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Ghaffar A, Khan N, Saleem MZ, Ali I, Rehman AU, Shah WA, Samiullah. Identification and Characterization of Evolutionary Conserved Muskmelon Non-coding miRNAs and Their Target Proteins. Biochem Genet 2024:10.1007/s10528-024-10829-y. [PMID: 38816671 DOI: 10.1007/s10528-024-10829-y] [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: 12/07/2023] [Accepted: 05/08/2024] [Indexed: 06/01/2024]
Abstract
MicroRNAs (miRNAs) are short, endogenously encoded small RNAs, 18-26 nucleotides in length, which can posttranscriptionally regulate gene expression through translation inhibition or endonucleolytic cleavage. The muskmelon is one of the most widely cultivated fruits in the Cucurbitaceae family. Despite its significance, only 120 miRNAs from different families have been reported in muskmelon. In this study, we aimed to expand this knowledge base by predicting 40 new miRNAs in muskmelon using a spectrum of genomic-based tools. Precursor and mature sequences were obtained from microRNA registry database as reference and analyzed via the basic local alignment search tool (Blastn) for ESTs identification. After removing the non-coding sequences, the remaining candidate sequences were analyzed using MFOLD to generate secondary structures for the newly predicted miRNAs. Additionally, the predicted muskmelon miRNAs were validated using a set of five randomly chosen primers and RT-PCR. Through gene ontology (GO) analysis, we identified 89 targets associated with newly predicted muskmelon miRNAs. Transcription factor-coding genes play a crucial role in plant growth and development. Additionally, the miR4249 has been found to have the same targets in muskmelon that have been linked to cell signaling and transcription factors. The identified targets are integral for diverse biological processes including plant growth, development, metabolism, aging, disease resistance, and resistance to environmental stresses, such as salt, cold, and oxidative stress. As a result, the outcomes of this study demonstrate that this mechanism not only contributes to the production of a higher quality crop but also enhances overall production.
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Affiliation(s)
- Abdul Ghaffar
- Colleges Higher and Technical Education Department Balochistan, Quetta, 87300, Pakistan.
- Department of Chemistry, University of Balochistan, Quetta, 87300, Pakistan.
| | - Naqeebullah Khan
- Department of Chemistry, University of Balochistan, Quetta, 87300, Pakistan
| | - Muhammad Zafar Saleem
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Lahore, Pakistan
| | - Irshad Ali
- Department of Chemistry, University of Balochistan, Quetta, 87300, Pakistan
| | - Attiq Ur Rehman
- Department of Chemistry, University of Balochistan, Quetta, 87300, Pakistan
| | - Waheed Ahmed Shah
- Department of Chemistry, University of Balochistan, Quetta, 87300, Pakistan
| | - Samiullah
- Department of Chemistry, University of Balochistan, Quetta, 87300, Pakistan
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2
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Bo C, Liu M, You Q, Liu X, Zhu Y, Duan Y, Wang D, Xue T, Xue J. Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings. BMC Genomics 2024; 25:398. [PMID: 38654150 DOI: 10.1186/s12864-024-10318-x] [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: 09/28/2023] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the "sprout tumble" phenomenon because of high temperatures, resulting in a significant yield reduction. However, the molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat-response genes, microRNAs (miRNAs), and key miRNA-target pairs in P. ternata that differed between heat-stress and room-temperature conditions. Transcriptome analysis revealed extensive reprogramming of 4,960 genes across various categories, predominantly associated with cellular and metabolic processes, responses to stimuli, biological regulation, cell parts, organelles, membranes, and catalytic and binding activities. miRNAome sequencing identified 1,597 known/conserved miRNAs that were differentially expressed between the two test conditions. According to the analysis, genes and miRNAs associated with the regulation of transcription, DNA template, transcription factor activity, and sequence-specific DNA binding pathways may play a major role in the resistance to heat stress in P. ternata. Integrated analysis of the transcriptome and miRNAome expression data revealed 41 high-confidence miRNA-mRNA pairs, forming 25 modules. MYB-like proteins and calcium-responsive transcription coactivators may play an integral role in heat-stress resistance in P. ternata. Additionally, the candidate genes and miRNAs were subjected to quantitative real-time polymerase chain reaction to validate their expression patterns. These results offer a foundation for future studies exploring the mechanisms and critical genes involved in heat-stress resistance in P. ternata.
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Affiliation(s)
- Chen Bo
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Mengmeng Liu
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Qian You
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Xiao Liu
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yanfang Zhu
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yongbo Duan
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Dexin Wang
- College of Agriculture and Bioengineering, Heze University, Heze, 274000, China.
| | - Tao Xue
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
| | - Jianping Xue
- Anhui Provincial Engineering Laboratory for Efficient Utilization of Featured Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
- Huaibei Key Laboratory of Efficient Cultivation and Utilization of Resource Plants, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
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Chaudhary V, Kumar M, Chauhan C, Sirohi U, Srivastav AL, Rani L. Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120326. [PMID: 38387349 DOI: 10.1016/j.jenvman.2024.120326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/14/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.
