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Hu C, Deng B, Fang W, Guo B, Chen P, Lu C, Dong Z, Pan M. Transgenic overexpression of bmo-miR-6498-5p increases resistance to Nosema bombycis in the silkworm, Bombyx mori. Appl Environ Microbiol 2024:e0027024. [PMID: 39240120 DOI: 10.1128/aem.00270-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/23/2024] [Indexed: 09/07/2024] Open
Abstract
Microsporidia are unfriendly microorganisms, and their infections cause considerable damage to economically or environmentally important insects like silkworms and honeybees. Thus, the identification of measures to improve host resistance to microsporidia infections is critically needed. Here, an overexpressed miR-6498-5p transgenic silkworm line was constructed. Importantly, the survival rates and median lethal doses of the transgenic line were clearly higher after infection with Nosema bombycis. H&E staining and RT-qPCR analyses revealed an inhibitory effect on the proliferation of N. bombycis in the transgenic larvae. Metabolomics analysis further revealed the presence of 56 differential metabolites between the two lines. KEGG analysis of these 56 metabolites found that they were involved in various amino acid and vitamin metabolism pathways. Notably, VB6 metabolism was enriched among the metabolites, and the pathway was well known for its involvement in the synthesis, interconversion, and degradation of amino acids. These suggest that miR-6498-5p modifies parasitic environments to inhibit the proliferation of N. bombycis by affecting the host amino acid metabolism. These results demonstrate the potential of microRNAs as biomolecules that can promote resistance to microsporidia and provide new insights and a new approach to generate microsporidia-resistant biological materials.IMPORTANCEMicrosporidia have an extremely wide host range and are capable of infecting a wide variety of insects and vertebrates, including humans, and their lethality to multiple species often poses significant environmental management challenge. Here, we successfully constructed a microsporidium-resistant line in the silkworm, based on the overexpression of miR-6498-5p. Our results strongly support the hypothesis that miR-6498-5p efficiently suppresses the proliferation of Nosema bombycis by regulating the host VB6 metabolism, a key pathway for enzymes involved in amino acid transport and protein metabolism. Our study provides new insights for understanding host anti-pathogen defenses toward microsporidia.
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Affiliation(s)
- Congwu Hu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- School of Chemical Engineering, Sichuan University of Science & Engineering, Zigong, Sichuan, China
| | - Boyuan Deng
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Wenxuan Fang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Bingyu Guo
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
| | - Peng Chen
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Cheng Lu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Zhanqi Dong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
| | - Minhui Pan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Chongqing, China
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Reynolds JA. MicroRNAs in the developmental toolbox - a comparative approach to understanding their role in regulating insect development. CURRENT OPINION IN INSECT SCIENCE 2024; 66:101256. [PMID: 39214418 DOI: 10.1016/j.cois.2024.101256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/10/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
MicroRNAs are ubiquitous in the genomes of metazoans. Since their discovery during the late 20th century, our understanding of these small, noncoding RNAs has grown rapidly. However, there are still many unknowns about the functional significance of miRNAs - especially in non-model insects. Here I discuss the accumulating evidence that microRNAs are part of gene regulatory networks that determine not only the developmental outcome but also mediate transitions between stages and alternative developmental pathways. During the last 20 years, researchers have published a multitude of profiling studies that describe changes in miRNAs that may be important for development and catalog potential targets. Proof-of-principle studies document phenotypic changes that occur when candidate genes and/or miRNAs are inhibited or overexpressed. Studies that use both of these approaches, along with methods for confirming miRNA-mRNA interaction, demonstrate the necessary roles for miRNAs within gene networks. Together, all of these types of studies provide essential clues for understanding the function of miRNAs in the developmental toolbox.
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Affiliation(s)
- Julie A Reynolds
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA.
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Wang YP, Chen XY, Pu DQ, Yi CY, Liu CH, Zhang CC, Wei ZZ, Guo JW, Yu WJ, Chen S, Liu HL. Identification and Prediction of Differentially Expressed MicroRNAs Associated with Detoxification Pathways in Larvae of Spodoptera frugiperda. Genes (Basel) 2024; 15:1021. [PMID: 39202382 PMCID: PMC11353827 DOI: 10.3390/genes15081021] [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: 07/06/2024] [Revised: 07/29/2024] [Accepted: 08/02/2024] [Indexed: 09/03/2024] Open
Abstract
Spodoptera frugiperda poses a severe threat to crops, causing substantial economic losses. The increased use of chemical pesticides has led to resistance in S. frugiperda populations. Micro ribonucleic acids (MicroRNAs or miRNAs) are pivotal in insect growth and development. This study aims to identify miRNAs across different developmental stages of S. frugiperda to explore differential expression and predict target gene functions. High-throughput sequencing of miRNAs was conducted on eggs, 3rd instar larvae, pupae, and adults. Bioinformatics analyses identified differentially expressed miRNAs specifically in larvae, with candidate miRNAs screened to predict target genes, particularly those involved in detoxification pathways. A total of 184 known miRNAs and 209 novel miRNAs were identified across stages. Comparative analysis revealed 54, 15, and 18 miRNAs differentially expressed in larvae, compared to egg, pupa, and adult stages, respectively. Eight miRNAs showed significant differential expression across stages, validated by quantitative reverse transcription PCR (qRT-PCR). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses predicted target genes' functions, identifying eight differentially expressed miRNAs targeting 10 gene families associated with detoxification metabolism, including P450s, glutathione S-transferase (GSTs), ATP-binding cassette (ABC) transporters, and sodium channels. These findings elucidate the species-specific miRNA profiles and regulatory mechanisms of detoxification-related genes in S. frugiperda larvae, offering insights and strategies for effectively managing this pest.
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Affiliation(s)
- Yan-Ping Wang
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Xing-Yu Chen
- Science and Technology Security Center, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China;
| | - De-Qiang Pu
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Chun-Yan Yi
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Chang-Hua Liu
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Cui-Cui Zhang
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Zhen-Zhen Wei
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Jing-Wei Guo
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Wen-Juan Yu
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Song Chen
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
| | - Hong-Ling Liu
- Key Laboratory of Integrated Pest Management of Southwest Crops, Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China; (Y.-P.W.); (D.-Q.P.); (C.-Y.Y.); (C.-H.L.); (C.-C.Z.); (Z.-Z.W.); (J.-W.G.); (W.-J.Y.); (S.C.)
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Zhang R, Liu W, Zhang Z. miR-306-5p is involved in chitin metabolism in Aedes albopictus pupae via linc8338-miR-306-5p-XM_019678125.2 axis. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 200:105811. [PMID: 38582583 DOI: 10.1016/j.pestbp.2024.105811] [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: 09/13/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 04/08/2024]
Abstract
Aedes albopictus can transmit several lethal arboviruses. This mosquito has become a sever public health threat due to its rapidly changing global distribution. Chitin, which is the major component of the cuticle and peritrophic membrane (PM), is crucial for the growth and development of insect. microRNAs (miRNAs) play important roles in the posttranscriptional level regulation of gene expression, thereby influencing many biological processes in insects. In this study, an attempt was made to evaluate the role of miR-306-5p in regulating chitin metabolism in Ae. albopictus pupae. Overexpression of miR-306-5p resulted in a significantly reduced survival rate in pupae and an increased malformation rate in adults. Both in vivo and in vitro evidence confirmed the presence of the competing endogenous RNA (ceRNA) regulatory axis (linc8338-miR-306-5p-XM_019678125.2). RNAi of linc8338 and XM_019678125.2 had effects on pupae similar to those of miR-306-5p. The highest expression level of miR-306-5p was found in the midgut, and alteration in the expression of miR-306-5p, XM_019678125.2 and linc8338 induced increased transcript levels of chitin synthase 2 (AaCHS2) and decreased chitinase 10 (AaCht10); as well as increased thickness of the midgut and enlarged midgut epithelial cells. The results of this study highlight the potential of miR-306-5p as a prospective target in mosquito control and confirm that the ceRNA mechanism is involved in chitin metabolism. These findings will provide a basis for further studies to uncover the molecular mechanisms through which ncRNAs regulate chitin metabolism.
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Affiliation(s)
- Ruiling Zhang
- School of Clinical and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan 250117, China; School of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan 250117, China.
| | - Wenjuan Liu
- School of Clinical and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan 250117, China
| | - Zhong Zhang
- School of Clinical and Basic Medical Science, Shandong First Medical University (Shandong Academy of Medical Sciences), Jinan 250117, China.
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5
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Asad S, Mehdi AM, Pujhari S, Rückert C, Ebel GD, Rasgon JL. Identification of MicroRNAs in the West Nile Virus Vector Culex tarsalis (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY 2023; 60:182-293. [PMID: 36477983 PMCID: PMC10216877 DOI: 10.1093/jme/tjac182] [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: 05/09/2022] [Indexed: 05/28/2023]
Abstract
MicroRNAs (miRNAs) are a group of small noncoding RNAs that regulate gene expression during important biological processes including development and pathogen defense in most living organisms. Presently, no miRNAs have been identified in the mosquito Culex tarsalis (Diptera: Culicidae), one of the most important vectors of West Nile virus (WNV) in North America. We used small RNA sequencing data and in vitro and in vivo experiments to identify and validate a repertoire of miRNAs in Cx. tarsalis mosquitoes. Using bioinformatic approaches we analyzed small RNA sequences from the Cx. tarsalis CT embryonic cell line to discover orthologs for 86 miRNAs. Consistent with other mosquitoes such as Aedes albopictus and Culex quinquefasciatus, miR-184 was found to be the most abundant miRNA in Cx. tarsalis. We also identified 20 novel miRNAs from the recently sequenced Cx. tarsalis genome, for a total of 106 miRNAs identified in this study. The presence of selected miRNAs was biologically validated in both the CT cell line and in adult Cx. tarsalis mosquitoes using RT-qPCR and sequencing. These results will open new avenues of research into the role of miRNAs in Cx. tarsalis biology, including development, metabolism, immunity, and pathogen infection.
