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Odhiambo CA, Derilus D, Impoinvil LM, Omoke D, Saizonou H, Okeyo S, Dada N, Mulder N, Nyamai D, Nyanjom S, Lenhart A, Djogbénou LS, Ochomo E. Key gene modules and hub genes associated with pyrethroid and organophosphate resistance in Anopheles mosquitoes: a systems biology approach. BMC Genomics 2024; 25:665. [PMID: 38961324 PMCID: PMC11223346 DOI: 10.1186/s12864-024-10572-z] [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: 01/12/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
Indoor residual spraying (IRS) and insecticide-treated nets (ITNs) are the main methods used to control mosquito populations for malaria prevention. The efficacy of these strategies is threatened by the spread of insecticide resistance (IR), limiting the success of malaria control. Studies of the genetic evolution leading to insecticide resistance could enable the identification of molecular markers that can be used for IR surveillance and an improved understanding of the molecular mechanisms associated with IR. This study used a weighted gene co-expression network analysis (WGCNA) algorithm, a systems biology approach, to identify genes with similar co-expression patterns (modules) and hub genes that are potential molecular markers for insecticide resistance surveillance in Kenya and Benin. A total of 20 and 26 gene co-expression modules were identified via average linkage hierarchical clustering from Anopheles arabiensis and An. gambiae, respectively, and hub genes (highly connected genes) were identified within each module. Three specific genes stood out: serine protease, E3 ubiquitin-protein ligase, and cuticular proteins, which were top hub genes in both species and could serve as potential markers and targets for monitoring IR in these malaria vectors. In addition to the identified markers, we explored molecular mechanisms using enrichment maps that revealed a complex process involving multiple steps, from odorant binding and neuronal signaling to cellular responses, immune modulation, cellular metabolism, and gene regulation. Incorporation of these dynamics into the development of new insecticides and the tracking of insecticide resistance could improve the sustainable and cost-effective deployment of interventions.
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Affiliation(s)
- Cynthia Awuor Odhiambo
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya.
| | - Dieunel Derilus
- Division of Parasitic Diseases and Malaria, Entomology Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Lucy Mackenzie Impoinvil
- Division of Parasitic Diseases and Malaria, Entomology Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Diana Omoke
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Helga Saizonou
- Tropical Infectious Diseases Research Center (TIDRC), University of Abomey-Calavi (UAC), Cotonou, Benin
| | - Stephen Okeyo
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
| | - Nsa Dada
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Nicola Mulder
- Human, Heredity, and Health in Africa H3A Bionet Network, Cape Town, South Africa
| | - Dorothy Nyamai
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Steven Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Audrey Lenhart
- Division of Parasitic Diseases and Malaria, Entomology Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Center (TIDRC), University of Abomey-Calavi (UAC), Cotonou, Benin
- Regional Institute of Public Health (IRSP), Ouidah, Benin
| | - Eric Ochomo
- Kenya Medical Research Institute (KEMRI), Centre for Global Health Research (CGHR), Kisumu, Kenya
- Liverpool School of Tropical Medicine, Liverpool, UK
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Gao H, Li Y, Tian Y, Zhang H, Kim K, Li B. Gene family expansion analysis and identification of the histone family in Spodoptera frugiperda. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101142. [PMID: 37713926 DOI: 10.1016/j.cbd.2023.101142] [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: 08/09/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
Spodoptera frugiperda, a major invasive pest, causes severe damage to various economically important crops. Previous comparative genomics studies have revealed a close association between the invasiveness of S. frugiperda and its genome. In recent years, a vast amount of genome from lepidopteran species has become available, offering an opportunity for a more detailed and comprehensive understanding of the biological characteristics of S. frugiperda. In this study, we conducted a comprehensive comparative genomics analysis of S. frugiperda using genome from 46 lepidopteran species. We found the highest number of gene family expansion events in S. frugiperda, indicating that gene family expansion is a crucial mechanism in its adaptive evolution. The expanded gene families are enriched in various biological processes, including nutrient metabolism, development, stress response, reproduction, and immune processes, suggesting that the expansion of these gene families likely contributes to the strong environmental adaptability of S. frugiperda. Furthermore, we identified the expansion of histone gene families in S. frugiperda which resulted from chromosome segmental duplications after the divergence from closely related species. Expression analysis of histone genes indicated that certain members might exert an influence on the growth and reproduction processes of S. frugiperda. Overall, our study deepens our understanding of the biological characteristics of S. frugiperda, providing a theoretical basis for the comprehensive management and sustained control of S. frugiperda and other lepidopteran pests in the future.
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Affiliation(s)
- Han Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Ying Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Hui Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - KumChol Kim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; Department of Life-Science, University of Science, Pyongyang, Democratic People's Republic of Korea
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, 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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Li F, Xing G, Li Y, Chen P, Hu Q, Chen M, Li Y, Cao H, Huang Y. Expressions and functions of RR-1 cuticular protein genes in the integument of Mythimna separata. JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:963-972. [PMID: 36964708 DOI: 10.1093/jee/toad053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 06/14/2023]
Abstract
As the most outer layer between itself and the environment, integuments are necessary for insects with various important functions. Cuticular proteins (CPs) are the main components in integuments, while the functions of CP genes remain unknown in Mythimna separata (Walker), which is a devastating agricultural pest. In this study, 79 CP genes were identified from the transcriptomes of larval integuments, 57 of which were from the family containing conserved Rebers & Riddiford (R&R) consensus (CPR family). Amongst these CPRs, 44 genes belonged to the subfamily with RR-1 motif (RR-1 genes) and clustered into three clades, with the top 15 most abundant RR-1 genes identified based on fragments per kilobase per million mapped fragments (FPKM) values. RT-qPCR analysis showed that most of RR-1 genes such as MsCPR1-4 were highly expressed at larval stages and in their integuments. The expression levels of RR-1 genes were generally decreased at the beginning but increased at the late stage of molting process. RNAi was applied for six RR-1 genes, and MsCPR1-4 were knocked down significantly. Silence of MsCPR2 resulted in abnormal integument formed after molting, while knockdown of MsCPR3 and MsCPR4 led to failure of molting, respectively. No phenotype was obtained for the RNAi of MsCPR1. Therefore, the expression of RR-1 genes and their functions were analyzed in the development of integuments in M. separata, providing new insights of RR-1 genes and potential targets for the development of growth regulators and new insecticides for M. separata.
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Affiliation(s)
- Fuyuan Li
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, PR China
| | - Gaoliang Xing
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, PR China
| | - Yixuan Li
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, PR China
| | - Peng Chen
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, PR China
| | - Qin Hu
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, PR China
| | - Ming Chen
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, PR China
| | - Yiyu Li
- Institute of New Rural Development, Anhui Agricultural University, Hefei, PR China
| | - Haiqun Cao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, PR China
| | - Yong Huang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, School of Plant Protection, Anhui Agricultural University, Hefei, PR China
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