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Affiliation(s)
- Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, Uttar-Pradesh, India
| | - Mukesh Kumar
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Chetan Chauhan
- Department of Floriculture and Landscaping Architecture, College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | - Ujjwal Sirohi
- National Institute of Plant Genome Research, New Delhi, India
| | - Arun Lal Srivastav
- Chitkara University School of Engineering and Technology, Chitkara University, Himachal Pradesh, India.
| | - Lata Rani
- Chitkara School of Pharmacy, Chitkara University, Himachal Pradesh, India
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Rumyantsev SD, Veselova SV, Burkhanova GF, Alekseev VY, Maksimov IV. Bacillus subtilis 26D Triggers Induced Systemic Resistance against Rhopalosiphum padi L. by Regulating the Expression of Genes AGO, DCL and microRNA in Bread Spring Wheat. Microorganisms 2023; 11:2983. [PMID: 38138127 PMCID: PMC10745712 DOI: 10.3390/microorganisms11122983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Bacillus subtilis 26D is a plant growth-promoting endophytic bacteria capable of inducing systemic resistance through the priming mechanism, which includes plant genome reprogramming and the phenomenon of RNA interference (RNAi) and microRNA (miRNAs). The phloem-feeding insect bird cherry-oat aphid Rhopalosiphum padi L. is a serious pest that causes significant damage to crops throughout the world. However, the function of plant miRNAs in the response to aphid infestation remains unclear. The results of this work showed that B. subtilis 26D stimulated aphid resistance in wheat plants, inducing the expression of genes of hormonal signaling pathways ICS, WRKY13, PR1, ACS, EIN3, PR3, and ABI5. In addition, B. subtilis 26D activated the RNAi mechanism and regulated the expression of nine conserved miRNAs through activation of the ethylene, salicylic acid (SA), and abscisic acid (ABA) signaling pathways, which was demonstrated by using treatments with phytohormones. Treatment of plants with SA, ethylene, and ABA acted in a similar manner to B. subtilis 26D on induction of the expression of the AGO4, AGO5 and DCL2, DCL4 genes, as well as the expression of nine conserved miRNAs. Different patterns of miRNA expression were found in aphid-infested plants and in plants treated with B. subtilis 26D or SA, ethylene, and ABA and infested by aphids, suggesting that miRNAs play multiple roles in the plant response to phloem-feeding insects, associated with effects on hormonal signaling pathways, redox metabolism, and the synthesis of secondary metabolites. Our study provides new data to further elucidate the fine mechanisms of bacterial-induced priming. However, further extensive work is needed to fully unravel these mechanisms.
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Affiliation(s)
| | - Svetlana V. Veselova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya, 71, 450054 Ufa, Russia; (S.D.R.); (G.F.B.); (V.Y.A.); (I.V.M.)
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Payne D, Li Y, Govindan G, Kumar A, Thomas J, Addo-Quaye CA, Pereira A, Sunkar R. High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness. Int J Mol Sci 2023; 24:11631. [PMID: 37511395 PMCID: PMC10380806 DOI: 10.3390/ijms241411631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.
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Affiliation(s)
- David Payne
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Yongfang Li
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ganesan Govindan
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Charles A Addo-Quaye
- Department of Computer Science and Cybersecurity, Metropolitan State University, Saint Paul, MN 55106, USA
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Han WH, Wang JX, Zhang FB, Liu YX, Wu H, Wang XW. Small RNA and Degradome Sequencing Reveal Important MicroRNA Function in Nicotiana tabacum Response to Bemisia tabaci. Genes (Basel) 2022; 13:361. [PMID: 35205405 PMCID: PMC8871844 DOI: 10.3390/genes13020361] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/07/2022] [Accepted: 02/15/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs), a class of small non-coding regulatory RNAs, are key molecules in many biological and metabolic processes of plant growth, development and stress response via targeting mRNAs. The phloem-feeding insect whitefly Bemisia tabaci (Hemiptera, Aleyrodidae) is a serious pest that causes devastating harm to agricultural production worldwide. However, the function of host miRNAs in the response to whitefly infestation remains unclear. Here, we sequenced the small RNA and degradome of tobacco (Nicotiana tabacum L.), after and before infestation by B. tabaci. We identified 1291 miRNAs belonging to 138 miRNA families including 706 known miRNAs and 585 novel miRNAs. A total of 47 miRNAs were differentially expressed, of which 30 were upregulated and 17 were downregulated by whitefly exposure. Then, computational analysis showed that the target genes of differential miRNAs were involved in R gene regulation, plant innate immunity, plant pathogen defense, the plant hormone signal pathway and abiotic stress tolerance. Furthermore, degradome analysis demonstrated that 253 mRNAs were cleaved by 66 miRNAs. Among them, the targets cleaved by upregulated miR6025, miR160, miR171, miR166 and miR168 are consistent with our prediction, suggesting that pathogen-related miRNAs may function in plant defense against whitefly. Moreover, our results show that plant miRNA response and miRNA-mediated post-transcriptional regulation for phloem-feeding insect infestation are similar to pathogen invasion. Our study provides additional data to further elucidate how host plants respond and defend the phloem-feeding insects.