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Affiliation(s)
- Sultan Asad
- Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Ahmed M Mehdi
- The University of Queensland, Brisbane, Australia Diamantina Institute, Faculty of Medicine, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Sujit Pujhari
- Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Pharmacology Physiology and Neuroscience, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Claudia Rückert
- Department of Biochemistry and Molecular Biology, University of Nevada Reno, Reno, NV, 89557, USA
- Department of Microbiology, Immunology and Pathology, Center for Vector-borne Infectious Diseases, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USAand
| | - Gregory D Ebel
- Department of Microbiology, Immunology and Pathology, Center for Vector-borne Infectious Diseases, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USAand
| | - Jason L Rasgon
- Department of Entomology, The Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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6
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Wang N, Zhang C, Chen M, Shi Z, Zhou Y, Shi X, Zhou W, Zhu Z. Characterization of MicroRNAs Associated with Reproduction in the Brown Planthopper, Nilaparvata lugens. Int J Mol Sci 2022; 23:7808. [PMID: 35887156 PMCID: PMC9316625 DOI: 10.3390/ijms23147808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Insects have a robust capacity to produce offspring for propagation, and the reproductive events of female insects have been achieved at the molecular and physiological levels via regulatory gene pathways. However, the roles of MicroRNAs (miRNAs) in the reproductive development of the brown planthopper (BPH), Nilaparvata lugens, remain largely unexplored. To understand the roles of miRNAs in reproductive development, miRNAs were identified by Solexa sequencing in short-winged (SW) female adults of BPH. Small RNA libraries derived from three developmental phases (1 day, 3 days, and 5 days after emergence) were constructed and sequenced. We identified 905 miRNAs, including 263 known and 642 novel miRNAs. Among them, a total of 43 miRNAs were differentially expressed in the three developmental phases, and 14,568 putative targets for 43 differentially expressed miRNAs (DEMs) were predicted by TargetScan and miRanda. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the predicted miRNA targets illustrated the putative roles for these DEMs in reproduction. The progress events were annotated, including oogenesis, lipid biosynthetic process, and related pathways such as apoptosis, ABC transporters, and amino acid metabolism. Four highly abundant DEMs (miR-9a-5p, miR-34-5p, miR-275-3p, and miR-317-3p) were further screened, and miR-34-5p was confirmed to be involved in the regulation of reproduction. Overexpression of miR-34-5p via injecting its mimics reduced fecundity and decreased Vg expression. Moreover, target genes prediction for miR-34-5p showed they might be involved in 20E signaling cascades, apoptosis, and gonadal development, including hormone receptor 4 (HR4), caspase-1 (Cp-1), and spermatogenesis-associated protein 20 (SPATA20). These findings provide a valuable resource for future studies on the role of miRNAs in BPH reproductive development.
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Affiliation(s)
- Ni Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (N.W.); (C.Z.); (M.C.); (Z.S.); (X.S.); (W.Z.)
- Hainan Research Institute, Zhejiang University, Sanya 572000, China;
| | - Chao Zhang
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (N.W.); (C.Z.); (M.C.); (Z.S.); (X.S.); (W.Z.)
- Hainan Research Institute, Zhejiang University, Sanya 572000, China;
| | - Min Chen
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (N.W.); (C.Z.); (M.C.); (Z.S.); (X.S.); (W.Z.)
- Hainan Research Institute, Zhejiang University, Sanya 572000, China;
| | - Zheyi Shi
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (N.W.); (C.Z.); (M.C.); (Z.S.); (X.S.); (W.Z.)
- Hainan Research Institute, Zhejiang University, Sanya 572000, China;
| | - Ying Zhou
- Hainan Research Institute, Zhejiang University, Sanya 572000, China;
| | - Xiaoxiao Shi
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (N.W.); (C.Z.); (M.C.); (Z.S.); (X.S.); (W.Z.)
| | - Wenwu Zhou
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (N.W.); (C.Z.); (M.C.); (Z.S.); (X.S.); (W.Z.)
- Hainan Research Institute, Zhejiang University, Sanya 572000, China;
| | - Zengrong Zhu
- State Key Laboratory of Rice Biology, Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects Pests, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (N.W.); (C.Z.); (M.C.); (Z.S.); (X.S.); (W.Z.)
- Hainan Research Institute, Zhejiang University, Sanya 572000, China;
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Deng Z, Zhang Y, Li L, Xie X, Huang J, Zhang M, Ni X, Li X. A dual-luciferase reporter system for characterization of small RNA target genes in both mammalian and insect cells. INSECT SCIENCE 2022; 29:631-644. [PMID: 34232550 DOI: 10.1111/1744-7917.12945] [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: 04/13/2021] [Revised: 06/04/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs) are regulatory RNA molecules that bind to target messenger RNAs (mRNAs) and affect the stability or translational efficiency of the bound mRNAs. Single or dual-luciferase reporter systems have been successfully used to identify miRNA target genes in mammalian cells. These reporter systems, however, are not sensitive enough to verify miRNA-target gene relationships in insect cell lines because the promoters of the target luciferase (usually Renilla) used in these reporter systems are too weak to drive sufficient expression of the target luciferase in insect cells. In this study, we replaced the SV40 promoter in the psiCHECK-2 reporter vector, which is widely used with mammalian cell lines, with the HSV-TK or AC5.1 promoter to yield two new dual-luciferase reporter vectors, designated psiCHECK-2-TK and psiCHECK-2-AC5.1, respectively. Only psiCHECK-2 and psiCHECK-2-AC5.1 had suitable target (Renilla)/reference (firefly) luciferase activity ratios in mammalian (HeLa and HEK293) and insect (Sf9, S2, Helicoverpa zea fat body and ovary) cell lines, while psiCHECK-2-TK had suitable Renilla/firefly luciferase activity ratios regardless of the cell line. Moreover, psiCHECK-2-TK successfully detected the interaction between Helicoverpa armigera miRNA9a and its target, the 3'-untranslated region of heat shock protein 90, in both mammalian and H. zea cell lines, but psiCHECK-2 failed to do so in H. zea cell lines. Furthermore, psiCHECK-2-TK with the target sequence, HzMasc (H. zea Masculinizer), accurately differentiated between H. zea cell lines with or without the negative regulation factor (miRNA or piRNA) of HzMasc. These data demonstrate that psiCHECK-2-TK can be used to functionally characterize small RNA target genes in both mammalian and insect cells.
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Affiliation(s)
- Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuting Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Leyao Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xingcheng Xie
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinyong Huang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Min Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Xinzhi Ni
- USDA-ARS, Crop Genetics and Breeding Research Unit, University of Georgia-Tifton Campus, Tifton, Georgia, USA
| | - Xianchun Li
- Department of Entomology and BIO5 Institute, University of Arizona, Tucson, Arizona, USA
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8
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Villagra C, Frías-Lasserre D. Epigenetic Molecular Mechanisms in Insects. NEOTROPICAL ENTOMOLOGY 2020; 49:615-642. [PMID: 32514997 DOI: 10.1007/s13744-020-00777-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.
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Affiliation(s)
- C Villagra
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - D Frías-Lasserre
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile
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9
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Liu W, Guo J, Luo J, Ren Q, Chen Z, Qu Z, Wu Z, Ni J, Xu X, Rashid M, Luo J, Yin H, Yang Z, Liu G. Analysis of microRNA expression profiles dynamic in different life stages of Haemaphysalis longicornis ticks by deep sequencing of small RNA libraries. Ticks Tick Borne Dis 2020; 11:101427. [PMID: 32370927 DOI: 10.1016/j.ttbdis.2020.101427] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 03/18/2020] [Accepted: 03/23/2020] [Indexed: 10/24/2022]
Abstract
The three-host tick Haemaphysalis longicornis is an obligate blood-sucking ectoparasite. In life-stage transitions, microRNAs (miRNAs) show a variety of expression changes. To investigate these changes, deep sequencing technology was applied to identify the conserved and potentially novel miRNAs expressed during the different life stages of H. longicornis. Total RNA from eggs, unfed larvae, unfed nymphs and unfed adults was extracted for deep sequence analysis. Deep sequencing on a Hiseq 4000 generated a total of 111,192,069 reads, grouped into four small RNA (sRNA) libraries, one for each of the four developmental stages of H. longicornis. Among these sequences, 78 conserved and 55 potentially novel miRNAs were identified, including stage-specific and differentially expressed miRNAs. Gene ontology (GO) analysis indicated significantly enriched GO terms related to cell proliferation and differentiation, including specific terms for the processes of development, growth, metabolism, regulation of biological functions, reproduction, and membrane enzyme regular activity. Kyoto Encyclopedia of Gene and Genomes (KEGG) analysis revealed a significant enrichment of the insulin, notch, Hippo, and Wnt signaling pathways for growth and development. Our data highlight the abundance of miRNA changes (conserved and potentially novel) in the different life stages of H. longicornis. In particular, stage-specific miRNAs, as observed, are essential regulators for the development of H. longicornis.
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Affiliation(s)
- Wenge Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China; College of Animal Veterinary Medicine, Northwest A & F University, Yangling, China.
| | - Junhui Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Jin Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Qiaoyun Ren
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Ze Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Zhiqiang Qu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Zegong Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Jun Ni
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Xiaofeng Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Muhammad Rashid
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
| | - Hong Yin
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
| | - Zengqi Yang
- College of Animal Veterinary Medicine, Northwest A & F University, Yangling, China.
| | - Guangyuan Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Science, Lanzhou, China.
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10
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Qian P, Wang X, Li J, Jiang T, Tang X, Huixiang G, Shen X. Bmo-miR-2780a regulates the expression of the sericin-1 gene of Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21627. [PMID: 31701579 DOI: 10.1002/arch.21627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/31/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Silk production in Bombyx mori L. is largely determined by the expression of genes encoding fibroin and sericin. Here, we examined the regulatory function of a microRNA (miRNA) on silk gene expression using the sericin-1 gene (BmSer-1). First, we downloaded whole mature miRNAs of silkworm from miRBase and identified bmo-miR-2780a as a candidate miRNA for the regulation of BmSer-1 expression. We used semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) with stem-loop primers to investigate the expression profile of bmo-miR-2780a and its predicted target gene BmSer-1 in seven different tissues from 5th instar day-3 larvae, including head, fat body, anterior silk gland (ASG), middle silk gland (MSG), posterior silk gland (PSG), middle gut, and hemolymph. Our results showed that bmo-miR-2780a was specifically expressed in the MSG and that the expression level of BmSer-1 was significantly higher in the MSG than in other tissues. Recombinant plasmids carrying both pri-mir-2780a and Ser1-3'UTR were constructed and then used to cotransfect BmN cells. We further detected the effect of bmo-miR-2780a on Ser-1 in vivo. These results showed that the target gene was significantly decreased by miR-2780a compared with the control group (p < .05), thus indicating that bmo-miR-2780a might negatively regulate the expression of Ser-1.
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Affiliation(s)
- Ping Qian
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Zhenjiang, Jiangsu, China
| | - Xin Wang
- Silkworm Eggs Administration Department of Jiangsu Province, Wuxi, Jiangsu, China
| | - Jiashuang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Tao Jiang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Zhenjiang, Jiangsu, China
- Department of Evolutionary & Environmental Biology, The Faculty of Natural Sciences, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Xudong Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Guan Huixiang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Xingjia Shen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Zhenjiang, Jiangsu, China
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11
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Ma SY, Smagghe G, Xia QY. Genome editing in Bombyx mori: New opportunities for silkworm functional genomics and the sericulture industry. INSECT SCIENCE 2019; 26:964-972. [PMID: 29845729 DOI: 10.1111/1744-7917.12609] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/29/2018] [Accepted: 05/07/2018] [Indexed: 06/08/2023]
Abstract
In recent years, research in life sciences has been remarkably revolutionized owing to the establishment, development and application of genome editing technologies. Genome editing has not only accelerated fundamental research but has also shown promising applications in agricultural breeding and therapy. In particular, the clustered, regularly interspaced, short palindromic repeat (CRISPR) technology has become an indispensable tool in molecular biology owing to its high efficacy and simplicity. Genome editing tools have also been established in silkworm (Bombyx mori), a model organism of Lepidoptera insects with high economic importance. This has remarkably improved the level and scope of silkworm research and could reveal new mechanisms or targets in basic entomology and pest management studies. In this review, we summarize the progress and potential of genome editing in silkworm and its applications in functional genomic studies for generating novel genetic materials.
