathway. These findings provide important insights into the mechanisms of virus-host interaction and the applications of baculoviruses as biological insecticides.
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Affiliation(s)
- Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Min Cai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Yu-Jie Feng
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Cong Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Zhan-Qi Dong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Wen-Fu Xiao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China; Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Liang Tang
- Sericulture Technology Promotion Station of Guangxi, Nanning 530007, China
| | - Yan Zhu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Ting Tian
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Bo-Yuan Deng
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Min-Hui Pan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China.
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China.
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Jia Z, Yang X, Yang H, Dai R, Zeng Q, Jin D. Interaction Analysis of lncRNA and mRNA Based on the Full-Length Transcriptome of the Nymph-to-Adult Developmental Transition of Sogatella furcifera. INSECTS 2023; 14:308. [PMID: 37103123 PMCID: PMC10141146 DOI: 10.3390/insects14040308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Little is known on how long noncoding RNAs (lncRNAs) and mRNAs cooperatively participate in regulating the nymph-to-adult development transition of Sogatella furcifera. Herein, lncRNA and mRNA libraries were constructed in three different developmental stages of S. furcifera, namely, prior to (PE), during (DE), and after (AE) ecdysis. Overall, 4649 lncRNAs were identified and divided into intergenic (53.90%), intronic (1.33%), sense (8.99%), antisense (21.75%), and bidirectional (3.94%) lncRNAs. Moreover, 795 differentially expressed lncRNAs were identified. Specifically, upon comparing PE and DE, 2719 target mRNAs were predicted for 574 lncRNAs. Upon comparing PE and AE, 2816 target mRNAs were predicted for 627 lncRNAs. Finally, upon comparing DE and AE, 51 target mRNAs were predicted for 35 lncRNAs. Kyoto Encyclopedia of Genes and Genome functional enrichment analysis revealed that the target genes of 795 lncRNAs were enriched in metabolic pathways, amino sugar and nucleotide sugar metabolism, and fatty acid metabolism. Subsequently, interaction analysis indicated that MSTRG.16086.1, MSTRG.16087.1, and MSTRG.2447.1 were functionally associated with cuticle protein and chitin biosynthesis. Finally, 11 differentially expressed lncRNAs were significantly enriched in 3rd and 4th instar nymphs. Our findings suggest that lncRNAs play a critical regulatory role during the molting of S. furcifera.
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Zheng SY, Pan LX, Cheng FP, Jin MJ, Wang ZL. A Global Survey of the Full-Length Transcriptome of Apis mellifera by Single-Molecule Long-Read Sequencing. Int J Mol Sci 2023; 24:ijms24065827. [PMID: 36982901 PMCID: PMC10059051 DOI: 10.3390/ijms24065827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/30/2023] Open
Abstract
As important pollinators, honey bees play a crucial role in both maintaining the ecological balance and providing products for humans. Although several versions of the western honey bee genome have already been published, its transcriptome information still needs to be refined. In this study, PacBio single-molecule sequencing technology was used to sequence the full-length transcriptome of mixed samples from many developmental time points and tissues of A. mellifera queens, workers and drones. A total of 116,535 transcripts corresponding to 30,045 genes were obtained. Of these, 92,477 transcripts were annotated. Compared to the annotated genes and transcripts on the reference genome, 18,915 gene loci and 96,176 transcripts were newly identified. From these transcripts, 136,554 alternative splicing (AS) events, 23,376 alternative polyadenylation (APA) sites and 21,813 lncRNAs were detected. In addition, based on the full-length transcripts, we identified many differentially expressed transcripts (DETs) between queen, worker and drone. Our results provide a complete set of reference transcripts for A. mellifera that dramatically expand our understanding of the complexity and diversity of the honey bee transcriptome.
