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Huang X, Li Q, Xu Y, Li A, Wang S, Chen Y, Zhang C, Zhang X, Wang H, Lv C, Sun B, Li S, Kang L, Chen B. A neural m 6A pathway regulates behavioral aggregation in migratory locusts. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1242-1254. [PMID: 38478296 DOI: 10.1007/s11427-023-2476-1] [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: 08/12/2023] [Accepted: 10/07/2023] [Indexed: 06/07/2024]
Abstract
RNA N6-methyladenosine (m6A), as the most abundant modification of messenger RNA, can modulate insect behaviors, but its specific roles in aggregation behaviors remain unexplored. Here, we conducted a comprehensive molecular and physiological characterization of the individual components of the methyltransferase and demethylase in the migratory locust Locusta migratoria. Our results demonstrated that METTL3, METTL14 and ALKBH5 were dominantly expressed in the brain and exhibited remarkable responses to crowding or isolation. The individual knockdown of methyltransferases (i.e., METTL3 and METTL14) promoted locust movement and conspecific attraction, whereas ALKBH5 knockdown induced a behavioral shift toward the solitary phase. Furthermore, global transcriptome profiles revealed that m6A modification could regulate the orchestration of gene expression to fine tune the behavioral aggregation of locusts. In summary, our in vivo characterization of the m6A functions in migratory locusts clearly demonstrated the crucial roles of the m6A pathway in effectively modulating aggregation behaviors.
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Affiliation(s)
- Xianliang Huang
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Qing Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanan Xu
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Ang Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shanzheng Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yusheng Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunrui Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xia Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cong Lv
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100101, China
| | - Baofa Sun
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shaoqin Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Le Kang
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, 071002, China.
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Bing Chen
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, 071002, China.
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2
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He J, Kang L. Regulation of insect behavior by non-coding RNAs. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1106-1118. [PMID: 38443665 DOI: 10.1007/s11427-023-2482-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/26/2023] [Indexed: 03/07/2024]
Abstract
The adaptation of insects to environments relies on a sophisticated set of behaviors controlled by molecular and physiological processes. Over the past several decades, accumulating studies have unveiled the roles of non-coding RNAs (ncRNAs) in regulating insect behaviors. ncRNAs assume particularly pivotal roles in the behavioral plasticity of insects by rapidly responding to environmental stimuli. ncRNAs also contribute to the maintenance of homeostasis of insects by fine-tuning the expression of target genes. However, a comprehensive review of ncRNAs' roles in regulating insect behaviors has yet to be conducted. Here, we present the recent progress in our understanding of how ncRNAs regulate various insect behaviors, including flight and movement, social behavior, reproduction, learning and memory, and feeding. We refine the intricate mechanisms by which ncRNAs modulate the function of neural, motor, reproductive, and other physiological systems, as well as gene expression in insects like fruit flies, social insects, locusts, and mosquitos. Furthermore, we discuss potential avenues for future studies in ncRNA-mediated insect behaviors.
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Affiliation(s)
- Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, Hebei University, Baoding, 071002, China.
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3
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Zhu YN, He J, Wang J, Guo W, Liu H, Song Z, Kang L. Parental experiences orchestrate locust egg hatching synchrony by regulating nuclear export of precursor miRNA. Nat Commun 2024; 15:4328. [PMID: 38773155 PMCID: PMC11109280 DOI: 10.1038/s41467-024-48658-7] [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: 06/14/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Parental experiences can affect the phenotypic plasticity of offspring. In locusts, the population density that adults experience regulates the number and hatching synchrony of their eggs, contributing to locust outbreaks. However, the pathway of signal transmission from parents to offspring remains unclear. Here, we find that transcription factor Forkhead box protein N1 (FOXN1) responds to high population density and activates the polypyrimidine tract-binding protein 1 (Ptbp1) in locusts. FOXN1-PTBP1 serves as an upstream regulator of miR-276, a miRNA to control egg-hatching synchrony. PTBP1 boosts the nucleo-cytoplasmic transport of pre-miR-276 in a "CU motif"-dependent manner, by collaborating with the primary exportin protein exportin 5 (XPO5). Enhanced nuclear export of pre-miR-276 elevates miR-276 expression in terminal oocytes, where FOXN1 activates Ptbp1 and leads to egg-hatching synchrony in response to high population density. Additionally, PTBP1-prompted nuclear export of pre-miR-276 is conserved in insects, implying a ubiquitous mechanism to mediate transgenerational effects.