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Affiliation(s)
- San-Yuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Qing-You Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing, China
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12
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Zhang L, Jing X, Chen W, Bai J, Vasseur L, He W, You M. Selection of reference genes for expression analysis of plant-derived microRNAs in Plutella xylostella using qRT-PCR and ddPCR. PLoS One 2019; 14:e0220475. [PMID: 31369618 PMCID: PMC6675394 DOI: 10.1371/journal.pone.0220475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/16/2019] [Indexed: 01/22/2023] Open
Abstract
The establishment of an expression quantification system that can be easily applied for the comparison of microRNAs (miRNAs) from biological samples is an important step toward understanding functional mechanisms in organisms. However, there is lack of attention on the selection of reference genes for miRNA expression profiling in insect herbivores. Here, we explored the candidate reference genes in a notorious pest of cruciferous crops, Plutella xylostella, for normalization of miRNA expression in developmental stages and tissues and in response to a change of food source from artificial diet to host plant Arabidopsis thaliana. We first compared the expression levels and stability of eight small RNAs using qRT-PCR, and found that miR11 was the most suitable reference gene for expression quantification of the miRNAs. We then confirmed this finding using digital droplet PCR and further validated with a well-studied cross-kingdom miRNA derived from A. thaliana (ath-miR159a). However, none of the reference genes was applicable for all experimental conditions, and multiple reference genes were sometimes required within the same experiment. Our work provides a method for the selection of reference genes for quantification of plant-derived miRNAs, which paves the way for unveiling their roles in the insect-plant coevolution.
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Affiliation(s)
- Lingling Zhang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodong Jing
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianlin Bai
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liette Vasseur
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Weiyi He
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (MSY); (WYH)
| | - Minsheng You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (MSY); (WYH)
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Chen J, Li TC, Pang R, Yue XZ, Hu J, Zhang WQ. Genome-Wide Screening and Functional Analysis Reveal That the Specific microRNA nlu-miR-173 Regulates Molting by Targeting Ftz-F1 in Nilaparvata lugens. Front Physiol 2018; 9:1854. [PMID: 30618850 PMCID: PMC6306441 DOI: 10.3389/fphys.2018.01854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/07/2018] [Indexed: 01/28/2023] Open
Abstract
Background: Molting is a crucial physiological behavior during arthropod growth. In the past few years, molting as well as chitin biosynthesis triggered by molting, is subject to regulation by miRNAs. However, how many miRNAs are involved in insect molting at the genome-wide level remains unknown. Results: We deeply sequenced four samples obtained from nymphs at the 2nd-3rd and 4th-5th instars, and then identified 61 miRNAs conserved in the Arthropoda and 326 putative novel miRNAs in the brown planthopper Nilaparvata lugens, a fearful pest of rice. A total of 36 mature miRNAs with significant different expression levels at the genome scale during molting, including 19 conserved and 17 putative novel miRNAs were identified. After comparing the expression profiles, we found that most of the targets of 36 miRNAs showing significantly differential expression were involved in energy and hormone pathways. One of the 17 putative novel miRNAs, nlu-miR-173 was chosen for functional study. nlu-miR-173 acts in 20-hydroxyecdysone signaling through its direct target, N. lugens Ftz-F1(NlFtz-F1), a transcription factor. Furthermore, we found that the transcription of nlu-miR-173 was promoted by Broad-Complex (BR-C), suggesting that its involvement in the 20-hydroxyecdysone pathway contributes to proper molting function. Conclusion: We provided a comprehensive resource of miRNAs associated with insect molting and identified a novel miRNA as a potential target for pest control.
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Affiliation(s)
- Jie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Teng Chao Li
- 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
| | - Xiang Zhao Yue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian Hu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen Qing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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14
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Sun X, Zhang S, Qin S, Hou C, Zhang G, Li M. MicroRNA Expression Analysis of Naked Silkworms. JOURNAL OF ECONOMIC ENTOMOLOGY 2018; 111:2876-2883. [PMID: 30124955 DOI: 10.1093/jee/toy235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 06/08/2023]
Abstract
The silk gland (SG) is characterized by the synthesis and secretion of silk protein in the economically important silkworm, Bombyx mori L. (Lepidoptera: Bombycidae). Nd and Nd-s are two fibroin-secretion-deficient silkworm mutants. MicroRNA (miRNA) plays an important role in many biological processes, such as cell proliferation, differentiation, and apoptosis. Using the Dazao silkworm as a control, we explored the miRNA expression profiles in the SGs of u02 (Nd) and u05 (Nd-s) to reveal the potential functions of miRNAs in silk protein expression and SG development. Here, we sequenced small RNA libraries made from the whole SGs of three strains. There are 260, 236, and 233 known miRNAs and 20, 18, and 18 potential new miRNAs identified from Dazao, u02, and u05, respectively. Fifty-three miRNAs are differentially expressed between Dazao and u02, 51 between Dazao and u05, and 16 between u02 and u05. Gene ontology/KEGG analyses show that most of the predicted target genes of differentially expressed miRNAs were assigned to functional categories involved in cell proliferation, organ development, and cellular compartment structures. The miRNA expression profile of naked silkworms will pave the way for the understanding of SG development and the regulation of silk protein expression.
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Affiliation(s)
- Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Shu Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Chengxiang Hou
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Guozheng Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Muwang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
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15
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Balan RK, Ramasamy A, Hande RH, Gawande SJ, Krishna Kumar NK. Genome-wide identification, expression profiling, and target gene analysis of microRNAs in the Onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae), vectors of tospoviruses (Bunyaviridae). Ecol Evol 2018; 8:6399-6419. [PMID: 30038744 PMCID: PMC6053560 DOI: 10.1002/ece3.3762] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 11/08/2017] [Accepted: 11/27/2017] [Indexed: 11/06/2022] Open
Abstract
Thrips tabaci Lindeman is an important polyphagous insect pest species estimated to cause losses of more than U.S. $1 billion worldwide annually. Chemical insecticides are of limited use in the management of T. tabaci due to the thigmokinetic behavior and development of resistance to insecticides. There is an urgent need to find alternative management strategies. Small noncoding RNAs (sncRNAs) especially microRNAs (miRNAs) hold great promise as key regulators of gene expression in a wide range of organisms. MiRNAs are a group of endogenously originated sncRNA known to regulate gene expression in animals, plants, and protozoans. In this study, we explored these RNAs in T. tabaci using deep sequencing to provide a basis for future studies of their biological and physiological roles in governing gene expression. Apart from snoRNAs and piRNAs, our study identified nine novel and 130 known miRNAs from T. tabaci. Functional classification of the targets for these miRNAs predicted that majority are involved in regulating transcription, translation, signal transduction and genetic information processing. The higher expression of few miRNAs (such as tta-miR-281, tta-miR-184, tta-miR-3533, tta-miR-N1, tta-miR-N7, and tta-miR-N9) in T. tabaci pupal and adult stages reflected their possible role in larval and adult development, metamorphosis, parthenogenesis, and reproduction. This is the first exploration of the miRNAome in T. tabaci, which not only provides insights into their possible role in insect metamorphosis, growth, and development but also offer an important resource for future pest management strategies.
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Affiliation(s)
- Rebijith K. Balan
- Department of Physiology, Development, and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Asokan Ramasamy
- Division of BiotechnologyICAR‐Indian Institute of Horticultural ResearchBangaloreIndia
| | - Ranjitha H. Hande
- Division of BiotechnologyICAR‐Indian Institute of Horticultural ResearchBangaloreIndia
| | - Suresh J. Gawande
- Crop Protection SectionICAR‐Directorate of Onion and Garlic ResearchPuneIndia
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16
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Yu T, Li X, Coates BS, Zhang Q, Siegfried BD, Zhou X. microRNA profiling between Bacillus thuringiensis Cry1Ab-susceptible and -resistant European corn borer, Ostrinia nubilalis (Hübner). INSECT MOLECULAR BIOLOGY 2018; 27:279-294. [PMID: 29451334 DOI: 10.1111/imb.12376] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transgenic maize hybrids that express insecticidal Bacillus thuringiensis (Bt) crystalline (Cry) protein toxins effectively protect against the European corn borer, Ostrinia nubilalis, a devastating maize pest. Field monitoring and laboratory selections have detected varying levels of O. nubilalis resistance to Cry1Ab toxin. MicroRNAs (miRNAs) are short noncoding RNAs that are involved in post-transcriptional gene regulation. Their potential roles in the evolution of Bt resistance, however, remain largely unknown. Sequencing of small RNA libraries from the midgut of Cry1Ab-susceptible and resistant O. nubilalis larvae resulted in the discovery of 277 miRNAs, including 248 conserved and 29 novel. Comparative analyses of miRNA expression profiles between the laboratory strains predicted 26 and nine significantly up- and down-regulated transcripts, respectively, in the midgut of Cry1Ab resistant larvae. Amongst 15 differentially regulated miRNAs examined by quantitative real-time PCR, nine (60%) were validated as cosegregating with Cry1Ab resistance in a backcross progeny. Differentially expressed miRNAs were predicted to affect transcripts involved in cell membrane components with functions in metabolism and binding, and the putative Bt-resistance genes aminopeptidase N and cadherin. These results lay the foundation for future investigation of the potential role of miRNAs in the evolution of Bt resistance.
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Affiliation(s)
- T Yu
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - X Li
- Department of Entomology, University of Kentucky, Lexington, KY, USA
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - B-S Coates
- Corn Insects & Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Q Zhang
- Department of Entomology, University of Kentucky, Lexington, KY, USA
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - B-D Siegfried
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - X Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, USA
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17
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Jia X, Zhou M, Zou Z, Lin P, Wang Y, Zhang Z. Identification and comparative analysis of the ovary and testis microRNAome of mud crab Scylla paramamosain. Mol Reprod Dev 2018; 85:519-531. [DOI: 10.1002/mrd.22989] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/19/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Xiwei Jia
- Fisheries College; Jimei University; Xiamen China
| | - Mingcan Zhou
- Fisheries College; Jimei University; Xiamen China
| | - Zhihua Zou
- Fisheries College; Jimei University; Xiamen China
| | - Peng Lin
- Fisheries College; Jimei University; Xiamen China
| | - Yilei Wang
- Fisheries College; Jimei University; Xiamen China
| | - Ziping Zhang
- College of Animal Science; Fujian Agriculture and Forestry University; Fuzhou China
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18
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Hearn J, Chow FWN, Barton H, Tung M, Wilson PJ, Blaxter M, Buck A, Little TJ. Daphnia magna microRNAs respond to nutritional stress and ageing but are not transgenerational. Mol Ecol 2018; 27:1402-1412. [PMID: 29420841 DOI: 10.1111/mec.14525] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/01/2018] [Indexed: 12/20/2022]
Abstract
Maternal effects, where the performance of offspring is determined by the condition of their mother, are widespread and may in some cases be adaptive. The crustacean Daphnia magna shows strong maternal effects: offspring size at birth and other proxies for fitness are altered when their mothers are older or when mothers have experienced dietary restriction. The mechanisms for this transgenerational transmission of maternal experience are unknown, but could include changes in epigenetic patterning. MicroRNAs (miRNAs) are regulators of gene expression that have been shown to play roles in intergenerational information transfer, and here, we test whether miRNAs are involved in D. magna maternal effects. We found that miRNAs were differentially expressed in mothers of different ages or nutritional state. We then examined miRNA expression in their eggs, their adult daughters and great granddaughters, which did not experience any treatments. The maternal (treatment) generation exhibited differential expression of miRNAs, as did their eggs, but this was reduced in adult daughters and lost by great granddaughters. Thus, miRNAs are a component of maternal provisioning, but do not appear to be the cause of transgenerational responses under these experimental conditions. MicroRNAs may act in tandem with egg provisioning (e.g., with carbohydrates or fats), and possibly other small RNAs or epigenetic modifications.