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Affiliation(s)
| | | | | | | | | | - Xiao-Wei Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; (W.-H.H.); (J.-X.W.); (F.-B.Z.); (Y.-X.L.); (H.W.)
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7
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Villalba-Bermell P, Marquez-Molins J, Marques MC, Hernandez-Azurdia AG, Corell-Sierra J, Picó B, Monforte AJ, Elena SF, Gomez GG. Combined Stress Conditions in Melon Induce Non-additive Effects in the Core miRNA Regulatory Network. FRONTIERS IN PLANT SCIENCE 2021; 12:769093. [PMID: 34899791 PMCID: PMC8656716 DOI: 10.3389/fpls.2021.769093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/14/2021] [Indexed: 06/14/2023]
Abstract
Climate change has been associated with a higher incidence of combined adverse environmental conditions that can promote a significant decrease in crop productivity. However, knowledge on how a combination of stresses might affect plant development is still scarce. MicroRNAs (miRNAs) have been proposed as potential targets for improving crop productivity. Here, we have combined deep-sequencing, computational characterization of responsive miRNAs and validation of their regulatory role in a comprehensive analysis of response of melon to several combinations of four stresses (cold, salinity, short day, and infection with a fungus). Twenty-two miRNA families responding to double and/or triple stresses were identified. The regulatory role of the differentially expressed miRNAs was validated by quantitative measurements of the expression of the corresponding target genes. A high proportion (ca. 60%) of these families (mainly highly conserved miRNAs targeting transcription factors) showed a non-additive response to multiple stresses in comparison with that observed under each one of the stresses individually. Among those miRNAs showing non-additive response to stress combinations, most interactions were negative, suggesting the existence of functional convergence in the miRNA-mediated response to combined stresses. Taken together, our results provide compelling pieces of evidence that the response to combined stresses cannot be easily predicted from the study individual stresses.
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Affiliation(s)
- Pascual Villalba-Bermell
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - Joan Marquez-Molins
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - María-Carmen Marques
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - Andrea G. Hernandez-Azurdia
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - Julia Corell-Sierra
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
| | - Belén Picó
- Instituto de Conservacióny Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Antonio J. Monforte
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universitat Politècnica de València (UPV), Valencia, Spain
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
- The Santa Fe Institute, Santa Fe, NM, United States
| | - Gustavo G. Gomez
- Instituto de Biología Integrativa de Sistemas (ISysBio), Consejo Superior de Investigaciones Científicas (CSIC), Universitat de València (UV), Valencia, Spain
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Nanda S, Yuan SY, Lai FX, Wang WX, Fu Q, Wan PJ. Identification and analysis of miRNAs in IR56 rice in response to BPH infestations of different virulence levels. Sci Rep 2020; 10:19093. [PMID: 33154527 PMCID: PMC7645692 DOI: 10.1038/s41598-020-76198-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/26/2020] [Indexed: 12/23/2022] Open
Abstract
Rice production and sustainability are challenged by its most dreadful pest, the brown planthopper (Nilaparvata lugens Stål, BPH). Therefore, the studies on rice-BPH interactions and their underlying mechanisms are of high interest. The rice ontogenetic defense, such as the role of microRNAs (miRNAs) has mostly been investigated against the pathogens, with only a few reports existing against the insect infestations. Thus, revealing the involvement of rice miRNAs in response to BPH infestations will be beneficial in understanding these complex interactions. In this study, the small RNA profiling of the IR56 rice in response to separate BPH infestations of varied virulence levels identified the BPH-responsive miRNAs and revealed the differential transcript abundance of several miRNAs during a compatible and incompatible rice-BPH interaction. The miRNA sequence analysis identified 218 known and 28 novel miRNAs distributed in 54 miRNA families. Additionally, 138 and 140 numbers of differentially expressed (DE) miRNAs were identified during the compatible and incompatible interaction, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the target gene candidates of DE miRNAs (including osa-miR2871a-3p, osa-miR172a, osa-miR166a-5p, osa-miR2120, and osa-miR1859) that might be involved in the IR56 rice defense responses against BPH infestation. Conversely, osa-miR530-5p, osa-miR812s, osa-miR2118g, osa-miR156l-5p, osa-miR435 and two of the novel miRNAs, including novel_16 and novel_52 might negatively modulate the IR56 rice defense. The expressional validation of the selected miRNAs and their targets further supported the IR56 rice defense regulatory network. Based on our results, we have proposed a conceptual model depicting the miRNA defense regulatory network in the IR56 rice against BPH infestation. The findings from the study add further insights into the molecular mechanisms of rice-BPH interactions and will be helpful for the future researches.