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Affiliation(s)
- Ya Nan Zhu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiawen Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hongran Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhuoran Song
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, Hebei University, Baoding, Hebei, 071002, China.
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4
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Dayal S, Chaubey D, Joshi DC, Ranmale S, Pillai B. Noncoding RNAs: Emerging regulators of behavioral complexity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1847. [PMID: 38702948 DOI: 10.1002/wrna.1847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 05/06/2024]
Abstract
The mammalian genome encodes thousands of non-coding RNAs (ncRNAs), ranging in size from about 20 nucleotides (microRNAs or miRNAs) to kilobases (long non-coding RNAs or lncRNAs). ncRNAs contribute to a layer of gene regulation that could explain the evolution of massive phenotypic complexity even as the number of protein-coding genes remains unaltered. We propose that low conservation, poor expression, and highly restricted spatiotemporal expression patterns-conventionally considered ncRNAs may affect behavior through direct, rapid, and often sustained regulation of gene expression at the transcriptional, post-transcriptional, or translational levels. Besides these direct roles, their effect during neurodevelopment may manifest as behavioral changes later in the organism's life, especially when exposed to environmental cues like stress and seasonal changes. The lncRNAs affect behavior through diverse mechanisms like sponging of miRNAs, recruitment of chromatin modifiers, and regulation of alternative splicing. We highlight the need for synthesis between rigorously designed behavioral paradigms in model organisms and the wide diversity of behaviors documented by ethologists through field studies on organisms exquisitely adapted to their environmental niche. Comparative genomics and the latest advancements in transcriptomics provide an unprecedented scope for merging field and lab studies on model and non-model organisms to shed light on the role of ncRNAs in driving the behavioral responses of individuals and groups. We touch upon the technical challenges and contentious issues that must be resolved to fully understand the role of ncRNAs in regulating complex behavioral traits. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Sanovar Dayal
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Divya Chaubey
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dheeraj Chandra Joshi
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Samruddhi Ranmale
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
| | - Beena Pillai
- CSIR-Institute of Genomics and Integrative Biology (IGIB), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Chen Y, Chen Y, Yu XQ, Feng Q, Wang X, Liu L. Expression profiles of lncRNAs, miRNAs, and mRNAs and interaction analysis indicate their potential involvement during testicular fusion in Spodoptera litura. Genomics 2024; 116:110758. [PMID: 38065236 DOI: 10.1016/j.ygeno.2023.110758] [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: 08/25/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024]
Abstract
Testicular fusion of Spodoptera litura occures during metamorphosis, which benefits sperms development. Previous research identified involvement of ECM-integrin interaction pathways, MMPs in testicular fusion, but the regulatory mechanism remains unclear. RNA-seq was performed to analyze long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in testes, aiming to uncover potential regulatory mechanisms of testicular fusion. 2150 lncRNAs, 2742 targeted mRNAs, and 347 miRNAs were identified in testes at three different developmental stages. Up-regulated DElncRNAs and DEmRNAs, as well as down-regulated DEmiRNAs, were observed during testicular fusion, while the opposite expression pattern was observed after fusion. Enrichment analysis of DEmRNAs revealed that cAMP signal pathway, ECM remodeling enzymes, ECM-integrin interaction pathways, and cell adhesion molecules were potentially associated with testicular fusion. The identified DElncRNA-DEmiRNA-DEmRNA regulatory network related to cAMP signal pathway, ECM remodeling enzymes suggests their roles during testicular fusion. Our research will provide new targets for studying the mechanism of testicular fusion.