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Affiliation(s)
- Jack Hearn
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Franklin Wang-Ngai Chow
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Harriet Barton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Matthew Tung
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Philip J Wilson
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Amy Buck
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tom J Little
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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19
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He K, Sun Y, Xiao H, Ge C, Li F, Han Z. Multiple miRNAs jointly regulate the biosynthesis of ecdysteroid in the holometabolous insects, Chilo suppressalis. RNA (NEW YORK, N.Y.) 2017; 23:1817-1833. [PMID: 28860304 PMCID: PMC5689003 DOI: 10.1261/rna.061408.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/18/2017] [Indexed: 05/30/2023]
Abstract
The accurate rise and fall of active hormones is important for insect development. The ecdysteroids must be cleared in a timely manner. However, the mechanism of suppressing the ecdysteroid biosynthesis at the right time remains unclear. Here, we sequenced a small RNA library of Chilo suppressalis and identified 300 miRNAs in this notorious rice insect pest. Microarray analysis yielded 54 differentially expressed miRNAs during metamorphosis development. Target prediction and in vitro dual-luciferase assays confirmed that seven miRNAs (two conserved and five novel miRNAs) jointly targeted three Halloween genes in the ecdysteroid biosynthesis pathway. Overexpression of these seven miRNAs reduced the titer of 20-hydroxyecdysone (20E), induced mortality, and retarded development, which could be rescued by treatment with 20E. Comparative analysis indicated that the miRNA regulation of metamorphosis development is a conserved process but that the miRNAs involved are highly divergent. In all, we present evidence that both conserved and lineage-specific miRNAs have crucial roles in regulating development in insects by controlling ecdysteroid biosynthesis, which is important for ensuring developmental convergence and evolutionary diversity.
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Affiliation(s)
- Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yang Sun
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Institute of Plant Protection, Jiangxi Academy of Agricultural Science, Nanchang 330200, China
| | - Huamei Xiao
- College of Life Sciences and Resource Environment, Yichun University, Yichun 336000, China
| | - Chang Ge
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhaojun Han
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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20
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Differentially expressed microRNAs in diapausing versus HCl-treated Bombyx embryos. PLoS One 2017; 12:e0180085. [PMID: 28700597 PMCID: PMC5507411 DOI: 10.1371/journal.pone.0180085] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 06/10/2017] [Indexed: 02/05/2023] Open
Abstract
Differentially expressed microRNAs were detected to explore the molecular mechanisms of diapause termination. The total small RNA of diapause-destined silkworm eggs and HCl-treated eggs was extracted and then sequenced using HiSeq high-throughput method. 44 novel miRNAs were discovered. Compared to those in the diapause-destined eggs, 61 miRNAs showed significant changes in the acid-treated eggs, with 23 being up-regulated and 38 being down-regulated. The potential target genes of differentially expressed miRNAs were predicted by miRanda. Gene Ontology and KEGG pathway enrichment analysis of these potential target genes revealed that they were mainly located within cells and organelles, involved in cellular and metabolic processes, and participated in protein production, processing and transportation. Two differentially expressed genes, Bombyx mori SDH and Bmo-miR-2761-3p, were further analyzed with qRT-PCR. BmSDH was significantly up-regulated in the HCl-treated eggs, while Bmo-miR-2761-3p was down-regulated. These results suggested that these two genes were well coordinated in silkworm eggs. Dual luciferase reporter assay demonstrated that Bmo-miR-2761-3p inhibited the expression of BmSDH.
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21
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Su Y, Zhang Y, Huang N, Liu F, Su W, Xu L, Ahmad W, Wu Q, Guo J, Que Y. Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection. BMC Genomics 2017; 18:325. [PMID: 28438123 PMCID: PMC5404671 DOI: 10.1186/s12864-017-3716-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 04/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The present study was the first to use two sugarcane genotypes, YA05-179 (smut-resistant) and ROC22 (smut-susceptible), to identify differentially expressed miRNAs in sugarcane challenged with S. scitamineum by using high-throughput sequencing. RESULTS The predicted target gene number corresponding to known differentially expressed miRNAs in YA05-179 was less than that in ROC22, however most of them were in common. Expression of differential miRNAs under S. scitamineum challenge was mostly downregulated, with similar trends in the two varieties. Gene ontology (GO) analysis showed that the target gene classification of known miRNAs was similar to that of the newly identified miRNAs. These were mainly associated with cellular processes and metabolic processes in the biological process category, as well as combination and catalytic activity in the molecular function category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that these predicted target genes involved in a series of physiological and biochemical pathways or disease resistance-related physiological metabolism and signal transduction pathways, suggesting that the molecular interaction mechanism between sugarcane and S. scitamineum was a complex network system. These findings also showed certain predicted target genes of miR5671, miR5054, miR5783, miR5221, and miR6478 play roles in the mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, and plant-pathogen interaction. Quantitative real-time PCR (qRT-PCR) analysis showed that majority of the known miRNAs and its predicted target genes followed a negatively regulated mode. Seven out of eight predicted target genes showed identical expression after 12 h treatment and reached the highest degree of matching at 48 h, indicating that the regulatory role of miRNAs on the target genes in sugarcane was maximized at 48 h after S. scitamineum challenge. CONCLUSIONS Taken together, our findings serve as evidence for the association of miRNA expression with the molecular mechanism underlying the pathogenesis of sugarcane smut, particularly on the significance of miRNA levels in relation to the cultivation of smut-resistant sugarcane varieties.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yuye Zhang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ning Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Feng Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Weihua Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Waqar Ahmad
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qibin Wu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jinlong Guo
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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22
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Allam M, Spillings BL, Abdalla H, Mapiye D, Koekemoer LL, Christoffels A. Identification and characterization of microRNAs expressed in the African malaria vector Anopheles funestus life stages using high throughput sequencing. Malar J 2016; 15:542. [PMID: 27825380 PMCID: PMC5101901 DOI: 10.1186/s12936-016-1591-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/28/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Over the past several years, thousands of microRNAs (miRNAs) have been identified in the genomes of various insects through cloning and sequencing or even by computational prediction. However, the number of miRNAs identified in anopheline species is low and little is known about their role. The mosquito Anopheles funestus is one of the dominant malaria vectors in Africa, which infects and kills millions of people every year. Therefore, small RNA molecules isolated from the four life stages (eggs, larvae, pupae and unfed adult females) of An. funestus were sequenced using next generation sequencing technology. RESULTS High throughput sequencing of four replicates in combination with computational analysis identified 107 mature miRNA sequences expressed in the An. funestus mosquito. These include 20 novel miRNAs without sequence identity in any organism and eight miRNAs not previously reported in the Anopheles genus but are known in non-anopheles mosquitoes. Finally, the changes in the expression of miRNAs during the mosquito development were determined and the analysis showed that many miRNAs have stage-specific expression, and are co-transcribed and co-regulated during development. CONCLUSIONS This study presents the first direct experimental evidence of miRNAs in An. funestus and the first profiling study of miRNA associated with the maturation in this mosquito. Overall, the results indicate that miRNAs play important roles during the growth and development. Silencing such molecules in a specific life stage could decrease the vector population and therefore interrupt malaria transmission.
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Affiliation(s)
- Mushal Allam
- SA Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Road, Cape Town, 7535 South Africa
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Johannesburg, 2131 South Africa
| | - Belinda L. Spillings
- Vector Control Reference Laboratory, Centre for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Johannesburg, 2131 South Africa
| | - Hiba Abdalla
- Vector Control Reference Laboratory, Centre for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Johannesburg, 2131 South Africa
- Faculty of Health Sciences, Wits Research Institute for Malaria, University of the Witwatersrand, 1 Jan Smuts Ave, Johannesburg, 2000 South Africa
- Vector Biology & Control Unit, Blue Nile National Institute for Communicable Disease, Wad Medani, Sudan
| | - Darlington Mapiye
- SA Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Road, Cape Town, 7535 South Africa
| | - Lizette L. Koekemoer
- Vector Control Reference Laboratory, Centre for Opportunistic, Tropical and Hospital Infections, National Institute for Communicable Diseases, National Health Laboratory Service, 1 Modderfontein Road, Johannesburg, 2131 South Africa
- Faculty of Health Sciences, Wits Research Institute for Malaria, University of the Witwatersrand, 1 Jan Smuts Ave, Johannesburg, 2000 South Africa
| | - Alan Christoffels
- SA Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Robert Sobukwe Road, Cape Town, 7535 South Africa
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23
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Wu N, Gaur U, Zhu Q, Chen B, Xu Z, Zhao X, Yang M, Li D. Expressed microRNA associated with high rate of egg production in chicken ovarian follicles. Anim Genet 2016; 48:205-216. [PMID: 27781291 DOI: 10.1111/age.12516] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2016] [Indexed: 01/28/2023]
Abstract
MicroRNA (miRNA) is a highly conserved class of small noncoding RNA about 19-24 nucleotides in length that function in a specific manner to post-transcriptionally regulate gene expression in organisms. Tissue miRNA expression studies have discovered a myriad of functions for miRNAs in various aspects, but a role for miRNAs in chicken ovarian tissue at 300 days of age has not hitherto been reported. In this study, we performed the first miRNA analysis of ovarian tissues in chickens with low and high rates of egg production using high-throughput sequencing. By comparing low rate of egg production chickens with high rate of egg production chickens, 17 significantly differentially expressed miRNAs were found (P < 0.05), including 11 known and six novel miRNAs. We found that all 11 known miRNAs were involved mainly in pathways of reproduction regulation, such as steroid hormone biosynthesis and dopaminergic synapse. Additionally, expression profiling of six randomly selected differentially regulated miRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR). Some miRNAs, such as gga-miR-34b, gga-miR-34c and gga-miR-216b, were reported to regulate processes such as proliferation, cell cycle, apoptosis and metastasis and were expressed differentially in ovaries of chickens with high rates of egg production, suggesting that these miRNAs have an important role in ovary development and reproductive management of chicken. Furthermore, we uncovered that a significantly up-regulated miRNA-gga-miR-200a-3p-is ubiquitous in reproduction-regulation-related pathways. This miRNA may play a special central role in the reproductive management of chicken, and needs to be further studied for confirmation.