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Affiliation(s)
- Satyabrata Nanda
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - San-Yue Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Feng-Xia Lai
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Wei-Xia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qiang Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Pin-Jun Wan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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Yan Y, Ham BK, Chong YH, Yeh SD, Lucas WJ. A Plant SMALL RNA-BINDING PROTEIN 1 Family Mediates Cell-to-Cell Trafficking of RNAi Signals. MOLECULAR PLANT 2020; 13:321-335. [PMID: 31812689 DOI: 10.1016/j.molp.2019.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/30/2019] [Accepted: 12/02/2019] [Indexed: 05/20/2023]
Abstract
In plants, RNA interference (RNAi) plays a pivotal role in growth and development, and responses to environmental inputs, including pathogen attack. The intercellular and systemic trafficking of small interfering RNA (siRNA)/microRNA (miRNA) is a central component in this regulatory pathway. Currently, little is known with regards to the molecular agents involved in the movement of these si/miRNAs. To address this situation, we employed a biochemical approach to identify and characterize a conserved SMALL RNA-BINDING PROTEIN 1 (SRBP1) family that mediates non-cell-autonomous small RNA (sRNA) trafficking. In Arabidopsis, AtSRBP1 is a glycine-rich (GR) RNA-binding protein, also known as AtGRP7, which we show binds single-stranded siRNA. A viral vector, Zucchini yellow mosaic virus (ZYMV), was employed to functionally characterized the AtSRBP1-4 (AtGRP7/2/4/8) RNA recognition motif and GR domains. Cellular-based studies revealed the GR domain as being necessary and sufficient for SRBP1 cell-to-cell movement. Taken together, our findings provide a foundation for future research into the mechanism and function of mobile sRNA signaling agents in plants.
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Affiliation(s)
- Yan Yan
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Byung-Kook Ham
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Yee Hang Chong
- Department of Plant Pathology, National Chung-Hsing University, Taichung
| | - Shyi-Dong Yeh
- Department of Plant Pathology, National Chung-Hsing University, Taichung
| | - William J Lucas
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA.
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Analysis of Small RNAs of Barley Genotypes Associated with Resistance to Barley Yellow Dwarf Virus. PLANTS 2020; 9:plants9010060. [PMID: 31906504 PMCID: PMC7020447 DOI: 10.3390/plants9010060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/13/2019] [Accepted: 12/24/2019] [Indexed: 11/29/2022]
Abstract
Barley yellow dwarf virus (BYDV) causes an often-devastating disease of cereals that is most effectively controlled by using plant genotypes that are resistant or tolerant to the virus. New barley lines Vir8:3 and Vir13:8, with pyramided resistance genes against different pathogens and resistance gene Ryd2 against BYDV, are currently being tested. Because microRNAs (miRNAs) are associated with antiviral plant defense, here we compared the miRNA profiles in these lines and in cultivar Wysor (carrying one resistance gene, Ryd2), with and without BYDV infection and after feeding by virus-free aphids, to determine whether the miRNA profile in the resistant variety bear similarities with the newly developed lines. The BYDV titer for each group was also determined and compared to the titer in sensitive cultivar Graciosa. Among 746 miRNAs identified in barley, 66 were known miRNAs, and 680 were novel. The expression of 73 miRNAs differed significantly after BYDV infection, including the strong, specific upregulation of novel miRNA10778 that was conserved across all the barley genotypes. This miRNA belongs to the H box and ACA box (H/ACA) snoR14 family of RNAs (Rf01280) and is associated with pseudourydilation. The expression of 48 miRNAs also differed depending on the barley genotype. The profile of miRNAs expressed in Vir8:3 and Vir13:8 in response to BYDV was similar and differed from that of Wysor. Insights into the expression patterns of miRNAs in response to BYDV in barley provided here will benefit further studies toward understanding the resistance mechanisms and developing novel strategies against virus infections.