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Affiliation(s)
- Yaqing Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yu Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiao-Qiang Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Xiaoyun Wang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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6
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Guo B, Li T, Wang L, Liu F, Chen B. Long non-coding RNAs regulate heavy metal-induced apoptosis in embryo-derived cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:121956. [PMID: 37271361 DOI: 10.1016/j.envpol.2023.121956] [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: 11/23/2022] [Revised: 05/14/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
Heavy metal pollution has been a worldwide prevalent problem, and particularly a threat to ecosystem integrity and animals' health. Previous studies on the mechanisms of heavy metal toxicity have focused on protein-coding genes, whereas most genomic transcripts are long non-coding RNAs (lncRNAs). Although lncRNAs are known to play important regulatory roles in biological processes, their role in heavy metal stress regulation is still not fully understood. We here developed an insect embryo cell model for studying metal toxicity and the underlying regulatory mechanisms. We performed genome-wide screening and functional characterization of lncRNAs induced by two essential and two non-essential heavy metals in Drosophila embryo-derived S2 cells. We identified 4894 lncRNAs, of which 1410 were novel. Forty-one lncRNAs, together with 328 mRNAs, were induced by all the four heavy metals. LncRNA-mRNA co-expression network and pathway enrichment analysis showed that detoxification metabolism, circadian rhythm, and apoptosis regulation pathways were activated in response to heavy metal stress. LncRNA CR44138 was remarkably upregulated in cells exposed to the four heavy metals and was associated with the apoptosis pathway. Expression interference confirmed that CR44138 aggravated cytotoxicity-induced apoptosis in cells under heavy metals stress. This study highlights the important role of lncRNAs in regulating the cellular response to heavy metals. This study also lays the foundation for discovering the novel regulatory mechanisms and developing diagnostic biomarkers of the toxic effects of heavy metal pollutants on organisms.
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Affiliation(s)
- Boyang Guo
- College of Life Science, Hebei University, Baoding 071002, China
| | - Ting Li
- School of Life Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, 271016, Shandong Province, China
| | - Lingyan Wang
- College of Life Science, Hebei University, Baoding 071002, China
| | - Fengsong Liu
- College of Life Science, Hebei University, Baoding 071002, China
| | - Bing Chen
- College of Life Science, Hebei University, Baoding 071002, China.
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7
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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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Cytosolic and mitochondrial ribosomal proteins mediate the locust phase transition via divergence of translational profiles. Proc Natl Acad Sci U S A 2023; 120:e2216851120. [PMID: 36701367 PMCID: PMC9945961 DOI: 10.1073/pnas.2216851120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The phase transition from solitary to gregarious locusts is crucial in outbreaks of locust plague, which threaten agricultural yield and food security. Research on the regulatory mechanisms of phase transition in locusts has focused primarily on the transcriptional or posttranslational level. However, the translational regulation of phase transition is unexplored. Here, we show a phase-dependent pattern at the translation level, which exhibits different polysome profiles between gregarious and solitary locusts. The gregarious locusts exhibit significant increases in 60S and polyribosomes, while solitary locusts possess higher peaks of the monoribosome and a specific "halfmer." The polysome profiles, a molecular phenotype, respond to changes in population density. In gregarious locusts, ten genes involved in the cytosolic ribosome pathway exhibited increased translational efficiency (TE). In solitary locusts, five genes from the mitochondrial ribosome pathway displayed increased TE. The high expression of large ribosomal protein 7 at the translational level promotes accumulation of the free 60S ribosomal subunit in gregarious locusts, while solitary locusts employ mitochondrial small ribosomal protein 18c to induce the assembly of mitochondrial ribosomes, causing divergence of the translational profiles and behavioral transition. This study reveals the translational regulatory mechanism of locust phase transition, in which the locusts employ divergent ribosome pathways to cope with changes in population density.
