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Shu B, Lin Y, Qian G, Cai X, Liu L, Lin J. Integrated miRNA and transcriptome profiling to explore the molecular mechanism of Spodoptera frugiperda larval midgut in response to azadirachtin exposure. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 187:105192. [PMID: 36127051 DOI: 10.1016/j.pestbp.2022.105192] [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: 04/21/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
As a destructive agricultural pest, Spodoptera frugiperda has spread worldwide in the past few years. Azadirachtin, an environmentally friendly and most promising compound, showed adverse effects, including mortality and growth inhibition, against S. frugiperda. While the effects of azadirachtin on the midgut of this pest remain to be determined. In this study, structural damage was observed in the larval midguts of S. frugiperda with azadirachtin exposure. RNA-seq on the larval midguts with different azadirachtin treatments was performed. Compared to the control group, a total of 3344 and 4759 differentially expressed genes (DEGs) were identified in the midguts with 0.1 and 0.5 μg/g azadirachtin exposure, respectively. Among them, the DEGs encoding detoxification enzymes/proteins, immune-related proteins, digestion and absorption-related proteins, and transcript factors were further analyzed. High-throughput sequencing was also used for the identification of differentially expressed microRNAs in different treatments. A total of 153 conserved miRNAs and 147 novel miRNAs were identified, of which 11 and 29 miRNAs were affected by 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The integrated analysis found that 13 and 178 miRNA versus mRNA pairs were acquired in the samples with 0.1 and 0.5 μg/g azadirachtin treatments, respectively. The results of high-throughput sequencing were confirmed by real-time quantitative polymerase chain reaction (RT-qPCR). These results provide useful information for revealing the molecular mechanism of S. frugiperda larval midgut in response to azadirachtin.
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Affiliation(s)
- Benshui Shu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Yanzheng Lin
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Guozhao Qian
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Xueming Cai
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Luyang Liu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China
| | - Jintian Lin
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, PR China.
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Lyne R, Bazaga A, Butano D, Contrino S, Heimbach J, Hu F, Kalderimis A, Lyne M, Reierskog K, Stepan R, Sullivan J, Wise A, Yehudi Y, Micklem G. HumanMine: advanced data searching, analysis and cross-species comparison. Database (Oxford) 2022; 2022:6640317. [PMID: 35820040 PMCID: PMC9275753 DOI: 10.1093/database/baac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/07/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
HumanMine (www.humanmine.org) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated exploration and analysis of data compiled from experimental, computational and curated data sources. Built using the InterMine data integration platform, HumanMine includes genes, proteins, pathways, expression levels, Single nucleotide polymorphism (SNP), diseases and more, integrated into a single searchable database. HumanMine promotes integrative analysis, a powerful approach in modern biology that allows many sources of evidence to be analysed together. The data can be accessed through a user-friendly web interface as well as a powerful, scriptable web service Application programming interface (API) to allow programmatic access to data. The web interface includes a useful identifier resolution system, sophisticated query options and interactive results tables that enable powerful exploration of data, including data summaries, filtering, browsing and export. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other biological entities. HumanMine can be used for integrative multistaged analysis that can lead to new insights and uncover previously unknown relationships. Database URL: https://www.humanmine.org
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Affiliation(s)
- Rachel Lyne
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Adrián Bazaga
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Daniela Butano
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Sergio Contrino
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Joshua Heimbach
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Fengyuan Hu
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Alexis Kalderimis
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Mike Lyne
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Kevin Reierskog
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Radek Stepan
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Julie Sullivan
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Archie Wise
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Yo Yehudi
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
| | - Gos Micklem
- Department of Genetics, University of Cambridge , Downing Pl, Cambridge, CB2 3EH, UK
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Wu HP, Wang XY, Hu J, Su RR, Lu W, Zheng XL. Identification of neuropeptides and neuropeptide receptor genes in Phauda flammans (Walker). Sci Rep 2022; 12:9892. [PMID: 35701459 PMCID: PMC9198061 DOI: 10.1038/s41598-022-13590-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022] Open
Abstract
Neuropeptides and neuropeptide receptors are crucial regulators to insect physiological processes. The 21.0 Gb bases were obtained from Illumina sequencing of two libraries representing the female and male heads of Phauda flammans (Walker) (Lepidoptera: Phaudidae), which is a diurnal defoliator of ficus plants and usually outbreaks in the south and south-east Asia, to identify differentially expressed genes, neuropeptides and neuropeptide receptor whose tissue expressions were also evaluated. In total, 99,386 unigenes were obtained, in which 156 up-regulated and 61 down-regulated genes were detected. Fifteen neuropeptides (i.e., F1b, Ast, NP1, IMF, Y, BbA1, CAP2b, NPLP1, SIF, CCH2, NP28, NP3, PDP3, ARF2 and SNPF) and 66 neuropeptide receptor genes (e.g., A2-1, FRL2, A32-1, A32-2, FRL3, etc.) were identified and well-clustered with other lepidopteron. This is the first sequencing, identification neuropeptides and neuropeptide receptor genes from P. flammans which provides valuable information regarding the molecular basis of P. flammans.