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Sanz-Carbonell A, Marques MC, Martinez G, Gomez G. Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon. RNA Biol 2019; 17:292-308. [PMID: 31766933 DOI: 10.1080/15476286.2019.1697487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
miRNAs are small RNAs that regulate mRNAs at both transcriptional and posttranscriptional level. In plants, miRNAs are involved in the regulation of different processes including development and stress-response. Elucidating how stress-responsive miRNAs are regulated is key to understand the global response to stress but also to develop efficient biotechnological tools that could help to cope with stress. Here, we describe a computational approach based on sRNA sequencing, transcript quantification and degradome data to analyse the accumulation, function and structural organization of melon miRNAs reactivated under seven biotic and abiotic stress conditions at two and four days post-treatment. Our pipeline allowed us to identify fourteen stress-responsive miRNAs (including evolutionary conserved such as miR156, miR166, miR172, miR319, miR398, miR399, miR894 and miR408) at both analysed times. According to our analysis miRNAs were categorized in three groups showing a broad-, intermediate- or narrow- response range. miRNAs reactive to a broad range of environmental cues appear as central components in the stress-response network. The strictly coordinated response of miR398 and miR408 (broad response-range) to the seven stress treatments during the period analysed here reinforces this notion. Although both, the amplitude and diversity of the miRNA-related response to stress changes during the exposition time, the architecture of the miRNA-network is conserved. This organization of miRNA response to stress is also conserved in rice and soybean supporting the conservation of miRNA-network organization in other crops. Overall, our work sheds light into how miRNA networks in plants organize and function during stress.
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Affiliation(s)
- Alejandro Sanz-Carbonell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Paterna, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Maria Carmen Marques
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Paterna, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - German Martinez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Paterna, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Paterna, Spain.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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12
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Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction. Int J Mol Sci 2019; 20:ijms20215357. [PMID: 31661835 PMCID: PMC6861988 DOI: 10.3390/ijms20215357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/14/2019] [Accepted: 10/25/2019] [Indexed: 01/10/2023] Open
Abstract
Although the regulatory function of miRNAs and their targets have been characterized in model plants, a possible underlying role in the cotton response to herbivore infestation has not been determined. To investigate this, we performed small RNA and degradome sequencing between resistant and susceptible cotton cultivar following infestation with the generalist herbivore whitefly. In total, the 260 miRNA families and 241 targets were identified. Quantitative-PCR analysis revealed that several miRNAs and their corresponding targets exhibited dynamic spatio-temporal expression patterns. Moreover, 17 miRNA precursors were generated from 29 long intergenic non-coding RNA (lincRNA) transcripts. The genome-wide analysis also led to the identification of 85 phased small interfering RNA (phasiRNA) loci. Among these, nine PHAS genes were triggered by miR167, miR390, miR482a, and two novel miRNAs, including those encoding a leucine-rich repeat (LRR) disease resistance protein, an auxin response factor (ARF) and MYB transcription factors. Through combined modeling and experimental data, we explored and expanded the miR390-tasiARF cascade during the cotton response to whitefly. Virus-induced gene silencing (VIGS) of ARF8 from miR390 target in whitefly-resistant cotton plants increased auxin and jasmonic acid (JA) accumulation, resulting in increased tolerance to whitefly infestation. These results highlight the provides a useful transcriptomic resource for plant-herbivore interaction.
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13
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Ramesh SV, Govindasamy V, Rajesh MK, Sabana AA, Praveen S. Stress-responsive miRNAome of Glycine max (L.) Merrill: molecular insights and way forward. PLANTA 2019; 249:1267-1284. [PMID: 30798358 DOI: 10.1007/s00425-019-03114-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
MAIN CONCLUSION Analysis of stress-associated miRNAs of Glycine max (L.) Merrill reveals wider ramifications of small RNA-mediated (conserved and legume-specific miRNAs) gene regulatory foot prints in molecular adaptive responses. MicroRNAs (miRNAs) are indispensable components of gene regulatory mechanism of plants. Soybean is a crop of immense commercial potential grown worldwide for its edible oil and soy meal. Intensive research efforts, using the next generation sequencing and bioinformatics techniques, have led to the identification and characterization of numerous small RNAs, especially microRNAs (miRNAs), in soybean. Furthermore, studies have unequivocally demonstrated the significance of miRNAs during the developmental processes and various stresses in soybean. In this review, we summarize the current state of understanding of miRNA-based abiotic and biotic stress responses in soybean. In addition, the molecular insights gained from the stress-related soybean miRNAs have been compared to the miRNAs of other crops, especially legumes, and the core commonalities have been highlighted, though differences among them were not ignored. Nature of response of soybean-derived conserved miRNAs during various stresses was also analyzed to gain deeper insights regarding sRNAome-based defense responses. This review further provides way forward in legume small RNA transcriptomics based on the adaptive responses of soybean and other legume-derived miRNAs.
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Affiliation(s)
- S V Ramesh
- ICAR-Indian Institute of Soybean Research (ICAR-IISR), Indore, Madhya Pradesh, 452001, India.
