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Li C, Nong W, Boncan DAT, So WL, Yip HY, Swale T, Jia Q, Vicentin IG, Chung G, Bendena WG, Ngo JCK, Chan TF, Lam HM, Hui JHL. Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis. BMC Genomics 2024; 25:327. [PMID: 38565997 PMCID: PMC10985886 DOI: 10.1186/s12864-024-10232-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of food, protein and oil. Hence, it is imperative to maintain or to increase its yield under different conditions including challenges caused by abiotic and biotic stresses. In recent years, the soybean pod-sucking stinkbug Riptortus pedestris has emerged as an important agricultural insect pest in East, South and Southeast Asia. Here, we present a genomics resource for R. pedestris including its genome assembly, messenger RNA (mRNA) and microRNA (miRNA) transcriptomes at different developmental stages and from different organs. As insect hormone biosynthesis genes (genes involved in metamorphosis) and their regulators such as miRNAs are potential targets for pest control, we analyzed the sesquiterpenoid (juvenile) and ecdysteroid (molting) hormone biosynthesis pathway genes including their miRNAs and relevant neuropeptides. Temporal gene expression changes of these insect hormone biosynthesis pathways were observed at different developmental stages. Similarly, a diet-specific response in gene expression was also observed in both head and salivary glands. Furthermore, we observed that microRNAs (bantam, miR-14, miR-316, and miR-263) of R. pedestris fed with different types of soybeans were differentially expressed in the salivary glands indicating a diet-specific response. Interestingly, the opposite arms of miR-281 (-5p and -3p), a miRNA involved in regulating development, were predicted to target Hmgs genes of R. pedestris and soybean, respectively. These observations among others highlight stinkbug's responses as a function of its interaction with soybean. In brief, the results of this study not only present salient findings that could be of potential use in pest management and mitigation but also provide an invaluable resource for R. pedestris as an insect model to facilitate studies on plant-pest interactions.
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Affiliation(s)
- Chade Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Wenyan Nong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Delbert Almerick T Boncan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
| | - Wai Lok So
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | - Ho Yin Yip
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China
| | | | - Qi Jia
- Key Laboratory for Genetics Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Ignacio G Vicentin
- Instituto Nacional de Tecnologia Agropecuaria, Avenida Rivadavia, Ciudad de Buenos, 1439, Argentina
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, 59626, Korea
| | - William G Bendena
- Department of Biology, Queen's University, 116 Barrie St, Kingston, ON K7L 3N6, Canada
| | - Jacky C K Ngo
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Ting Fung Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
| | - Jerome H L Hui
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, China.
- Simon F.S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shat-in, HKSAR, China.
- Institute of Environment, Institute of Energy and Sustainability, The Chinese University of Hong Kong, Shatin, HKSAR, China.
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Maritz-Olivier C, Ferreira M, Olivier NA, Crafford J, Stutzer C. Mining gene expression data for rational identification of novel drug targets and vaccine candidates against the cattle tick, Rhipicephalus microplus. EXPERIMENTAL & APPLIED ACAROLOGY 2023; 91:291-317. [PMID: 37755526 PMCID: PMC10562289 DOI: 10.1007/s10493-023-00838-8] [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: 06/13/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023]
Abstract
Control of complex parasites via vaccination remains challenging, with the current combination of vaccines and small drugs remaining the choice for an integrated control strategy. Studies conducted to date, are providing evidence that multicomponent vaccines will be needed for the development of protective vaccines against endo- and ectoparasites, though multicomponent vaccines require an in-depth understanding of parasite biology which remains insufficient for ticks. With the rapid development and spread of acaricide resistance in ticks, new targets for acaricide development also remains to be identified, along with novel targets that can be exploited for the design of lead compounds. In this study, we analysed the differential gene expression of Rhipicephalus microplus ticks that were fed on cattle vaccinated with a multi-component vaccine (Bm86 and 3 putative Bm86-binding proteins). The data was scrutinised for the identification of vaccine targets, small drug targets and novel pathways that can be evaluated in future studies. Limitations associated with targeting novel proteins for vaccine and/or drug design is also discussed and placed into the context of challenges arising when targeting large protein families and intracellular localised proteins. Lastly, this study provide insight into how Bm86-based vaccines may reduce successful uptake and digestion of the bloodmeal and overall tick fecundity.
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Affiliation(s)
- Christine Maritz-Olivier
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa.
| | - Mariëtte Ferreira
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Nicholas A Olivier
- DNA Microarray Laboratory, Department of Plant Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Jan Crafford
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Christian Stutzer
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, Gauteng, South Africa.
