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Ma X, Liao Z, Cai R, Yin Z, Chen Q, Yan Y, Li H, Guo J. A novel lncRNA PDG1 targets NADP-ME to modulate TCA cycle and JH in Aspongopus chinensis diapause. Int J Biol Macromol 2025; 297:139848. [PMID: 39814299 DOI: 10.1016/j.ijbiomac.2025.139848] [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: 09/28/2024] [Revised: 12/29/2024] [Accepted: 01/12/2025] [Indexed: 01/18/2025]
Abstract
Diapause is essential for insect survival under adverse environmental conditions and plays a crucial role in regulating reproduction. However, the role of long non-coding RNAs (lncRNAs) in this process remains unclear. In this study, we investigated the function of lncRNAs in the diapause of Aspongopus chinensis. A total of 28,360 lncRNAs were identified across the transcriptomes, with 814 upregulated and 512 downregulated during diapause. Analysis revealed 48 key mRNAs regulated by these lncRNAs, primarily associated with energy metabolism. Among them, the NADP+-dependent malic enzyme (NADP-ME) gene was notably enriched in these pathways. Knockdown of NADP-ME resulted in decreased pyruvate levels and TCA activity. We identified a novel lncRNA, PDG1, which regulates NADP-ME expression, and RNA interference targeting PDG1 increased NADP-ME levels, leading to enhanced pyruvate levels and elevated TCA cycle activity, with dual luciferase assays confirming that PDG1 directly targeted NADP-ME and downregulated its expression. Furthermore, secondary structure analysis revealed that PDG1 exhibited significantly lower free energy compared to NADP-ME, with fewer hairpins and stem-loops. These findings highlight PDG1's critical role in regulating TCA cycle activity by targeting NADP-ME during A. chinensis diapause, revealing a novel mechanism through which lncRNAs modulate metabolic pathways to control insect diapause.
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Affiliation(s)
- Xinyi Ma
- Institute of Entomology, Guizhou University, Guiyang 550025, PR China
| | - Zixuan Liao
- Institute of Entomology, Guizhou University, Guiyang 550025, PR China
| | - Renlian Cai
- Zunyi Medical University, Zunyi, 563006, PR China
| | - Zhiyong Yin
- Institute of Entomology, Guizhou University, Guiyang 550025, PR China
| | - Qingting Chen
- Institute of Entomology, Guizhou University, Guiyang 550025, PR China
| | - Yufang Yan
- Institute of Entomology, Guizhou University, Guiyang 550025, PR China
| | - Haiyin Li
- Institute of Entomology, Guizhou University, Guiyang 550025, PR China.
| | - Jianjun Guo
- Institute of Entomology, Guizhou University, Guiyang 550025, PR China.
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Molik DC, Stahlke AR, Sharma SP, Simmonds TJ, Corpuz RL, Kauwe AN, Schrader JE, Mason CJ, Sim SB, Geib SM. otb: an automated HiC/HiFi pipeline assembles the Prosapia bicincta Genome. G3 (BETHESDA, MD.) 2024; 14:jkae129. [PMID: 38861413 PMCID: PMC11304988 DOI: 10.1093/g3journal/jkae129] [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: 05/01/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024]
Abstract
The implementation of a new genomic assembly pipeline named only the best (otb) has effectively addressed various challenges associated with data management during the development and storage of genome assemblies. otb, which incorporates a comprehensive pipeline involving a setup layer, quality checks, templating, and the integration of Nextflow and Singularity. The primary objective of otb is to streamline the process of creating a HiFi/HiC genome, aiming to minimize the manual intervention required in the genome assembly process. The 2-lined spittlebug, (Prosapia bicincta, Hemiptera: Cercopidae), a true bug insect herbivore, serves as a practical test case for evaluating otb. The 2-lined spittlebug is both a crucial agricultural pest and a genomically understudied insect belonging to the order Hemiptera. This insect is a significant threat to grasslands and pastures, leading to plant wilting and phytotoxemia when infested. Its presence in tropical and subtropical regions around the world poses a long-term threat to the composition of plant communities in grassland landscapes, impacting rangelands, and posing a substantial risk to cattle production.