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India.
| | - V Govindasamy
- ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
| | - M K Rajesh
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India
| | - A A Sabana
- ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, 671124, India
| | - Shelly Praveen
- ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
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14
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Sanz-Carbonell A, Marques MC, Bustamante A, Fares MA, Rodrigo G, Gomez G. Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon. BMC PLANT BIOLOGY 2019; 19:78. [PMID: 30777009 PMCID: PMC6379984 DOI: 10.1186/s12870-019-1679-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/07/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND MiRNAs have emerged as key regulators of stress response in plants, suggesting their potential as candidates for knock-in/out to improve stress tolerance in agricultural crops. Although diverse assays have been performed, systematic and detailed studies of miRNA expression and function during exposure to multiple environments in crops are limited. RESULTS Here, we present such pioneering analysis in melon plants in response to seven biotic and abiotic stress conditions. Deep-sequencing and computational approaches have identified twenty-four known miRNAs whose expression was significantly altered under at least one stress condition, observing that down-regulation was preponderant. Additionally, miRNA function was characterized by high scale degradome assays and quantitative RNA measurements over the intended target mRNAs, providing mechanistic insight. Clustering analysis provided evidence that eight miRNAs showed a broad response range under the stress conditions analyzed, whereas another eight miRNAs displayed a narrow response range. Transcription factors were predominantly targeted by stress-responsive miRNAs in melon. Furthermore, our results show that the miRNAs that are down-regulated upon stress predominantly have as targets genes that are known to participate in the stress response by the plant, whereas the miRNAs that are up-regulated control genes linked to development. CONCLUSION Altogether, this high-resolution analysis of miRNA-target interactions, combining experimental and computational work, Illustrates the close interplay between miRNAs and the response to diverse environmental conditions, in melon.
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Affiliation(s)
- Alejandro Sanz-Carbonell
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980 Paterna, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), CPI 8E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - María Carmen Marques
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980 Paterna, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), CPI 8E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Antonio Bustamante
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980 Paterna, Spain
- Instituto Nacional de Investigaciones Agropecuarias (INIAP), Estación Experimental Pichilingue, Km5 vía Quevedo El Empalme, Mocache, Ecuador
| | - Mario A. Fares
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980 Paterna, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), CPI 8E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980 Paterna, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), CPI 8E, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas (CSIC) - Universitat de València (UV), Parc Científic, Cat. Agustín Escardino 9, 46980 Paterna, Spain
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), CPI 8E, Av. de los Naranjos s/n, 46022 Valencia, Spain
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15
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Nalam V, Louis J, Shah J. Plant defense against aphids, the pest extraordinaire. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 279:96-107. [PMID: 30709498 DOI: 10.1016/j.plantsci.2018.04.027] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/02/2018] [Accepted: 04/30/2018] [Indexed: 05/20/2023]
Abstract
Aphids are amongst the most damaging pests of plants that use their stylets to penetrate the plant tissue to consume large amounts of phloem sap and thus deprive the plant of photoassimilates. In addition, some aphids vector important viral diseases of plants. Plant defenses targeting aphids are broadly classified as antibiosis, which interferes with aphid growth, survival and fecundity, and antixenosis, which influences aphid behavior, including plant choice and feeding from the sieve elements. Here we review the multitude of steps in the infestation process where these defenses can be exerted and highlight the progress made on identifying molecular factors and mechanisms that contribute to host defense, including plant resistance genes and signaling components, as well as aphid-derived effectors that elicit or attenuate host defenses. Also discussed is the impact of aphid-vectored plant viruses on plant-aphid interaction and the concept of tolerance, which allows plant to withstand or recover from damage resulting from the infestation.
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Affiliation(s)
- Vamsi Nalam
- Department of Biology, Indiana University-Purdue University, Fort Wayne, Indiana, 46805, USA.
| | - Joe Louis
- Department of Entomology and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
| | - Jyoti Shah
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA.
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16
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Li C, Wong AYP, Wang S, Jia Q, Chuang WP, Bendena WG, Tobe SS, Yang SH, Chung G, Chan TF, Lam HM, Bede JC, Hui JHL. miRNA-Mediated Interactions in and between Plants and Insects. Int J Mol Sci 2018; 19:E3239. [PMID: 30347694 PMCID: PMC6213987 DOI: 10.3390/ijms19103239] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 01/17/2023] Open
Abstract
Our understanding of microRNA (miRNA) regulation of gene expression and protein translation, as a critical area of cellular regulation, has blossomed in the last two decades. Recently, it has become apparent that in plant-insect interactions, both plants and insects use miRNAs to regulate their biological processes, as well as co-opting each others' miRNA systems. In this review article, we discuss the current paradigms of miRNA-mediated cellular regulation and provide examples of plant-insect interactions that utilize this regulation. Lastly, we discuss the potential biotechnological applications of utilizing miRNAs in agriculture.