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Affiliation(s)
- N Wu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - U Gaur
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - Q Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - B Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - Z Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - X Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - M Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
| | - D Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 610000, China
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24
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Comparative profiling of microRNAs in the winged and wingless English grain aphid, Sitobion avenae (F.) (Homoptera: Aphididae). Sci Rep 2016; 6:35668. [PMID: 27762301 PMCID: PMC5071838 DOI: 10.1038/srep35668] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/03/2016] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are short single-stranded non-coding RNAs that regulate gene expression, particularly during development. In this study, 345 miRNAs were identified from the English green aphid, Sitobion avenae (F.), of which 168 were conserved and 177 were S. avenae-specific. Quantitative comparison of miRNA expression levels indicated that 16 and 12 miRNAs were significantly up-regulated in winged and wingless S. avenae small RNA libraries, respectively. Differential expression of these miRNAs was confirmed by real-time quantitative RT-PCR validation. The putative transcript targets for these candidate miRNAs were predicted based on sequences from a model species Drosophila melanogaster and four aphid species Acyrthosiphon pisum, Myzus persicae, Toxoptera citricida, and Aphis gosspii. Gene Ontology and KEGG pathway analyses shed light on the potential functions of these miRNAs in the regulation of genes involved in the metabolism, development and wing polyphenism of S. avenae.
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25
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Rebijith KB, Asokan R, Hande HR, Krishna Kumar NK. The First Report of miRNAs from a Thysanopteran Insect, Thrips palmi Karny Using High-Throughput Sequencing. PLoS One 2016; 11:e0163635. [PMID: 27685664 PMCID: PMC5042526 DOI: 10.1371/journal.pone.0163635] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/12/2016] [Indexed: 12/15/2022] Open
Abstract
Thrips palmi Karny (Thysanoptera: Thripidae) is the sole vector of Watermelon bud necrosis tospovirus, where the crop loss has been estimated to be around USD 50 million annually. Chemical insecticides are of limited use in the management of T. palmi due to the thigmokinetic behaviour and development of high levels of resistance to insecticides. There is an urgent need to find out an effective futuristic management strategy, where the small RNAs especially microRNAs hold great promise as a key player in the growth and development. miRNAs are a class of short non-coding RNAs involved in regulation of gene expression either by mRNA cleavage or by translational repression. We identified and characterized a total of 77 miRNAs from T. palmi using high-throughput deep sequencing. Functional classifications of the targets for these miRNAs revealed that majority of them are involved in the regulation of transcription and translation, nucleotide binding and signal transduction. We have also validated few of these miRNAs employing stem-loop RT-PCR, qRT-PCR and Northern blot. The present study not only provides an in-depth understanding of the biological and physiological roles of miRNAs in governing gene expression but may also lead as an invaluable tool for the management of thysanopteran insects in the future.
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Affiliation(s)
- K. B. Rebijith
- Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India
- * E-mail: ;
| | - R. Asokan
- Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India
- * E-mail: ;
| | - H. Ranjitha Hande
- Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India
| | - N. K. Krishna Kumar
- Division of Horticultural Science, Indian Council of Agricultural Research, New Delhi, India
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26
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Chang ZX, Tang N, Wang L, Zhang LQ, Akinyemi IA, Wu QF. Identification and characterization of microRNAs in the white-backed planthopper, Sogatella furcifera. INSECT SCIENCE 2016; 23:452-68. [PMID: 27060479 DOI: 10.1111/1744-7917.12343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 03/14/2016] [Accepted: 03/28/2016] [Indexed: 05/14/2023]
Abstract
MicroRNAs (miRNAs) are a novel class of small, non-coding endogenous RNAs that play critical regulatory roles in many metabolic activities in eukaryotes. Reports of the identification of miRNAs in Sogatella furcifera (white-backed planthopper), the insect that acts as the only confirmed vector of the southern rice black-streaked dwarf virus (SRBSDV), are limited. In this study, a total of 382 miRNAs were identified in S. furcifera, including 106 conserved and 276 novel miRNAs, using high-throughput sequencing based on two small RNA libraries from viruliferous and non-viruliferous S. furcifera, and these miRNAs belonged to 52 conserved miRNA families and 58 S. furcifera-specific families, respectively. Comparison with miRNAs from 26 insect species and five other species in miRBase showed that more than half of the conserved miRNA families are highly conserved in Hexapoda, while other miRNAs are only conserved in non-dipterans. Furthermore, 4 117 target genes predicted for the 382 identified miRNAs could be categorized into 45 functional groups annotated by Gene Ontology. Compared with non-viruliferous cells, eight up-regulated miRNAs and four down-regulated miRNAs were identified in cells inoculated with SRBSDV, among which miR-14 and miR-n98a may be involved in the immune response to SRBSDV infection. Analyses of the identified miRNAs will provide insights into the roles of these miRNAs in the regulation and expression of genes involved in the metabolism, development and viral infection of S. furcifera.
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Affiliation(s)
- Zhao-Xia Chang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Nan Tang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lin Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Li-Qing Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ibukun A Akinyemi
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qing-Fa Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
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27
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Zhang Y, Xu Z, Wu Q, Peng M, Liu Y, Liu X, Shi L, Shen G, Pan Y, He L. Identification of Differentially Expressed microRNAs between the Fenpropathrin Resistant and Susceptible Strains in Tetranychus cinnabarinus. PLoS One 2016; 11:e0152924. [PMID: 27050424 PMCID: PMC4822788 DOI: 10.1371/journal.pone.0152924] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/20/2016] [Indexed: 11/18/2022] Open
Abstract
The carmine spider mite (Tetranychus cinnabarinus) is one of the most serious pests on crops and its control mainly depends on chemical acaricides. The excessive and improper acaricides use has resulted in mite resistance to many acaricides, including fenpropathrin. Previous studies have indicated fenpropathrin resistance is a complex development process involving many genes, but information on resistance mechanism of post-transcription regulation is rare. Using Illumina sequencing, several categories of sRNAs were identified from susceptible (TS) and fenpropathrin-resistant strains (TR) of T. cinnabarinus, including 75 known microRNAs (miRNAs) and 64 novel miRNAs, whose target genes containing 78592 miRNA-target pairs were predicted by 6 algorithms. Also, 12 significantly differently expressed miRNAs were identified between the TS and TR libraries and RT-qPCR validation also performed a well consistency with sequencing. The targets of significantly differentially expressed miRNAs included 7 glutathione S-transferase, 7 cytochrome P450 and 16 carboxyl/choline esterase genes, their function in fenpropathrin resistance were further analyzed. The present study provides the firstly large-scale characterization of miRNAs in T. cinnabarinus and the comparison between TS and TR strains gives a clue on how miRNA involves in fenpropathrin resistance.
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Affiliation(s)
- Yichao Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Zhifeng Xu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Qiong Wu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Miao Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Yanchao Liu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Xing Liu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Li Shi
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Guangmao Shen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Yu Pan
- College of Horticulture and Landscape Agriculture, Southwest University, Chongqing, China
| | - Lin He
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
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28
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Chen C, Fan YY, Wang X, Song F, Jiang T, Qian P, Tang SM, Shen XJ. bmo-miR-0001 and bmo-miR-0015 down-regulate expression of Bombyx mori fibroin light chain gene in vitro. J Zhejiang Univ Sci B 2016; 17:127-35. [PMID: 26834013 DOI: 10.1631/jzus.b1500078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Based on bioinformatic analysis, we selected two novel microRNAs (miRNAs), bmo-miR-0001 and bmo-miR-0015, from high-throughput sequencing of the Bombyx mori larval posterior silk gland (PSG). Firstly, we examined the expression of bmo-miR-0001 and bmo-miR 12 different tissues of the 5th instar Day-3 larvae of the silkworm. The results showed that the expression levels of both bmo-miR-0001 and bmo-miR-0015 were obviously higher in the PSG than in other tissues, implying there is a spatio-temporal condition for bmo-miR-0001 and bmo-miR-0015 to regulate the expression of BmFib-L. To test this hypothesis, we constructed pri-bmo-miR-0001 expressing the plasmid pcDNA3.0 and pri-bmo-miR-0015 expressing the plasmid pcDNA3.0 [ie1-egfp-pri-bmo-miR-0015-SV40]. Finally, the BmN cells were harvested and luciferase activity was detected. The results showed that luciferase activity was reduced significantly (P<0.05) in BmN cells co-transfected by pcDNA3.0 [ie1-egfp-pri-bmo-miR-0001-SV40] or pcDNA3.0 with pGL3.0 [A3-luc-Fib-L-3'UTR-SV40], suggesting that both bmo-miR-0001 and bmo-miR-0015 can down-regulate the expression of BmFib-L in vitro.
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Affiliation(s)
- Chen Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Yang-yang Fan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Xin Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Fei Song
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Tao Jiang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Ping Qian
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Shun-ming Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
| | - Xing-jia Shen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China
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29
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Nandety RS, Sharif A, Kamita SG, Ramasamy A, Falk BW. Identification of Novel and Conserved microRNAs in Homalodisca vitripennis, the Glassy-Winged Sharpshooter by Expression Profiling. PLoS One 2015; 10:e0139771. [PMID: 26440407 PMCID: PMC4595010 DOI: 10.1371/journal.pone.0139771] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/17/2015] [Indexed: 11/21/2022] Open
Abstract
The glassy-winged sharpshooter (GWSS) Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and an important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce’s disease of grapevines. MicroRNAs are a class of small RNAs that play an important role in the functional development of various organisms including insects. In H. vitripennis, we identified microRNAs using high-throughput deep sequencing of adults followed by computational and manual annotation. A total of 14 novel microRNAs that are not found in the miRBase were identified from adult H. vitripennis. Conserved microRNAs were also found in our datasets. By comparison to our previously determined transcriptome sequence of H. vitripennis, we identified the potential targets of the microRNAs in the transcriptome. This microRNA profile information not only provides a more nuanced understanding of the biological and physiological mechanisms that govern gene expression in H. vitripennis, but may also lead to the identification of novel mechanisms for biorationally designed management strategies through the use of microRNAs.