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Affiliation(s)
- Shuang-Yan Zheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Lu-Xia Pan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fu-Ping Cheng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang 330045, China
| | - Meng-Jie Jin
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zi-Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang 330045, China
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14
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Recent Advances and Future Potential of Long Non-Coding RNAs in Insects. Int J Mol Sci 2023; 24:ijms24032605. [PMID: 36768922 PMCID: PMC9917219 DOI: 10.3390/ijms24032605] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Over the last decade, long non-coding RNAs (lncRNAs) have witnessed a steep rise in interest amongst the scientific community. Because of their functional significance in several biological processes, i.e., alternative splicing, epigenetics, cell cycle, dosage compensation, and gene expression regulation, lncRNAs have transformed our understanding of RNA's regulatory potential. However, most knowledge concerning lncRNAs comes from mammals, and our understanding of the potential role of lncRNAs amongst insects remains unclear. Technological advances such as RNA-seq have enabled entomologists to profile several hundred lncRNAs in insect species, although few are functionally studied. This article will review experimentally validated lncRNAs from different insects and the lncRNAs identified via bioinformatic tools. Lastly, we will discuss the existing research challenges and the future of lncRNAs in insects.
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Huang S, Jing D, Xu L, Luo G, Hu Y, Wu T, Hu Y, Li F, He K, Qin W, Sun Y, Liu H. Genome-wide identification and functional analysis of long non-coding RNAs in Chilo suppressalis reveal their potential roles in chlorantraniliprole resistance. Front Physiol 2023; 13:1091232. [PMID: 36699669 PMCID: PMC9868556 DOI: 10.3389/fphys.2022.1091232] [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: 11/06/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Long non-coding RNAs, referred to as lncRNAs, perform essential functions in some biological processes, including reproduction, metamorphosis, and other critical life functions. Yet, lncRNAs are poorly understood in pesticide resistance, and no reports to date have characterized which lncRNAs are associated with chlorantraniliprole resistance in Chilo suppressalis. Here, RNA-seq was performed on two strains of C. suppressalis exposed to chlorantraniliprole: one is a susceptible strain (S), and the other is a resistant strain (R). In total, 3,470 lncRNAs were identified from 40,573 merged transcripts in six libraries, including 1,879 lincRNAs, 245 intronic lncRNAs, 853 sense lncRNAs, and 493 antisense lncRNAs. Moreover, differential expression analysis revealed 297 and 335 lncRNAs upregulated in S and R strains, respectively. Differentially expressed (DE) lncRNAs are usually assumed to be involved in the chlorantraniliprole resistance in C. suppressalis. As potential targets, adjacent protein-coding genes (within <1000 kb range upstream or downstream of DE lncRNAs), especially detoxification enzyme genes (cytochrome P450s, carboxyl/cholinesterases/esterases, and ATP-binding cassette transporter), were analyzed. Furthermore, the strand-specific RT-PCR was conducted to confirm the transcript orientation of randomly selected 20 DE lincRNAs, and qRT-PCR was carried out to verify the expression status of 8 out of them. MSTRG.25315.3, MSTRG.25315.6, and MSTRG.7482.1 were upregulated in the R strain. Lastly, RNA interference and bioassay analyses indicated overexpressed lincRNA MSTRG.7482.1 was involved in chlorantraniliprole resistance. In conclusion, we represent, for the first time, the genome-wide identification of chlorantraniliprole-resistance-related lncRNAs in C. suppressalis. It elaborates the views underlying the mechanism conferring chlorantraniliprole resistance in lncRNAs.