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Glutamate-GABA imbalance mediated by miR-8-5p and its STTM regulates phase-related behavior of locusts. Proc Natl Acad Sci U S A 2023; 120:e2215660120. [PMID: 36574679 PMCID: PMC9910461 DOI: 10.1073/pnas.2215660120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The aggregation of locusts from solitary to gregarious phases is crucial for the formation of devastating locust plagues. Locust management requires research on the prevention of aggregation or alternative and greener solutions to replace insecticide use, and insect-derived microRNAs (miRNAs) show the potential for application in pest control. Here, we performed a genome-wide screen of the differential expression of miRNAs between solitary and gregarious locusts and showed that miR-8-5p controls the γ-aminobutyric acid (GABA)/glutamate functional balance by directly targeting glutamate decarboxylase (Gad). Blocking glutamate-GABA neurotransmission by miR-8-5p overexpression or Gad RNAi in solitary locusts decreased GABA production, resulting in locust aggregation behavior. Conversely, activating this pathway by miR-8-5p knockdown in gregarious locusts induced GABA production to eliminate aggregation behavior. Further results demonstrated that ionotropic glutamate/GABA receptors tuned glutamate/GABA to trigger/hamper the aggregation behavior of locusts. Finally, we successfully established a transgenic rice line expressing the miR-8-5p inhibitor by short tandem target mimic (STTM). When locusts fed on transgenic rice plants, Gad transcript levels in the brain increased greatly, and aggregation behavior was lost. This study provided insights into different regulatory pathways in the phase change of locusts and a potential control approach through behavioral regulation in insect pests.
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10
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Liu K, Yuan L, Yue L, Chen W, Kang K, Lv J, Zhang W, Pang R. Population density modulates insect progenitive plasticity through the regulation of dopamine biosynthesis. INSECT SCIENCE 2022; 29:1773-1789. [PMID: 35230747 DOI: 10.1111/1744-7917.13019] [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: 10/20/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Insect fecundity is a quantitative phenotype strongly affected by genotypes and the environment. However, interactions between genotypes and environmental factors in modulating insect fecundity remain largely unknown. This study investigated the impact of population density on the fecundity of Nilaparvata lugens (brown planthopper; BPH) carrying homozygous high- (HFG) or low- (LFG) fecundity homozygous genotypes. Under low population densities, the fecundity and population growth rate of both genotypes showed similar increasing trends across generations, while the trends between HFG and LFG under high population densities were opposite. Through a combination of temporal analysis and weighted gene co-expression network analyses on RNA-seq data of HFG and LFG under low and high population densities in the 1st, 3rd, and 5th generations, we identified 2 gene modules that were associated with these density-dependent progenitive phenotypes. Four pathways related to the neural system were simultaneously enriched by the 2 gene modules. Furthermore, Nlpale, which encodes a tyrosine hydroxylase, was identified as a key gene. The RNA interference of this gene and manipulation of its downstream product dopamine significantly affected the basic and density-dependent progenitive phenotypes of BPH. These findings indicated that dopamine biosynthesis is the key regulatory factor that determines fecundity in response to density changes in different BPH genotypes. Thus, this study provides insights into the interaction of a typical environmental factor and insect genotype during the process of population regulation.
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Affiliation(s)
- Kai Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Innovative Institute for Plant Health, College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Longyu Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lei Yue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Weiwen Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Kui Kang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jun Lv
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Rui Pang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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11
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Alvarenga AB, Oliveira HR, Miller SP, Silva FF, Brito LF. Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits. Front Genet 2022; 13:794625. [PMID: 35444687 PMCID: PMC9014094 DOI: 10.3389/fgene.2022.794625] [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: 10/13/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen's safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1-6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal-human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.