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Affiliation(s)
- Raja Sekhar Nandety
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Almas Sharif
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Shizuo G. Kamita
- Department of Entomology & Nematology, University of California, Davis, California, United States of America
| | - Asokan Ramasamy
- Division of Biotechnology, Indian Institute of Horticultural Research, Bangalore, India
| | - Bryce W. Falk
- Department of Plant Pathology, University of California, Davis, California, United States of America
- * E-mail:
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30
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Characterization and profiling of MicroRNAs in posterior silk gland of the silkworm (Bombyx mori). Genes Genomics 2015. [DOI: 10.1007/s13258-015-0300-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Zhou L, Li H, Hao F, Li N, Liu X, Wang G, Wang Y, Tang H. Developmental Changes for the Hemolymph Metabolome of Silkworm (Bombyx mori L.). J Proteome Res 2015; 14:2331-47. [PMID: 25825269 DOI: 10.1021/acs.jproteome.5b00159] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Silkworm (Bombyx mori) is a lepidopteran-holometabolic model organism. To understand its developmental biochemistry, we characterized the larval hemolymph metabonome from the third instar to prepupa stage using (1)H NMR spectroscopy whilst hemolymph fatty acid composition using GC-FID/MS. We unambiguously assigned more than 60 metabolites, among which tyrosine-o-β-glucuronide, mesaconate, homocarnosine, and picolinate were reported for the first time from the silkworm hemolymph. Phosphorylcholine was the most abundant metabolite in all developmental stages with exception for the periods before the third and fourth molting. We also found obvious developmental dependence for the hemolymph metabonome involving multiple pathways including protein biosyntheses, glycolysis, TCA cycle, the metabolisms of choline amino acids, fatty acids, purines, and pyrimidines. Most hemolymph amino acids had two elevations during the feeding period of the fourth instar and prepupa stage. Trehalose was the major blood sugar before day 8 of the fifth instar, whereas glucose became the major blood sugar after spinning. C16:0, C18:0 and its unsaturated forms were dominant fatty acids in hemolymph. The developmental changes of hemolymph metabonome were associated with dietary nutrient intakes, biosyntheses of cell membrane, pigments, proteins, and energy metabolism. These findings offered essential biochemistry information in terms of the dynamic metabolic changes during silkworm development.
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Affiliation(s)
- Lihong Zhou
- †College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.,‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,¶College of Life Sciences, Jianghan University, Wuhan 430056, China
| | - Huihui Li
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Fuhua Hao
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ning Li
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xin Liu
- †College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guoliang Wang
- ¶College of Life Sciences, Jianghan University, Wuhan 430056, China
| | - Yulan Wang
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,⊥Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, China
| | - Huiru Tang
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,§State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Metabonomics and Systems Biology Laboratory, School of Life Sciences, Fudan University, Shanghai 200433, China
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Kakumani PK, Chinnappan M, Singh AK, Malhotra P, Mukherjee SK, Bhatnagar RK. Identification and characteristics of microRNAs from army worm, Spodoptera frugiperda cell line Sf21. PLoS One 2015; 10:e0116988. [PMID: 25693181 PMCID: PMC4333348 DOI: 10.1371/journal.pone.0116988] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/17/2014] [Indexed: 02/07/2023] Open
Abstract
microRNAs play important regulatory role in all intrinsic cellular functions. Amongst lepidopteran insects, miRNAs from only Bombyx mori have been studied extensively with a little focus on Spodoptera sp. In the present study, we identified a total of 226 miRNAs from Spodoptera frugiperda cell line Sf21. Of the total, 116 miRNAs were well conserved within other insects, like B. mori, Drosophila melanogaster and Tribolium castenum while the remaining 110 miRNAs were identified as novel based on comparative analysis with the insect miRNA data set. Landscape distribution analysis based on Sf21 genome assembly revealed clustering of few novel miRNAs. A total of 5 miRNA clusters were identified and the largest one encodes 5 miRNA genes. In addition, 12 miRNAs were validated using northern blot analysis and putative functional role assignment for 6 Sf miRNAs was investigated by examining their relative abundance at different developmental stages of Spodoptera litura and body parts of 6th instar larvae. Further, we identified a total of 809 potential target genes with GO terms for selected miRNAs, involved in different metabolic and signalling pathways of the insect. The newly identified miRNAs greatly enrich the repertoire of insect miRNAs and analysis of expression profiles reveal their involvement at various steps of biochemical pathways of the army worm.
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Affiliation(s)
- Pavan Kumar Kakumani
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mahendran Chinnappan
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashok K. Singh
- Department of Zoology, University of Delhi, Cavalry Lane, New Delhi, 110007, India
| | - Pawan Malhotra
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
- * E-mail: (PM); (SKM); (RKB)
| | - Sunil K. Mukherjee
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
- * E-mail: (PM); (SKM); (RKB)
| | - Raj K. Bhatnagar
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
- * E-mail: (PM); (SKM); (RKB)
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Identification of microRNAs by small RNA deep sequencing for synthetic microRNA mimics to control Spodoptera exigua. Gene 2015; 557:215-21. [DOI: 10.1016/j.gene.2014.12.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/12/2014] [Accepted: 12/16/2014] [Indexed: 12/26/2022]
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Papantonis A, Swevers L, Iatrou K. Chorion genes: a landscape of their evolution, structure, and regulation. ANNUAL REVIEW OF ENTOMOLOGY 2015; 60:177-194. [PMID: 25341099 DOI: 10.1146/annurev-ento-010814-020810] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Differential regulation at the level of transcription provides a means for controlling gene expression in eukaryotes, especially during development. Insect model systems have been extensively used to decipher the molecular basis of such regulatory cascades, and one of the oldest such model systems is the regulation of chorion gene expression during ovarian follicle maturation. Recent experimental and technological advances have shed new light onto the system, allowing us to revisit it. Thus, in this review we try to summarize almost 40 years' worth of studies on chorion gene regulation while-by comparing Bombyx mori and Drosophila melanogaster models-attempting to present a comprehensive, unified model of the various regulatory aspects of choriogenesis that takes into account the evolutionary conservation and divergence of the underlying mechanisms.
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Affiliation(s)
- Argyris Papantonis
- Research Group for Systems Biology of Chromatin, Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany;
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Duarte Junior FF, de Lima Neto QA, Rando FDS, de Freitas DVB, Pattaro Júnior JR, Polizelli LG, Munhoz REF, Seixas FAV, Fernandez MA. Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome. MOLECULAR BIOSYSTEMS 2014; 11:801-8. [PMID: 25521575 DOI: 10.1039/c4mb00595c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The small noncoding group of RNAs called stem-bulge RNAs (sbRNAs), first reported in Caenorhabditis elegans, is described as molecules homologous to the Y RNAs, a specific class of noncoding RNAs that is present in vertebrates. This homology indicates the possibility of the existence of sbRNAs in other invertebrate organisms. In this work, we used bioinformatic tools and conserved sequences of sbRNAs from C. Elegans and Y RNAs to search for homologous sbRNA sequences in the Bombyx mori genome. This analysis led to the discovery of one noncoding gene, which was translated into RNA segments and comparatively analysed with segments from human and hamster Y RNAs and C. elegans sbRNAs in molecular dynamic simulations. This gene represents the first evidence for a new sbRNA-like noncoding RNA, the BmsbRNA gene, in this Lepidoptera genome.
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Affiliation(s)
- Francisco Ferreira Duarte Junior
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo, 5790, 87020-900, Maringá, Paraná, Brasil.
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Ling L, Ge X, Li Z, Zeng B, Xu J, Aslam AFM, Song Q, Shang P, Huang Y, Tan A. MicroRNA Let-7 regulates molting and metamorphosis in the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 53:13-21. [PMID: 25016132 DOI: 10.1016/j.ibmb.2014.06.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/26/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous, non-coding, regulatory RNA molecules that post-transcriptionally regulate gene expression by binding to the 3'UTRs of mRNA targets and thus cause their degradation or translational inhibition. In insects, important roles of miRNAs in various biological processes have been demonstrated in Drosophila melanogaster. However, biological roles of miRNAs are barely unveiled in the majority of insect species due to limited genetic tools. In the present study, we introduce the transgenic miRNA sponge (miR-SP) technology combining with the binary GAL4/UAS system in the domesticated silkworm, Bombyx mori, to exploit the biological function of an evolutionally conserved miRNA, let-7. We successfully established transgenic silkworm lines in which a miRNA sponge construct targeting BmLet-7 seed region was expressed in a ubiquitous manner directed by A3-GAL4 driver. Transgenic animals showed decreased expression of BmLet-7, leading to developmental arrestment during the larval-larval and larval-pupal transition. Simultaneously, expression levels of the predicted BmLet-7 target genes, FTZ-F1 and Eip74EF (E74), key regulatory factors in the ecdysone pathway, were elevated in transgenic animals. The current study is the first report on application of the transgenic miR-SP technology in non-drosophilid insects, which will not only contribute to better understanding of let-7 biological roles, but also greatly facilitate future miRNA functional analysis in insects.
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Affiliation(s)
- Lin Ling
- Faculty of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China; Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xie Ge
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqian Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baosheng Zeng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Abu F M Aslam
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Peng Shang
- Faculty of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Anjiang Tan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Huang Y, Dou W, Liu B, Wei D, Liao CY, Smagghe G, Wang JJ. Deep sequencing of small RNA libraries reveals dynamic expression patterns of microRNAs in multiple developmental stages of Bactrocera dorsalis. INSECT MOLECULAR BIOLOGY 2014; 23:656-667. [PMID: 24957108 DOI: 10.1111/imb.12111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In eukaryotes, microRNAs (miRNAs) are small, conserved, noncoding RNAs that have emerged as critical regulators of gene expression. The oriental fruit fly Bactrocera dorsalis is one of the most economically important fruit fly pests in East Asia and the Pacific. Although transcriptome analyses have greatly enriched our knowledge of its structural genes, little is known about post-transcriptional regulation by miRNAs in this dipteran species. In this study, small RNA libraries corresponding to four B. dorsalis developmental stages (eggs, larvae, pupae and adults) were constructed and sequenced. Approximately 30.7 million reads of 18-30 nucleotides were obtained, with 123 known miRNAs and 60 novel miRNAs identified amongst these libraries. More than half of the miRNAs were stage-specific during the four developmental stages. A set of miRNAs was found to be up- or down-regulated during development by comparison of their reads at different developmental stages. Moreover, a small part of miRNAs owned both miR-#-3p and miR-#-5p types, with enormously variable miR-#-3p/miR-#-5p ratios in the same library and amongst different developmental stages for each miRNA. Taking these findings together, the current study has uncovered a number of miRNAs and provided insights into their possible involvement in developmental regulation by expression profiling of miRNAs. Further analyses of the expression and function of these miRNAs could increase our understanding of regulatory networks in this insect and lead to novel approaches for its control.