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Affiliation(s)
- Hai-Pan Wu
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Xiao-Yun Wang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Jin Hu
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Ran-Ran Su
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Wen Lu
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Xia-Lin Zheng
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning, 530004, China.
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Wu M, Qi G, Chen H, Ma J, Liu J, Jiang Y, Lee G, Otuka A, Hu G. Overseas immigration of fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), invading Korea and Japan in 2019. INSECT SCIENCE 2022; 29:505-520. [PMID: 34050604 PMCID: PMC9292357 DOI: 10.1111/1744-7917.12940] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 05/02/2023]
Abstract
The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith), spread rapidly in Africa and Asia recently, causing huge economic losses in crop production. Fall armyworm caterpillars were first detected in South Korea and Japan in June 2019. Here, the migration timing and path for FAW into the countries were estimated by a trajectory simulation approach implementing the insect's flight behavior. The result showed that FAWs found in both South Korea and Japan were estimated to have come from eastern China by crossing the Yellow Sea or the East China Sea in 10-36 h in three series of migrations. In the first series, FAW moths that arrived on Jeju Island during 22-24 May were estimated to be from Zhejiang, Anhui and Fujian Provinces after 1-2 nights' flights. In the second series, it was estimated that FAW moths landed in southern Korea and Kyushu region of Japan simultaneously or successively during 5-9 June, and these moths mostly came from Guangdong and Fujian Provinces. The FAW moths in the third series were estimated to have immigrated from Taiwan Province onto Okinawa Islands during 19-24 June. During these migrations, southwesterly low-level jets extending from eastern China to southern Korea and/or Japan were observed in the northwestern periphery of the western Pacific Subtropical High. These results, for the first time, suggested that the overseas FAW immigrants invading Korea and Japan came from eastern and southern China. This study is helpful for future monitoring, early warning and the source control of this pest in the two countries.
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Affiliation(s)
- Ming‐Fei Wu
- College of Plant ProtectionNanjing Agricultural UniversityNanjing210095China
| | - Guo‐Jun Qi
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection/Plant Protection Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou510640China
| | - Hui Chen
- College of Plant ProtectionNanjing Agricultural UniversityNanjing210095China
| | - Jian Ma
- College of Plant ProtectionNanjing Agricultural UniversityNanjing210095China
| | - Jie Liu
- Division of Pest ForecastingChina National Agro‐Tech Extension and Service CenterBeijing100026China
| | - Yu‐Ying Jiang
- Division of Pest ForecastingChina National Agro‐Tech Extension and Service CenterBeijing100026China
| | - Gwan‐Seok Lee
- Department of Agro‐food Safety and Crop ProtectionNational Institute of Agricultural SciencesWanju55365Korea
| | - Akira Otuka
- Institute of Agricultural MachineryNational Agriculture and Food Research OrganizationTsukuba3058517Japan
| | - Gao Hu
- College of Plant ProtectionNanjing Agricultural UniversityNanjing210095China
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