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Affiliation(s)
- Amanda B Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Stephen P Miller
- American Angus Association, Angus Genetics Inc., St Joseph, MO, United States
| | - Fabyano F Silva
- Department of Animal Sciences, Federal University of Vicosa, Viçosa, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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12
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Zhang X, Zhu YN, Chen B, Kang L. A Gypsy element contributes to the nuclear retention and transcriptional regulation of the resident lncRNA in locusts. RNA Biol 2022; 19:206-220. [PMID: 35067197 PMCID: PMC8786324 DOI: 10.1080/15476286.2021.2024032] [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] [Indexed: 11/17/2022] Open
Abstract
The majority of long noncoding RNAs (lncRNAs) contain transposable elements (TEs). PAHAL, a nuclear-retained lncRNA that is inserted by a Gypsy retrotransposon, has been shown to be a vital regulator of phenylalanine hydroxylase (PAH) gene expression that controls dopamine biosynthesis and behavioural aggregation in the migratory locust. However, the role of the Gypsy retrotransposon in the transcriptional regulation of PAHAL remains unknown. Here, we identified a Gypsy retrotransposon (named Gypsy element) as an inverted long terminal repeat located in the 3′ end of PAHAL, representing a feature shared by many other lncRNAs in the locust genome. The embedded Gypsy element contains a RNA nuclear localization signal motif, which promotes the stable accumulation of PAHAL in the nucleus. The Gypsy element also provides high-affinity SRSF2 binding sites for PAHAL that induce the recruitment of SRSF2, resulting in the PAHAL-mediated transcriptional activation of PAH. Thus, our data demonstrate that TEs provide discrete functional domains for lncRNA organization and highlight the contribution of TEs to the regulatory significance of lncRNAs.
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Affiliation(s)
- Xia Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Ya Nan Zhu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Bing Chen
- School of Life Sciences, Hebei University, Baoding, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.,School of Life Sciences, Hebei University, Baoding, China.,Beijing Institute of Life Sciences, Chinese Academy of Sciences, Beijing, China
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13
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Shang F, Ding BY, Zhang YT, Wu JJ, Pan ST, Wang JJ. Genome-wide analysis of long non-coding RNAs and their association with wing development in Aphis citricidus (Hemiptera: Aphididae). INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 139:103666. [PMID: 34619323 DOI: 10.1016/j.ibmb.2021.103666] [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: 06/03/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) play critical roles in the various physiological processes of insects. The wing is a successful adaptation allowing insects to escape from unfavorable environments, while information on lncRNAs related to wing development is limited. In this study, we constructed 12 libraries from two RNA-seq comparisons: 4th instar winged nymphs versus winged adults and 4th instar wingless nymphs versus wingless adults in the brown citrus aphid Aphis citricidus, to identify the wing development-associated lncRNAs. A total of 2914 lncRNAs were identified and 50 lncRNAs were differentially expressed during the 4th instar winged nymphs to winged adults transition, and 28 lncRNAs changed during the 4th instar wingless nymphs to wingless adults transition. The differentially expressed lncRNAs were grouped into six clusters according to the expression patterns in the combined two-winged morphs. lncRNA Ac_lnc54106.1 was up-regulated during 4th instar winged nymphs to winged adults transition, but a lack of change during the 4th instar wingless nymphs to wingless adults transition implied a critical role in the specific regulation of wing development. RNA interference of Ac_lnc54106.1 resulted in malformed wings. Targets prediction, expression patterns, and RNAi assay results showed that Ac_lnc54106.1 may target the PiggyBac transposable element-derived protein 4 (PGBD4) gene, decrease expression of the canonical wing development-related genes, and finally regulate wing development. The systematic identification of lncRNAs in an aphid increases our understanding of how non-coding RNA mediates the wing plasticity of insects.
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Affiliation(s)
- Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
| | - Yong-Te Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Jin-Jin Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Si-Tong Pan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China.