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Zhang R, Zhang S, Li T, Li H, Zhang H, Zheng W. RNA sequencing identifies an ovary-enriched microRNA, miR-311-3p, involved in ovarian development and fecundity by targeting Endophilin B1 in Bactrocera dorsalis. PEST MANAGEMENT SCIENCE 2023; 79:688-700. [PMID: 36239581 DOI: 10.1002/ps.7236] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The oriental fruit fly, Bactrocera dorsalis, is a highly invasive pest in East Asia and the Pacific. With the development of pesticides resistance, environment-friendly pesticides are urgently needed. MicroRNAs (miRNAs) are critical regulators of numerous biological processes, including reproduction. Thus, it is significant to identify reproductive-related miRNAs in this notorious pest to facilitate its control, such as RNAi-based biopesticides targeting essential miRNAs. RESULTS A high-throughput sequencing was carried out to identify miRNAs involved in reproduction from the ovary and fat body at four developmental stages [1 day (d), 5, 9, and 13 days post-eclosion] in female B. dorsalis. Results showed that 98 and 74 miRNAs were differentially expressed in ovary and fat body, respectively, during sexual maturation. Gene ontology analysis showed that target genes involved in oogenesis and lipid particle accounted for 33% and 15% of the total targets, respectively. Among these differentially expressed miRNAs, we found by qPCR that miR-311-3p was enriched in the ovary and down-regulated during sexual maturation. Injection of agomir-miR-311-3p resulted in arrested ovarian development, reduced egg deposition and progeny viability. Endophilin B1 was confirmed to be the target of miR-311-3p, via dual-luciferase assay and expression profiling. Knockdown of Endophilin B1 resulted in reproductive defects similar to those caused by injection of miR-311-3p agomir. Thus, miR-311-3p might play a critical role in female reproduction by targeting Endophilin B1. CONCLUSION Our data not only provides knowledge on the abundance of reproductive-related miRNAs and target genes, but also promotes new control strategies for this pest. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Rui Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengfeng Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tianran Li
- Key Laboratory of Horticultural Plant Biology (MOE), Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Haozhe Li
- Key Laboratory of Horticultural Plant Biology (MOE), Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongyu Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weiwei Zheng
- Key Laboratory of Horticultural Plant Biology (MOE), Hubei Key Laboratory of Insect Resource Application and Sustainable Pest Control, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Aksoy E, Raikhel AS. Juvenile hormone regulation of microRNAs is mediated by E75 in the Dengue vector mosquito Aedes aegypti. Proc Natl Acad Sci U S A 2021; 118:e2102851118. [PMID: 34266957 PMCID: PMC8307694 DOI: 10.1073/pnas.2102851118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that play critical roles in controlling posttranscriptional gene regulation and have a profound effect on mosquito reproduction and metabolism. Juvenile hormone (JH) is critical for achieving reproductive competence in the main vector of human arboviral diseases, Aedes aegypti We report a JH-mediated mechanism governing miRNA expression. Using a transcription factor screen with multiple primary miRNA (pri-miRNA) promoters, we identified that the Ecdysone-induced protein E75 (E75) isoform (E75-RD) induced miRNA gene promoter activity. E75 binding sites were determined in miRNA promoters by means of cell transfection assay. E75-RD was found to be up-regulated by JH, as shown by the JH application and RNA interference (RNAi) of the JH receptor Methoprene-tolerant (Met). Small RNA sequencing from RNAi of Met and E75 displayed an overlapping miRNA cohort, suggesting E75 to be an intermediate component within the JH hierarchical network controlling miRNAs. Further experiments confirmed that E75-RD positively regulates several miRNAs including miR-2940. Reducing miR-2940 resulted in the arrest of follicle development and number of eggs laid. Performing miRNA target predictions and RT-qPCR from antagomir Ant-2940-3p-treated fat body tissues identified the mRNA target Clumsy (AAEL002518) The molecular interaction between this gene target and miR-2940 was confirmed using an in vitro dual luciferase assay in Drosophila S2 cells and in Ae. aegypti Aag2 cell lines. Finally, we performed a phenotypic rescue experiment to demonstrate that miR-2940/Clumsy is responsible for the disruption in egg development. Collectively, these results established the role of JH-mediated E75-RD in regulation of miRNA gene expression during the mosquito reproductive cycle.
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Affiliation(s)
- Emre Aksoy
- Department of Entomology, University of California, Riverside, CA 92521
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA 92521
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Alexander S Raikhel
- Department of Entomology, University of California, Riverside, CA 92521;
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
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