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Affiliation(s)
- Y Huang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
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Xu F, Wang X, Feng Y, Huang W, Wang W, Li L, Fang X, Que H, Zhang G. Identification of conserved and novel microRNAs in the Pacific oyster Crassostrea gigas by deep sequencing. PLoS One 2014; 9:e104371. [PMID: 25137038 PMCID: PMC4138081 DOI: 10.1371/journal.pone.0104371] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 07/12/2014] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in regulatory processes in various organisms. To date many studies have been performed in the investigation of miRNAs of numerous bilaterians, but limited numbers of miRNAs have been identified in the few species belonging to the clade Lophotrochozoa. In the current study, deep sequencing was conducted to identify the miRNAs of Crassostrea gigas (Lophotrochozoa) at a genomic scale, using 21 libraries that included different developmental stages and adult organs. A total of 100 hairpin precursor loci were predicted to encode miRNAs. Of these, 19 precursors (pre-miRNA) were novel in the oyster. As many as 53 (53%) miRNAs were distributed in clusters and 49 (49%) precursors were intragenic, which suggests two important biogenetic sources of miRNAs. Different developmental stages were characterized with specific miRNA expression patterns that highlighted regulatory variation along a temporal axis. Conserved miRNAs were expressed universally throughout different stages and organs, whereas novel miRNAs tended to be more specific and may be related to the determination of the novel body plan. Furthermore, we developed an index named the miRNA profile age index (miRPAI) to integrate the evolutionary age and expression levels of miRNAs during a particular developmental stage. We found that the swimming stages were characterized by the youngest miRPAIs. Indeed, the large-scale expression of novel miRNAs indicated the importance of these stages during development, particularly from organogenetic and evolutionary perspectives. Some potentially important miRNAs were identified for further study through significant changes between expression patterns in different developmental events, such as metamorphosis. This study broadened the knowledge of miRNAs in animals and indicated the presence of sophisticated miRNA regulatory networks related to the biological processes in lophotrochozoans.
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Affiliation(s)
- Fei Xu
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xiaotong Wang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Wen Huang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Li
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | | | - Huayong Que
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Guofan Zhang
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
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Li DD, Liu ZC, Huang L, Jiang QL, Zhang K, Qiao HL, Jiao ZJ, Yao LG, Liu RY, Kan YC. The expression analysis of silk gland-enriched intermediate-size non-coding RNAs in silkworm Bombyx mori. INSECT SCIENCE 2014; 21:429-438. [PMID: 24124013 DOI: 10.1111/1744-7917.12063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/22/2013] [Indexed: 06/02/2023]
Abstract
Small non-protein coding RNAs (ncRNAs) play important roles in development, stress response and other cellular processes. Silkworm is an important model for studies on insect genetics and control of Lepidopterous pests. We have previously identified 189 novel intermediate-size ncRNAs in silkworm Bombyx mori, including 40 ncRNAs that showed altered expression in different developmental stages. Here we characterized the functions of these 40 ncRNAs by measuring their expressions in six tissues of the fifth instar larvae using Northern blot and real-time polymerase chain reaction assays. We identified nine ncRNAs (four small nucleolar RNAs and five unclassified ncRNAs) that were enriched in silk gland, including four ncRNAs that showed silk gland-specific expression. We further showed that three of nine silk gland-enriched ncRNAs were predominantly expressed in the anterior silk gland, whereas another three ncRNAs were highly accumulated in the posterior silk gland, suggesting that they may play different roles in fibroin synthesis. Furthermore, an unclassified ncRNA, Bm-152, exhibited converse expression pattern with its antisense host gene gartenzwerg in diverse tissues, and might regulate the expression of gartenzwerg through RNA-protein complex. In addition, two silk gland-enriched ncRNAs Bm-102 and Bm-159 can be found in histone modification complex, which indicated that they might play roles through epigenetic modifications. Taken together, we provided the first expression and preliminary functional analysis of silk gland-enriched ncRNAs, which will help understand the molecular mechanism of silk gland-development and fibroin synthesis.
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Affiliation(s)
- Dan-Dan Li
- China-UK-NYNU-RRes Joint Libratory of Insect Biology, Nanyang Normal University, Nanyang, Henan, China
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Hong YH, Dinh H, Lillehoj HS, Song KD, Oh JD. Differential regulation of microRNA transcriptome in chicken lines resistant and susceptible to necrotic enteritis disease. Poult Sci 2014; 93:1383-95. [DOI: 10.3382/ps.2013-03666] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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Li J, Cai Y, Ye L, Wang S, Che J, You Z, Yu J, Zhong B. MicroRNA expression profiling of the fifth-instar posterior silk gland of Bombyx mori. BMC Genomics 2014; 15:410. [PMID: 24885170 PMCID: PMC4045974 DOI: 10.1186/1471-2164-15-410] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/07/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The growth and development of the posterior silk gland and the biosynthesis of the silk core protein at the fifth larval instar stage of Bombyx mori are of paramount importance for silk production. RESULTS Here, aided by next-generation sequencing and microarry assay, we profile 1,229 microRNAs (miRNAs), including 728 novel miRNAs and 110 miRNA/miRNA* duplexes, of the posterior silk gland at the fifth larval instar. Target gene prediction yields 14,222 unique target genes from 1,195 miRNAs. Functional categorization classifies the targets into complex pathways that include both cellular and metabolic processes, especially protein synthesis and processing. CONCLUSION The enrichment of target genes in the ribosome-related pathway indicates that miRNAs may directly regulate translation. Our findings pave a way for further functional elucidation of these miRNAs and their targets in silk production.
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Affiliation(s)
- Jisheng Li
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
- />Institute of Sericulture, Chengde Medical University, Chengde, 067000 P.R. China
| | - Yimei Cai
- />Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
| | - Lupeng Ye
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
| | - Shaohua Wang
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
| | - Jiaqian Che
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
| | - Zhengying You
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
| | - Jun Yu
- />Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
| | - Boxiong Zhong
- />College of Animal Sciences, Zhejiang University, Hangzhou, Hangzhou, 310058 P.R. China
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Yi S, Lu D, Peng W, Wang T, Zhang Y, Lin H. Differential expression profiling of spleen microRNAs in response to two distinct type II interferons in Tetraodon nigroviridis. PLoS One 2014; 9:e96336. [PMID: 24800866 PMCID: PMC4011704 DOI: 10.1371/journal.pone.0096336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 04/04/2014] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs are endogenous, small non-coding RNAs approximately 18-26 nucleotides in length that regulate target gene expression at the post-transcription level. Interferon-γ (IFN-γ) is a Th1 cytokine that is involved in both the innate and adaptive immune responses. We previously identified two IFN-γ genes in green-spotted puffer fish (Tetraodon nigroviridis). To determine whether miRNAs participate in IFN-γ-related immune responses, T. nigroviridis spleen cells were treated with recombinant IFN-γ isoforms, and a Solexa high-throughput sequencing method was used to identify miRNAs. In total, 1,556, 1,538 and 1,573 miRNAs were found in the three samples, and differentially expressed miRNAs were determined. In total, 398 miRNAs were differentially expressed after rIFN-γ1 treatment, and 438 miRNAs were differentially expressed after rIFN-γ2 treatment; additionally, 403 miRNAs were differentially expressed between the treatment groups. Ten differentially expressed miRNAs were chosen for validation using qRT-PCR. Target genes for the differentially expressed miRNAs were predicted, and GO and KEGG analyses were performed. This study provides basic knowledge regarding fish IFN-γ-induced miRNAs and offers clues for further studies into the mechanisms underlying fish IFN-γ-mediated immune responses.
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Affiliation(s)
- Shibai Yi
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Danqi Lu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
- * E-mail: (DL); (HL)
| | - Wan Peng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Ting Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
| | - Haoran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen (Zhongshan) University, Guangzhou, PR China
- * E-mail: (DL); (HL)
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Ling YH, Ren CH, Guo XF, Xu LN, Huang YF, Luo JC, Zhang YH, Zhang XR, Zhang ZJ. Identification and characterization of microRNAs in the ovaries of multiple and uniparous goats (Capra hircus) during follicular phase. BMC Genomics 2014; 15:339. [PMID: 24886377 PMCID: PMC4035069 DOI: 10.1186/1471-2164-15-339] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 04/30/2014] [Indexed: 12/14/2022] Open
Abstract
Background Superior kidding rate is an important economic trait in production of meat goat, and ovulation rate is the precondition of kidding rate. MicroRNAs (miRNAs) play critical roles in almost all ovarian biological processes, including folliculogenesis, follicle development, follicle atresia, luteal development and regression. To find out the different ovarian activity and follicle recruitment with miRNA-mediated posttranscriptional regulation, the small RNAs expressed pattern in the ovarian tissues of multiple and uniparous Anhui White goats during follicular phase was analyzed using Solexa sequencing data. Results 1008 miRNAs co-expressed, 309 and 433 miRNAs specifically expressed in the ovaries of multiple and uniparous goats during follicular phase were identified. The 10 most highly expressed miRNAs in the multiple library were also the highest expressed in the uniparous library, and there were no significantly different between each other. The highest specific expressed miRNA in the multiple library was miR-29c, and the one in the uniparous library was miR-6406. 35 novel miRNAs were predicted in total. GO annotation and KEGG Pathway analyses were implemented on target genes of all miRNA in two libraries. RT-PCR was applied to detect the expression level of 5 randomly selected miRNAs in multiple and uniparous hircine ovaries, and the results were consistent with the Solexa sequencing data. Conclusions In the present study, the different expression of miRNAs in the ovaries of multiple and uniparous goats during follicular phase were characterized and investigated using deep sequencing technology. The result will help to further understand the role of miRNAs in kidding rate regulation and also may help to identify miRNAs which could be potentially used to increase hircine ovulation rate and kidding rate in the future. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-339) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Xiao-Rong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, No, 130 Changjiang west road, Hefei 230036, P,R, China.
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Sha Z, Gong G, Wang S, Lu Y, Wang L, Wang Q, Chen S. Identification and characterization of Cynoglossus semilaevis microRNA response to Vibrio anguillarum infection through high-throughput sequencing. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 44:59-69. [PMID: 24296438 DOI: 10.1016/j.dci.2013.11.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 11/25/2013] [Accepted: 11/25/2013] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNA) play key regulatory roles in diverse biological processes. Cynoglossus semilaevis is an important commercial mariculture fish species in China. To identify miRNAs and investigate immune-related miRNAs of C. semilaevis, we performed high-throughput sequencing on three small RNA libraries prepared from C. semilaevis immune tissues (liver, head kidney, spleen, and intestine). One library was prepared under normal conditions (control, CG); two were prepared during Vibrio anguillarum infection, where vibriosis symptoms were obvious and non-obvious (HOSG and NOSG, respectively). We obtained 11,216,875, 12,313,404, and 11,398,695 clean reads per library, respectively. Bioinformatic analysis identified 452 miRNAs, including 24 putative novel miRNAs. We analyzed differentially expressed miRNAs between two libraries using pairwise comparison. For NOSG-CG, there was significant differential expression of 175 (38.72%) miRNAs. There was significant differential expression of 215 (47.57%) miRNAs between HOSG and CG. Compared with CG, The HOSG-NOSG comparison revealed significantly different expression of 122 (26.99%) miRNAs respectively. Real-time quantitative PCR (RT-qPCR) experiments were performed for 10 miRNAs of the three samples, and agreement was found between the sequencing and RT-qPCR data. For miRNAs that were significantly differentially expressed, functional annotation of target genes by Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that a set of miRNAs that were expressed highly abundantly and significantly differentially were might involved in immune system development and immune response. To our understanding, this is the first report of comprehensive identification of C. semilaevis miRNAs being differentially regulated in immune tissues (liver, head kidney, spleen, and intestine) in normal conditions relating to V. anguillarum infection. Many miRNAs were differentially regulated upon pathogen exposure. This work provides an opportunity for further understanding of the molecular mechanisms of miRNA regulation in C. semilaevis host-pathogen interactions.