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Affiliation(s)
- Shuijin Huang
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Dong Jing
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lu Xu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Guanghua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, China
| | - Yanyue Hu
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Ting Wu
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yao Hu
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang City, China
| | - Fei Li
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Kang He
- Institute of Insect Sciences/Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenjing Qin
- Institute of Soil Fertilizer and Environmental Resource, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Yang Sun
- Institute of Plant Protection, Jiangxi Academy of Agricultural Sciences, Nanchang, China,*Correspondence: Yang Sun, ; Hui Liu,
| | - Hui Liu
- Institute of Red Soil and Germplasm Resources in Jiangxi, Nanchang, China,*Correspondence: Yang Sun, ; Hui Liu,
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Shi L, Li WL, Zeng HX, Shi Y, Liao XL. Systematic identification and functional analysis of long noncoding RNAs involved in indoxacarb resistance in Spodoptera litura. INSECT SCIENCE 2022; 29:1721-1736. [PMID: 35150054 DOI: 10.1111/1744-7917.13015] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts that are more than 200 nucleotides long. They play essential roles in regulating a variety of biological processes in many species, including insects, and some lncRNAs have been found to be associated with insecticide resistance. However, the characteristics and biological functions of lncRNAs involved in indoxacarb resistance are unknown in Spodoptera litura. We performed RNA sequencing in the SS, InRS, and FInRS of S. litura and identified 11 978 lncRNAs, including 3 136 intergenic lncRNAs, 7 393 intronic lncRNAs, and 1 449 anti-sense lncRNAs. Compared with the SS, 51 lncRNAs were upregulated and 134 lncRNAs were downregulated in the two resistant strains, and 908 differentially expressed mRNAs were predicted as the target genes of the 185 differentially expressed lncRNAs. Further analysis showed that 112 of differentially expressed lncRNAs may be associated with indoxacarb resistance by regulating the expression of 14 P450s, seven CCEs, one GST, six UGTs, five ABC transporters, and 24 cuticle protein genes, and 79 of differentially expressed lncRNAs may regulate the expression of 14 detoxification genes and 19 cuticle protein genes to participate in indoxacarb resistance by sponging 10 microRNAs. Interestingly, 47 of differentially expressed lncRNAs may mediate indoxacarb resistance through both lncRNA-mRNA and lncRNA-miRNA-mRNA regulatory pathways. Furthermore, quantitative PCR, RNA interference, and indoxacarb bioassay analyses indicated that overexpressed LNC_004867 and LNC_006576 were involved in indoxacarb resistance. This study provides comprehensive information for lncRNAs of S. litura, and presents evidence that lncRNAs have key roles in conferring insecticide resistance in S. litura.
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Affiliation(s)
- Li Shi
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
| | - Wen-Lin Li
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
| | - Hai-Xin Zeng
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
| | - Yao Shi
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
| | - Xiao-Lan Liao
- Hunan Provincial Engineering and Technology Research Center for Bio-pesticide and Formulation Processing, College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Changsha, China
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Zha W, Li S, Xu H, Chen J, Liu K, Li P, Liu K, Yang G, Chen Z, Shi S, Zhou L, You A. Genome-wide identification of long non-coding (lncRNA) in Nilaparvata lugens's adaptability to resistant rice. PeerJ 2022; 10:e13587. [PMID: 35910769 PMCID: PMC9332332 DOI: 10.7717/peerj.13587] [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: 02/11/2022] [Accepted: 05/24/2022] [Indexed: 01/22/2023] Open
Abstract
Background The brown planthopper (BPH), Nilaparvata lugens (Stål), is a very destructive pest that poses a major threat to rice plants worldwide. BPH and rice have developed complex feeding and defense strategies in the long-term co-evolution. Methods To explore the molecular mechanism of BPH's adaptation to resistant rice varieties, the lncRNA expression profiles of two virulent BPH populations were analyzed. The RNA-seq method was used to obtain the lncRNA expression data in TN1 and YHY15. Results In total, 3,112 highly reliable lncRNAs in TN1 and YHY15 were identified. Compared to the expression profiles between TN1 and YHY15, 157 differentially expressed lncRNAs, and 675 differentially expressed mRNAs were identified. Further analysis of the possible regulation relationships between differentially expressed lncRNAs and differentially expressed mRNAs, identified three pair antisense targets, nine pair cis-regulation targets, and 3,972 pair co-expressed targets. Function enriched found arginine and proline metabolism, glutathione metabolism, and carbon metabolism categories may significantly affect the adaptability in BPH when it is exposed to susceptible and resistant rice varieties. Altogether, it provided scientific data for the study of lncRNA regulation of brown planthopper resistance to rice. These results are helpful in the development of new control strategies for host defense against BPH and breeding rice for high yield.