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Affiliation(s)
- Chade Li
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Annette Y P Wong
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Shuang Wang
- Key Laboratory of Soil Environment and Plant Nutrition of Heilongjiang Province, Institute of Soil Fertilizer and Environment Resources, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, 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, China.
| | - Wen-Po Chuang
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan.
| | - William G Bendena
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
| | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada.
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
| | - Ting-Fung Chan
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hon-Ming Lam
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Jacqueline C Bede
- Department of Plant Science, McGill University, 21,111 Lakeshore, Ste-Anne-de-Bellevue, Montreal, QC H9X 3V9, Canada.
| | - Jerome H L Hui
- State Key Laboratory of Agrobiotechnology, Centre of Soybean Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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17
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Transcriptome and miRNA analyses of the response to Corynespora cassiicola in cucumber. Sci Rep 2018; 8:7798. [PMID: 29773833 PMCID: PMC5958113 DOI: 10.1038/s41598-018-26080-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 05/04/2018] [Indexed: 01/11/2023] Open
Abstract
Cucumber (Cucumis sativus L.) target leaf spot (TLS), which is caused by the fungus Corynespora cassiicola (C. cassiicola), seriously endangers the production of cucumber. In this assay, we performed comprehensive sequencing of the transcriptome and microRNAs (miRNAs) of a resistant cucumber (Jinyou 38) during C. cassiicola inoculation using the Illumina NextSeq 500 platform. The possible genes related to the response to C. cassiicola were associated with plant hormones, transcription factors, primary metabolism, Ca2+ signaling pathways, secondary metabolism and defense genes. In total, 150 target genes of these differentially expressed miRNAs were predicted by the bioinformatic analysis. By analyzing the function of the target genes, several candidate miRNAs that may be related to the response to C. cassiicola stress were selected. We also predicted 7 novel miRNAs and predicted their target genes. Moreover, the expression patterns of the candidate genes and miRNAs were tested by quantitative real-time RT-PCR. According to the analysis, genes and miRNAs associated with secondary metabolism, particularly the phenylpropanoid biosynthesis pathway, may play a major role in the resistance to C. cassiicola stress in cucumber. These results offer a foundation for future studies exploring the mechanism and key genes of resistance to cucumber TLS.
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18
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Yates AD, Michel A. Mechanisms of aphid adaptation to host plant resistance. CURRENT OPINION IN INSECT SCIENCE 2018; 26:41-49. [PMID: 29764659 DOI: 10.1016/j.cois.2018.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/11/2018] [Accepted: 01/14/2018] [Indexed: 05/27/2023]
Abstract
Host-plant resistant (HPR) crops can play a major role in preventing insect damage, but their durability is limited due to insect adaptation. Research in basal plant resistance provides a framework to investigate adaptation against HPR. Resistance and adaptation are predicted to follow the gene-for-gene and zigzag models of plant defense. These models also highlight the importance of insect effectors, which are small molecules that modulate host plant defense signaling. We highlight research in insect adaptation to plant resistance, and then draw parallels to virulence adaptation. We focus on virulent biotype evolution within the Aphididae, since this group has the highest number of described virulent biotypes. Understanding how virulence occurs will lead to more durable insect management strategies and enhance food production and security.
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Affiliation(s)
- Ashley D Yates
- Center for Applied Plant Sciences, and The Ohio State Center for Soybean Research, USA
| | - Andy Michel
- Center for Applied Plant Sciences, and The Ohio State Center for Soybean Research, USA; Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH, USA.
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19
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Zhang H, Yin L, Wang H, Wang G, Ma X, Li M, Wu H, Fu Q, Zhang Y, Yi H. Genome-wide identification of Hami melon miRNAs with putative roles during fruit development. PLoS One 2017; 12:e0180600. [PMID: 28742088 PMCID: PMC5524408 DOI: 10.1371/journal.pone.0180600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/16/2017] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages. Small RNA sequencing yielded a total of 54,553,424 raw reads from eight libraries. 113 conserved miRNAs belonging to 30 miRNA families and nine novel miRNAs comprising nine miRNA families were identified. The expression of 42 conserved miRNAs and three Hami melon-specific miRNAs significantly changed during fruit development. Furthermore, 484 and 124 melon genes were predicted as putative targets of 29 conserved and nine Hami melon-specific miRNA families, respectively. GO enrichment analysis were performed on target genes, "transcription, DNA-dependent", "rRNA processing", "oxidation reduction", "signal transduction", "regulation of transcription, DNA-dependent", and "metabolic process" were the over-represented biological process terms. Cleavage sites of six target genes were validated using 5' RACE. Our results present a comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis towards understanding the regulatory mechanisms in programmed process of normal Hami fruit development and ripening. Specific miRNAs could be selected for further research and applications in breeding practices.