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Affiliation(s)
- Zhenxia Sha
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.
| | - Guangye Gong
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China
| | - Shaolin Wang
- Department of Psychiatry & Neurobiology Science, University of Virginia, VA 22911, USA
| | - Yang Lu
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China; College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, PR China
| | - Lei Wang
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China
| | - Qilong Wang
- Tengzhou Fisheries Service Center, Tengzhou 277500, PR China
| | - Songlin Chen
- Key Lab for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China.
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45
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Liu B, Dou W, Ding TB, Zhong R, Liao CY, Xia WK, Wang JJ. An analysis of the small RNA transcriptome of four developmental stages of the citrus red mite (Panonychus citri). INSECT MOLECULAR BIOLOGY 2014; 23:216-229. [PMID: 24330037 DOI: 10.1111/imb.12075] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The citrus red mite (Panonychus citri) can feed on more than 112 plant species around the world. Endogenous small RNAs (sRNAs) have proved to be important components of gene regulation in many eukaryotes. Recently, many sRNAs have been shown to be involved in various biological processes, such as development in many animals, including insects; however, to date, no sRNAs have been reported in the citrus red mite. Using Illumina sequencing, several categories of sRNAs were identified, including 594 known microRNAs (miRNAs) grouped into 206 families and 31 novel miRNAs in the four developmental stages of citrus red mite. In addition, according to bioinformatics analysis and S-Poly(T) miRNA assays, the expression level of many miRNAs varied among the developmental stages. Furthermore, the prediction of miRNAs target genes and their functional annotation indicated that miRNAs are involved in the regulation of multiple pathways in the citrus red mite. As the first report of the sRNA world in citrus red mite, the present study furthers our understanding of the roles played by sRNAs in the development of citrus red mite and the data may help to develop methods of controlling the pests in the field.
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Affiliation(s)
- B Liu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
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46
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Wang X, Tang SM, Shen XJ. Overview of research on Bombyx mori microRNA. JOURNAL OF INSECT SCIENCE (ONLINE) 2014; 14:133. [PMID: 25368077 PMCID: PMC4222307 DOI: 10.1093/jis/14.1.133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 05/03/2013] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) constitute some of the most significant regulatory factors involved at the post-transcriptional level after gene expression, contributing to the modulation of a large number of physiological processes such as development, metabolism, and disease occurrence. This review comprehensively and retrospectively explores the literature investigating silkworm, Bombyx mori L. (Lepidoptera: Bombicidae), miRNAs published to date, including discovery, identification, expression profiling analysis, target gene prediction, and the functional analysis of both miRNAs and their targets. It may provide experimental considerations and approaches for future study of miRNAs and benefit elucidation of the mechanisms of miRNAs involved in silkworm developmental processes and intracellular activities of other unknown non-coding RNAs.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang City 212018 Jiangsu Province, People's Republic of China
| | - Shun-ming Tang
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang City 212018 Jiangsu Province, People's Republic of China
| | - Xing-jia Shen
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang City 212018 Jiangsu Province, People's Republic of China
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47
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Liang P, Feng B, Zhou X, Gao X. Identification and developmental profiling of microRNAs in diamondback moth, Plutellaxylostella (L.). PLoS One 2013; 8:e78787. [PMID: 24236051 PMCID: PMC3827265 DOI: 10.1371/journal.pone.0078787] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/22/2013] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are a group of small RNAs involved in various biological processes through negative regulation of mRNAs at the post-transcriptional level. Although miRNA profiles have been documented in over two dozen insect species, few are agricultural pests. In this study, both conserved and novel miRNAs in the diamondback moth, Plutella xylostella L., a devastating insect pest of cruciferous crops worldwide, were documented. High-throughput sequencing of a small RNA library constructed from a mixed life stages of P. xylostella, including eggs, 1st to 4th (last) instar larvae, pupae and adults, identified 384 miRNAs, of which 174 were P. xylostella specific. In addition, temporal expressions of 234 miRNAs at various developmental stages were investigated using a customized microarray analysis. Among the 91 differentially expressed miRNAs, qRT-PCR analysis was used to validate highly expressed miRNAs at each stage. The combined results not only systematically document miRNA profiles in an agriculturally important insect pest, but also provide molecular targets for future functional analysis and, ultimately, genetic-based pest control practice.
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Affiliation(s)
- Pei Liang
- Department of Entomology, China Agricultural University, Beijing, P. R. China
| | - Bing Feng
- Department of Entomology, China Agricultural University, Beijing, P. R. China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, Kentucky, United States of America
- * E-mail: (XZ); (XG)
| | - Xiwu Gao
- Department of Entomology, China Agricultural University, Beijing, P. R. China
- * E-mail: (XZ); (XG)
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48
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Nie Z, Zhou F, Li D, Lv Z, Chen J, Liu Y, Shu J, Sheng Q, Yu W, Zhang W, Jiang C, Yao Y, Yao J, Jin Y, Zhang Y. RIP-seq of BmAgo2-associated small RNAs reveal various types of small non-coding RNAs in the silkworm, Bombyx mori. BMC Genomics 2013; 14:661. [PMID: 24074203 PMCID: PMC3849828 DOI: 10.1186/1471-2164-14-661] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 09/26/2013] [Indexed: 12/21/2022] Open
Abstract
Background Small non-coding RNAs (ncRNAs) are important regulators of gene expression in eukaryotes. Previously, only microRNAs (miRNAs) and piRNAs have been identified in the silkworm, Bombyx mori. Furthermore, only ncRNAs (50-500nt) of intermediate size have been systematically identified in the silkworm. Results Here, we performed a systematic identification and analysis of small RNAs (18-50nt) associated with the Bombyx mori argonaute2 (BmAgo2) protein. Using RIP-seq, we identified various types of small ncRNAs associated with BmAGO2. These ncRNAs showed a multimodal length distribution, with three peaks at ~20nt, ~27nt and ~33nt, which included tRNA-, transposable element (TE)-, rRNA-, snoRNA- and snRNA-derived small RNAs as well as miRNAs and piRNAs. The tRNA-derived fragments (tRFs) were found at an extremely high abundance and accounted for 69.90% of the BmAgo2-associated small RNAs. Northern blotting confirmed that many tRFs were expressed or up-regulated only in the BmNPV-infected cells, implying that the tRFs play a prominent role by binding to BmAgo2 during BmNPV infection. Additional evidence suggested that there are potential cleavage sites on the D, anti-codon and TψC loops of the tRNAs. TE-derived small RNAs and piRNAs also accounted for a significant proportion of the BmAgo2-associated small RNAs, suggesting that BmAgo2 could be involved in the maintenance of genome stability by suppressing the activities of transposons guided by these small RNAs. Finally, Northern blotting was also used to confirm the Bombyx 5.8 s rRNA-derived small RNAs, demonstrating that various novel small RNAs exist in the silkworm. Conclusions Using an RIP-seq method in combination with Northern blotting, we identified various types of small RNAs associated with the BmAgo2 protein, including tRNA-, TE-, rRNA-, snoRNA- and snRNA-derived small RNAs as well as miRNAs and piRNAs. Our findings provide new clues for future functional studies of the role of small RNAs in insect development and evolution.
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Affiliation(s)
- Zuoming Nie
- College of Life Sciences, Zhejiang Sci-Tech University, Hanghzou 310018, China.
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Identification of differentially expressed genes in American cockroach ovaries and testes by suppression subtractive hybridization and the prediction of its miRNAs. Mol Genet Genomics 2013; 288:627-38. [PMID: 23996145 DOI: 10.1007/s00438-013-0777-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/19/2013] [Indexed: 10/26/2022]
Abstract
Studies on the cockroach have contributed to our understanding of several important developmental processes, especially those that can be easily studied in the embryo. However, our knowledge on late events such as gonad differentiation in the cockroach is still limited. The major aim of the present study was to identify sex-specific genes between adult female and male Periplaneta americana. Two cDNA libraries were constructed using the suppression subtractive hybridization method; a total of 433 and 599 unique sequences were obtained from the forward library and the reverse library, respectively, by cluster assembly, and sequence alignment of 1,032 expressed sequence tags. The analysis of the differentially expressed gene functions allowed these genes to be categorized into three groups: biological process, molecular function, and cellular component. The differentially expressed genes were suggested to be related to the development of the gonads of P. americana. Twelve differentially expressed genes were randomly selected and verified using relative quantitative real-time polymerase chain reaction (qRT-PCR). Meanwhile, by adopting a range of filtering criteria, we predicted two potential microRNA sequences for P. americana, pam-miR100-3p and pam-miR7. To confirm the expression of potential microRNAs (miRNAs) in American cockroach, a qRT-PCR approach was also employed. The data presented here offer the insights into the molecular foundation of sex differences in American cockroach, and the first report for the miRNAs in this species. In addition, the results can be used as a reference for unraveling candidate genes associated with the sex and reproduction of cockroaches.
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Jiang J, Ge X, Li Z, Wang Y, Song Q, Stanley DW, Tan A, Huang Y. MicroRNA-281 regulates the expression of ecdysone receptor (EcR) isoform B in the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:692-700. [PMID: 23707601 DOI: 10.1016/j.ibmb.2013.05.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/25/2013] [Accepted: 05/07/2013] [Indexed: 06/02/2023]
Abstract
Insect development and metamorphosis are regulated by the coordination of ecdysone and juvenile hormones. Insect microRNAs (miRNAs) also act in insect development and metamorphosis by regulating genes in the ecdysone cascade. Although hundreds of insect miRNAs have been identified, the physiological functions of most remain poorly understood. Here, we report that a conserved insect miRNA, microRNA-281 (miR-281), regulates the ecdysone receptor (EcR), in an isoform-specific manner in the silkworm Bombyx mori. The B. mori EcR (BmEcR) gene encodes three isoforms: BmEcR-A, BmEcR-B1 and BmEcR-B2. The 3'UTR regions of A and B genes, which contain multiple potential microRNA targeting sites, are distinct. Target prediction revealed that miR-281 may specifically target the 3'UTR of BmEcR-B. Using a dual luciferase reporter assay in HEK293T cells, we confirmed that miR-281 suppressed transcription of BmEcR-B but not BmEcR-A. The expression of miR-281 and BmEcR-B are well coordinated in the Malpighian tubules from the fourth larval molt to pupation. In the Malpighian tubules of fifth instar larvae, BmEcR-B protein expression was down-regulated after injection of a miR-281 mimic while up-regulated after injection of a miR-281 inhibitor. miR-281 expression was suppressed by 20-hydroxyecdysone treatments but not affected by juvenile hormone treatments. Based on these findings, we propose that miR-281 participates in B. mori developmental regulation in the Malpighian tubules through suppression of BmEcR-B expression.
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Affiliation(s)
- Jianhao Jiang
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai 200032, China
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