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Affiliation(s)
- Wenjun Zha
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Sanhe Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Huashan Xu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Junxiao Chen
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Kai Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Peide Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Kai Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guocai Yang
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Zhijun Chen
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Shaojie Shi
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Lei Zhou
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Aiqing You
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China,Hubei Hongshan Laboratory, Wuhan, Hubei, China
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Peng T, Liu X, Tian F, Xu H, Yang F, Chen X, Gao X, Lv Y, Li J, Pan Y, Shang Q. Functional investigation of lncRNAs and target cytochrome P450 genes related to spirotetramat resistance in Aphis gossypii Glover. PEST MANAGEMENT SCIENCE 2022; 78:1982-1991. [PMID: 35092151 DOI: 10.1002/ps.6818] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/07/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Spirotetramat is a tetramic acid derivative insecticide with novel modes of action for controlling Aphis gossypii Glover in the field. Previous studies have shown that long noncoding RNAs (lncRNAs) and cytochrome P450 monooxygenases (P450s) are involved in the detoxification process. However, the functions of lncRNAs in regulating P450 gene expression in spirotetramat resistance in A. gossypii are unknown. RESULTS In this study, we found CYP4CJ1, CYP6CY7 and CYP6CY21 expression levels to be significantly upregulated in a spirotetramat-resistant (SR) strain compared with a susceptible (SS) strain. Furthermore, knockdown of CYP4CJ1, CYP6CY7 and CYP6CY21 increased nymph and adult mortality in the SR strain following exposure to spirotetramat. Drosophila ectopically expressing CYP380C6, CYP4CJ1, CYP6DA2, CYP6CY7 and CYP6CY21 showed significantly decreased mortality after spirotetramat exposure, and CYP380C6, CYP4CJ1 and CYP6CY21 are putative targets of six lncRNAs. Silencing of lncRNAs MSTRG.36649.2/5 and MSTRG.71880.1 changed CYP6CY21 and CYP380C6 expression, altering the sensitivity of the SR strain to spirotetramat. Moreover, MSTRG.36649.2/5 did not compete for microRNA (miRNA) binding to regulate CYP6CY21 expression. CONCLUSION Our results confirm that CYP380C6, CYP4CJ1, CYP6DA2, CYP6CY7 and CYP6CY21 are potentially involved in the development of spirotetramat resistance in A. gossypii, and MSTRG.36649.2/5 and MSTRG.71880.1 probably regulate CYP6CY21 and CYP380C6 expression other than through the "sponge effect" of competing for miRNA binding. Our results provide a favorable molecular basis for studying cotton aphid P450 genes and lncRNA functions in spirotetramat resistance development.