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400716, China; State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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14
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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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15
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Dai Z, Ren J, Tong X, Hu H, Lu K, Dai F, Han MJ. The Landscapes of Full-Length Transcripts and Splice Isoforms as Well as Transposons Exonization in the Lepidopteran Model System, Bombyx mori. Front Genet 2021; 12:704162. [PMID: 34594358 PMCID: PMC8476886 DOI: 10.3389/fgene.2021.704162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
The domesticated silkworm, Bombyx mori, is an important model system for the order Lepidoptera. Currently, based on third-generation sequencing, the chromosome-level genome of Bombyx mori has been released. However, its transcripts were mainly assembled by using short reads of second-generation sequencing and expressed sequence tags which cannot explain the transcript profile accurately. Here, we used PacBio Iso-Seq technology to investigate the transcripts from 45 developmental stages of Bombyx mori. We obtained 25,970 non-redundant high-quality consensus isoforms capturing ∼60% of previous reported RNAs, 15,431 (∼47%) novel transcripts, and identified 7,253 long non-coding RNA (lncRNA) with a large proportion of novel lncRNA (∼56%). In addition, we found that transposable elements (TEs) exonization account for 11,671 (∼45%) transcripts including 5,980 protein-coding transcripts (∼32%) and 5,691 lncRNAs (∼79%). Overall, our results expand the silkworm transcripts and have general implications to understand the interaction between TEs and their host genes. These transcripts resource will promote functional studies of genes and lncRNAs as well as TEs in the silkworm.
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Affiliation(s)
- Zongrui Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, China.,WESTA College, Southwest University, Chongqing, China
| | - Jianyu Ren
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, China
| | - Kunpeng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, China
| | - Min-Jin Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, China
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16
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Yang L, Wang YW, Lu YY, Li B, Chen KP, Li CJ. Genome-wide identification and characterization of long non-coding RNAs in Tribolium castaneum. INSECT SCIENCE 2021; 28:1262-1276. [PMID: 32978885 DOI: 10.1111/1744-7917.12867] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/19/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
Long non-coding RNAs (lncRNAs) are poorly understood in insects. In this study, we performed genome-wide analysis of lncRNAs in Tribolium castaneum by RNA-seq. In total, 4516 lncRNA transcripts corresponding to 3917 genes were identified from late embryos, early larvae, late larvae, early pupae, late pupae and early adults of T. castaneum, including 3152 novel lncRNAs and 1364 known lncRNAs. These lncRNAs have few exons and transcripts, and are short in length. During development, they exhibited nine different expression patterns. Functionally, they can act either by targeting messenger RNAs (1813 lncRNAs) and lncRNAs (45 lncRNAs) or as micro RNA (miRNA) precursors (46 lncRNAs). LncRNAs were observed to target the metabolic enzymes of glycolysis, TCA cycle and amino acids, demonstrating that lncRNAs control metabolism by regulating metabolic enzymes. Moreover, lncRNAs were shown to participate in cell differentiation and development via their targets. As miRNA precursors, lncRNAs could participate in the ecdysone signaling pathway. This study provides comprehensive information for lncRNAs of T. castaneum, and will promote functional analysis and target identification of lncRNAs in the insect.
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Affiliation(s)
- Liu Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, China
| | - You-Wei Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, China
| | - Yao-Yao Lu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ke-Ping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, China
| | - Cheng-Jun Li
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, China
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17
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Fischer EK, Hauber ME, Bell AM. Back to the basics? Transcriptomics offers integrative insights into the role of space, time and the environment for gene expression and behaviour. Biol Lett 2021; 17:20210293. [PMID: 34520681 DOI: 10.1098/rsbl.2021.0293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Fuelled by the ongoing genomic revolution, broadscale RNA expression surveys are fast replacing studies targeting one or a few genes to understand the molecular basis of behaviour. Yet, the timescale of RNA-sequencing experiments and the dynamics of neural gene activation are insufficient to drive real-time switches between behavioural states. Moreover, the spatial, functional and transcriptional complexity of the brain (the most commonly targeted tissue in studies of behaviour) further complicates inference. We argue that a Central Dogma-like 'back-to-basics' assumption that gene expression changes cause behaviour leaves some of the most important aspects of gene-behaviour relationships unexplored, including the roles of environmental influences, timing and feedback from behaviour-and the environmental shifts it causes-to neural gene expression. No perfect experimental solutions exist but we advocate that explicit consideration, exploration and discussion of these factors will pave the way toward a richer understanding of the complicated relationships between genes, environments, brain gene expression and behaviour over developmental and evolutionary timescales.