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Affiliation(s)
- David C Molik
- Arthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research, United States Department of Agriculture, Agricultural Research Service, 1515 College Ave, Manhattan, KS 66502, USA
| | - Amanda R Stahlke
- Department of Biological Sciences, Wubben Hall and Science Center, Colorado Mesa University, 1100 North Avenue, Grand Junction, CO 81501-3122, USA
| | - Sharu P Sharma
- Genome Informatics Facility, Iowa State University, 2200 Osborn Drive, Ames, IA 50011-4009, USA
| | - Tyler J Simmonds
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Renee L Corpuz
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Angela N Kauwe
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Jeremy E Schrader
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Charles J Mason
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Sheina B Sim
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
| | - Scott M Geib
- Tropical Pest Genetics and Molecular Biology Research Unit, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, 64 Nowelo St, Hilo, HI 96720, USA
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Yin Z, Yan Y, Khan S, Cai R, Li H, Guo J. Differential expression of microRNAs in diapause and non-diapause gonads of Aspongopus chinensis Dallas (Hemiptera: Dinidoridae): implications for reproductive control. JOURNAL OF INSECT SCIENCE (ONLINE) 2024; 24:22. [PMID: 38809688 PMCID: PMC11135359 DOI: 10.1093/jisesa/ieae021] [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: 10/18/2023] [Revised: 01/02/2024] [Accepted: 05/25/2024] [Indexed: 05/31/2024]
Abstract
Aspongopus chinensis Dallas, 1851 (Hemiptera: Dinidoridae), an edible and medicinal insect, usually found in China and Southeast Asia, offers substantial potential for various applications. The reproductive cycle of this particular insect occurs annually because of reproductive diapause, leading to inadequate utilization of available natural resources. Despite its considerable ecological importance, the precise mechanisms underlying diapause in A. chinensis are not yet well understood. In this study, we conducted an analysis of comparing the microRNA (miRNA) regulation in the diapause and non-diapause gonads of A. chinensis and identified 303 differentially expressed miRNAs, among which, compared with the diapause group, 76 miRNAs were upregulated and 227 miRNAs downregulated. The results, regarding the Enrichment analysis of miRNA-targeted genes, showed their involvement in several essential biological processes, such as lipid anabolism, energy metabolism, and gonadal growth. Interestingly, we observed that the ATP-binding cassette pathway is the only enriched pathway, demonstrating the capability of these targeted miRNAs to regulate the reproductive diapause of A. chinensis through the above essential pathway. The current study provided the role of gonadal miRNA expression in the control of reproductive diapause in A. chinensis, the specific regulatory mechanism behind this event remained unknown and needed more investigation.
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Affiliation(s)
- Zhiyong Yin
- Institute of Entomology, Guizhou University, Guiyang 550025, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang 550025, P. R. China
| | - Yufang Yan
- Institute of Entomology, Guizhou University, Guiyang 550025, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang 550025, P. R. China
| | - Samiullah Khan
- Institute of Entomology, Guizhou University, Guiyang 550025, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang 550025, P. R. China
| | - Renlian Cai
- Institute of Entomology, Guizhou University, Guiyang 550025, P. R. China
| | - Haiyin Li
- Institute of Entomology, Guizhou University, Guiyang 550025, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang 550025, P. R. China
| | - Jianjun Guo
- Institute of Entomology, Guizhou University, Guiyang 550025, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang 550025, P. R. China
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Cai R, Chen X, Khan S, Li H, Tan J, Tian Y, Zhao S, Yin Z, Jin D, Guo J. Aspongopus chinensis Dallas induces pro-apoptotic and cell cycle arresting effects in hepatocellular carcinoma cells by modulating miRNA and mRNA expression. Heliyon 2024; 10:e27525. [PMID: 38500987 PMCID: PMC10945178 DOI: 10.1016/j.heliyon.2024.e27525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/20/2024] Open
Abstract
Aspongopus chinensis Dallas is a traditional Chinese medicinal insect with several anticancer properties can inhibit cancer cell growth, by inhibiting cell division, autophagy and cell cycle. However, the precise therapeutics effects and mechanisms of this insect on liver cancer are still unknown. This study examined the inhibitory influence of A. chinensis on the proliferation of hepatocellular carcinoma (HCC) cells and explore the underlying mechanism using high-throughput sequencing. The results showed that A. chinensis substantially reduced the viability of Hep G2 cells. A total of 33 miRNAs were found to be upregulated, while 43 miRNAs were downregulated. Additionally, 754 mRNAs were upregulated and 863 mRNAs were downregulated. Significant enrichment of differentially expressed genes was observed in signaling pathways related to tumor cell growth, cell cycle regulation, and apoptosis. Differentially expressed miRNAs exhibited a targeting relationship with various target genes, including ARC, HSPA6, C11orf86, and others. Hence, cell cycle and apoptosis were identified by flow cytometry. These findings indicate that A. chinensis impeded cell cycle advancement, halted the cell cycle in the G0/G1 and S stages, and stimulated apoptosis. Finally, mouse experiments confirmed that A. chinensis significantly inhibits tumor growth in vivo. Therefore, our findings indicate that A. chinensis has a notable suppressive impact on the proliferation of HCC cells. The potential mechanism of action could involve the regulation of mRNA expression via miRNA, ultimately leading to cell cycle arrest and apoptosis. The results offer a scientific foundation for the advancement and application of A. chinensis in the management of HCC.