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Affiliation(s)
- Tianfei Peng
- College of Plant Science, Jilin University, Changchun, China
| | - Xuemei Liu
- College of Plant Science, Jilin University, Changchun, China
| | - Fayi Tian
- College of Plant Science, Jilin University, Changchun, China
| | - Hongfei Xu
- College of Plant Science, Jilin University, Changchun, China
| | - Fengting Yang
- College of Plant Science, Jilin University, Changchun, China
| | - Xuewei Chen
- School of Agricultural Science, Zhengzhou University, Zhengzhou, China
| | - Xiwu Gao
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yuntong Lv
- College of Plant Science, Jilin University, Changchun, China
| | - Jianyi Li
- College of Plant Science, Jilin University, Changchun, China
| | - Yiou Pan
- College of Plant Science, Jilin University, Changchun, China
| | - Qingli Shang
- College of Plant Science, Jilin University, Changchun, China
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Li WJ, Wei D, Han HL, Song YJ, Wang Y, Xu HQ, Smagghe G, Wang JJ. lnc94638 is a testis-specific long non-coding RNA involved in spermatozoa formation in Zeugodacus cucurbitae (Coquillett). INSECT MOLECULAR BIOLOGY 2021; 30:605-614. [PMID: 34318563 DOI: 10.1111/imb.12729] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/24/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) generally display tissue-specific distributions, and testis-specific lncRNAs form the highest proportion of lncRNAs in many species. Here, we presented a detailed analysis of testis-specific lncRNAs in the melon fly, Zeugodacus cucurbitae, a highly destructive insect pest of cucurbitaceous and other related crops. Most testis-specific lncRNAs were found to be long intergenic non-coding RNAs (lincRNA). The size distribution of these lncRNAs ranged between 600 and 1000 nucleotides. Testis-specific lncRNAs that harboured one isoform number and two exons were the most abundant. Compared to other male tissues, the testis had more highly expressed lncRNAs. The quantitative real-time polymerase chain reaction results of 10 randomly selected testis-specific lncRNAs showed expression patterns consistent with RNA-seq data. Further analysis of the most highly expressed testis-specific lncRNA, lnc94638, was undertaken. Fluorescent in situ hybridization assays localized lnc94638 to the apical region of the testis that contains mature spermatozoa. RNA interference-mediated knockdown of lnc94638 expression reduced spermatozoa numbers and impaired the fertility of Z. cucurbitae male. This study provides a catalogue of testis-specific lncRNAs, shows that the testis-specific lnc94638 is involved in spermatogenesis and has the potential to be used for treating male sterility.
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Affiliation(s)
- W-J Li
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - D Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - H-L Han
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Y-J Song
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Y Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - H-Q Xu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - G Smagghe
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - J-J Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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Peng T, Pan Y, Tian F, Xu H, Yang F, Chen X, Gao X, Li J, Wang H, Shang Q. Identification and the potential roles of long non-coding RNAs in regulating acetyl-CoA carboxylase ACC transcription in spirotetramat-resistant Aphis gossypii. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 179:104972. [PMID: 34802522 DOI: 10.1016/j.pestbp.2021.104972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/09/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) represent the largest class of non-coding transcripts. They act a pivotal part in various insect developmental processes and stress responses. However, the investigation of lncRNA functions in insecticide resistant remains at an early phase. Herein, we conducted whole-transcriptome RNA sequencing for two cotton aphid (Aphis gossypii Glover) strains, i.e., insecticide-susceptible (SS) and spirotetramat-resistant (SR). We discovered 6059 lncRNAs in the RNA-Seq data, and 874 lncRNAs showed differential expression. In addition, 5 lncRNAs among 874 lncRNAs were predicted as targets of acetyl-CoA carboxylase (ACC). Reverse transcription real-time quantitative PCR (RT-qPCR) combined with RNA interference (RNAi) confirmed that selected ACC lncRNA was related to the expression of ACC. Moreover, we also identified two transcription factors, i.e., C/EBP and C/EBPzeta, that regulate the transcription level of ACC lncRNA. These results provide a good basis for the study of cotton aphid lncRNA functions in insecticide resistance development.
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Affiliation(s)
- Tianfei Peng
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Yiou Pan
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Fayi Tian
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Hongfei Xu
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Fengting Yang
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Xuewei Chen
- School of Agricultural Science, Zhengzhou University, Zhengzhou 450001, PR China
| | - Xiwu Gao
- Department of Entomology, China Agricultural University, Beijing 100193, PR China
| | - Jianyi Li
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Haibao Wang
- College of Plant Science, Jilin University, Changchun 130062, PR China
| | - Qingli Shang
- College of Plant Science, Jilin University, Changchun 130062, PR China; School of Agricultural Science, Zhengzhou University, Zhengzhou 450001, PR China.
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