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Affiliation(s)
- Eva K Fischer
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
| | - Alison M Bell
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801, USA
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18
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Meng LW, Yuan GR, Chen ML, Dou W, Jing TX, Zheng LS, Peng ML, Bai WJ, Wang JJ. Genome-wide identification of long non-coding RNAs (lncRNAs) associated with malathion resistance in Bactrocera dorsalis. PEST MANAGEMENT SCIENCE 2021; 77:2292-2301. [PMID: 33423365 DOI: 10.1002/ps.6256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/09/2020] [Accepted: 01/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play important roles in the regulation of biological processes and have been identified in many species including insects. However, the association between lncRNAs and pesticide resistance in insect species such as Bactrocera dorsalis is unknown. RESULTS RNA-seq was performed on malathion resistant (MR1) and susceptible (MS) strains of B. dorsalis and a total of 6171 lncRNAs transcripts were identified. These included 3728 lincRNAs, 653 antisense lncRNAs, 1402 intronic lncRNAs, and 388 sense lncRNAs. A total of 40 and 52 upregulated lncRNAs were found in females and males of the MR1 strain compared to 54 and 49 in the same sexes of the MS strain, respectively. Twenty-seven of these lncRNAs showed the same trend of expression in both females and males in the MR1 strain, in which 15 lncRNAs were upregulated and 12 were downregulated. RT-qPCR results indicated that the differentially expressed lncRNAs were associated with malathion resistance. The lnc15010.10 and lnc3774.2 were highly expressed in the cuticle of the MR1 strain, indicating that these two lncRNAs may be related to malathion resistance. RNAi of lnc3774.2 and a bioassay showed that malathion resistance was possibly influenced by changes in the B. dorsalis cuticle. CONCLUSION LncRNAs of B. dorsalis potentially related to the malathion resistance were identified. Two lncRNAs appear to influence malathion resistance via modulating the structure, or components, of the cuticle. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Li-Wei Meng
- 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
| | - Guo-Rui Yuan
- 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
| | - Meng-Ling Chen
- 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
| | - Wei Dou
- 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
| | - Tian-Xing Jing
- 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
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Li-Sha Zheng
- 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
| | - Meng-Lan Peng
- 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
| | - Wen-Jie Bai
- 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
| | - Jin-Jun Wang
- 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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19
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Li WJ, Song YJ, Han HL, Xu HQ, Wei D, Smagghe G, Wang JJ. Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). BMC Genomics 2020; 21:600. [PMID: 32867696 PMCID: PMC7457495 DOI: 10.1186/s12864-020-07014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/20/2020] [Indexed: 12/14/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited. Results We constructed 24 RNA-seq libraries from eight tissues (midgut, Malpighian tubules, fat body, ovary, and testis) of Z. cucurbitae adults. A total of 3124 lncRNA transcripts were identified. Among those, 1464 were lincRNAs, 1037 were intronic lncRNAs, 301 were anti-sense lncRNAs, and 322 were sense lncRNAs. The majority of lncRNAs contained two exons and one isoform. Differentially expressed lncRNAs were analyzed between tissues, and Malpighian tubules versus testis had the largest number. Some lncRNAs exhibited strong tissue specificity. Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. cucurbitae based on their expression levels. Four midgut-specific lncRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR), and the data were consistent with RNA-seq data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process. Conclusions This was the first systematic identification of lncRNA in the melon fly. Expressions of lncRNAs in multiple adult tissues were evaluated by quantitative transcriptomic analysis. These qualitative and quantitative analyses of lncRNAs, especially the tissue-specific lncRNAs in Z. cucurbitae, provide useful data for further functional studies.
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Affiliation(s)
- Wei-Jun Li
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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, 400715, China
| | - Yu-Jia Song
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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, 400715, China
| | - Hong-Liang Han
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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, 400715, China
| | - Hui-Qian Xu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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, 400715, China
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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, 400715, China
| | - Guy Smagghe
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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, 400715, China. .,Department of Plants and Crops, Ghent University, 9000, Ghent, Belgium.
| | - Jin-Jun Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, 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, 400715, China.
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