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Affiliation(s)
- Renlian Cai
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
- Department of Histology and Embryology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Xumei Chen
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Samiullah Khan
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Haiyin Li
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Jun Tan
- Department of Histology and Embryology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Ying Tian
- Department of Histology and Embryology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Shuai Zhao
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Zhiyong Yin
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Daochao Jin
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Jianjun Guo
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
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Ma X, Yin Z, Li H, Guo J. HSP gene superfamily in Aspongopus chinensis Dallas: unravelling identification, characterisation and expression patterns during diapause and non-diapause stages. BULLETIN OF ENTOMOLOGICAL RESEARCH 2024:1-11. [PMID: 38425077 DOI: 10.1017/s0007485324000075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Aspongopus chinensis Dallas 1851, an insect of important economic value, faces challenges in artificial breeding due to mandatory diapause and limited access to wild resources. Heat shock proteins (Hsps) are thought to influence diapause in insects, but little is known about their role in A. chinensis during diapause. This study used genomic methods to identify 25 Hsp genes in A. chinensis, including two Hsp90, 14 Hsp70, four Hsp60 and five small Hsp genes, were located on seven chromosomes, respectively. The gene structures among the same families are relatively conserved. Meanwhile, the motif compositions and secondary structures of A. chinensis Hsps (AcHsps) were predicted. RNA-seq data and fluorescence quantitative PCR analysis showed that there were differences in the expression patterns of AcHsps in diapause and non-diapause stages, and AcHsp70-5 was significantly differentially expressed in both analysis, which was enriched in the pathway of response to hormone. All the results showed that Hsps play an important role in the diapause mechanism of A. chinensis. Our observations highlight the molecular evolution of the Hsp gene and their effect on diapause in A. chinensis.
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Affiliation(s)
- Xinyi Ma
- Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang, P. R. China
| | - Zhiyong Yin
- Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang, P. R. China
| | - Haiyin Li
- Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang, P. R. China
| | - Jianjun Guo
- Institute of Entomology, Guizhou University, Guiyang, P. R. China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Ministry of Agriculture and Rural Affairs of the P. R. China, Guiyang, P. R. China
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Wang YH, Luan YX, Luo JY, Men Y, Engel MS, Damgaard J, Khila A, Chen PP, Figueiredo Moreira FF, Rafael JA, Xie Q. 300 Million years of coral treaders (Insecta: Heteroptera: Hermatobatidae) back to the ocean in the phylogenetic context of Arthropoda. Proc Biol Sci 2023; 290:20230855. [PMID: 37357866 PMCID: PMC10291715 DOI: 10.1098/rspb.2023.0855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/06/2023] [Indexed: 06/27/2023] Open
Abstract
Among hundreds of insect families, Hermatobatidae (commonly known as coral treaders) is one of the most unique. They are small, wingless predaceous bugs in the suborder Heteroptera. Adults are almost black in colour, measuring about 5 mm in body length and 3 mm in width. Thirteen species are known from tropical coral reefs or rocky shores, but their origin and evolutionary adaptation to their unusual marine habitat were unexplored. We report here the genome and metagenome of Hermatobates lingyangjiaoensis, hitherto known only from its type locality in the South China Sea. We further reconstructed the evolutionary history and origin of these marine bugs in the broader context of Arthropoda. The dated phylogeny indicates that Hexapoda diverged from their marine sister groups approximately 498 Ma and that Hermatobatidae originated 192 Ma, indicating that they returned to an oceanic life some 300 Myr after their ancestors became terrestrial. Their origin is consistent with the recovery of tropical reef ecosystems after the end-Triassic mass extinction, which might have provided new and open niches for them to occupy and thrive. Our analyses also revealed that both the genome changes and the symbiotic bacteria might have contributed to adaptations necessary for life in the sea.
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Affiliation(s)
- Yan-hui Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 Xingangxi Road, Guangzhou 510275, Guangdong, China
| | - Yun-xia Luan
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, 55 West of Zhongshan Avenue, Guangzhou 510631, China
| | - Jiu-yang Luo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 Xingangxi Road, Guangzhou 510275, Guangdong, China
| | - Yu Men
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 Xingangxi Road, Guangzhou 510275, Guangdong, China
| | - Michael S. Engel
- Division of Entomology, Natural History Museum, and Department of Ecology and Evolutionary Biology, University of Kansa, 1501 Crestline Drive – Suite 140, Lawrence, KS 66045, USA
| | - Jakob Damgaard
- Natural History Museum of Denmark, Zoological Museum, Universitetsparken 15, 2100 Copenhagen Ø, Denmark
| | - Abderrahman Khila
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Ping-ping Chen
- Netherlands Centre of Biodiversity Naturalis, 2300 RA, Leiden, The Netherlands
| | | | - José A. Rafael
- Instituto Nacional de Pesquisas da Amazônia, INPA, Caixa Postal 478, 69011-970 Manaus, Amazonas, Brazil
| | - Qiang Xie
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 135 Xingangxi Road, Guangzhou 510275, Guangdong, China
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