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Affiliation(s)
- Hong Zhang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Lan Yin
- ABLife, Inc., Wuhan, Hubei, China
| | - Huaisong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guangzhi Wang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Xinli Ma
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Meihua Li
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Haibo Wu
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Qiushi Fu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yi Zhang
- ABLife, Inc., Wuhan, Hubei, China
| | - Hongping Yi
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
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20
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Nicolis VF, Greyling SM, Venter E. Isolation of Early-Responsive MicroRNA From Diuraphis noxia (Hemiptera: Aphididae)-Resistant Wheat. JOURNAL OF ECONOMIC ENTOMOLOGY 2017; 110:1298-1306. [PMID: 28407081 DOI: 10.1093/jee/tox103] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Indexed: 05/10/2023]
Abstract
The Russian wheat aphid (Diuraphis noxia Kurdjumov) is an economically important pest of small grains in many countries. The past decades have seen the deployment of resistance-carrying wheat (Triticum aestivum L.) cultivars to control D. noxia. However, the emergence of resistance-breaking biotypes is negating this strategy. The role that noncoding RNA (ncRNA) molecules play in the wheat-D. noxia interaction has not been studied to date. This study aimed to isolate differentially regulated microRNA from a resistant and susceptible near-isogenic wheat line after aphid infestation. Twenty-seven identified miRNA were mostly related to stress-linked miRNA, and their predicted targets were linked with known D. noxia-feeding regulated proteins. These included transcription factors, signaling proteins, carbohydrate metabolism, and disease resistance pathways. Gene expression of three putative miRNAs and a predicted nucleotide-binding leucine-rich repeat gene with an identified miRNA target site in the NB-ARC domain displayed differential regulation between the resistant and susceptible plants. This study marks the initial investigation into understanding the role of ncRNA in a D. noxia-resistant wheat line after infestation and reports a correlation between a miRNA and its putative target for this interaction.
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Affiliation(s)
- Vittorio F Nicolis
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa (; ; )
| | - Sonia-Mari Greyling
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa (; ; )
| | - Eduard Venter
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa ( ; ; )
- Corresponding author, e-mail:
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21
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Kundu A, Paul S, Dey A, Pal A. High throughput sequencing reveals modulation of microRNAs in Vigna mungo upon Mungbean Yellow Mosaic India Virus inoculation highlighting stress regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 257:96-105. [PMID: 28224923 DOI: 10.1016/j.plantsci.2017.01.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/23/2017] [Accepted: 01/28/2017] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotides long non-coding RNAs known to play important regulatory roles during biotic and abiotic stresses by controlling gene expression. Blackgram (Vigna mungo), an economically important grain legume is highly susceptible to pathogenic begomovirus Mungbean Yellow Mosaic India Virus (MYMIV) and resulting in high yield loss. In this study two different leaf-small-RNA libraries were prepared from the pooled RNA at three different time points of resistant V. mungo inbred line VM84 inoculated either with viruliferous or non-viruliferous whiteflies carrying MYMIV and performed high-throughput Illumina sequencing. Sequencing followed by bioinformatics analysis of the small RNA reads indicated that the expression patterns of most of the known and novel miRNAs were altered in resistant line over mock-inoculated sample during the plant virus incompatible interaction. Highly altered miRNAs belong to the families of miR156, miR159, miR160, miR166, miR398, miR1511, miR1514, miR2118 and novel vmu-miRn7, vmu-miRn8, vmu-miRn13 and vmu-miRn14. These results were validated using qPCR, and most of the miRNAs showed similar pattern of expression like that of Illumina reads. The expression patterns of some selected known and novel miRNAs were also compared between the infected MYMIV-resistant and -susceptible genotypes and most of these were modulated after MYMIV-inoculation. Target transcripts like NB-LRR, NAC, MYB, Zinc finger, CCAAT-box transcription factor, fructose 2-6 bisphosphate, HDZIP protein that confers immune response were predicted as targets amongst identified miRNAs using psRNATarget server. Some selected target transcripts including NB-LRR, ARF, SOD, SPB, Basic blue copper protein were validated and their differential expression were demonstrated between MYMIV-resistant and -susceptible V. mungo by qPCR data analyses. In the present study we have identified miRNAs that implicate in the regulation of MYMIV-induced stress response in V. mungo; and generated genomic resources for a non-model legume with the aid of bioinformatics tools supplemented by experimental validation.
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Affiliation(s)
- Anirban Kundu
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India; Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata, 7000118, India
| | - Sujay Paul
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India; Laboratorio de Micología y Biotecnología, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima, 12, Peru.
| | - Avishek Dey
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Amita Pal
- Division of Plant Biology, Bose Institute, P 1/12 CIT Scheme VII M, Kolkata, 700054, India.
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Boissot N, Schoeny A, Vanlerberghe-Masutti F. Vat, an Amazing Gene Conferring Resistance to Aphids and Viruses They Carry: From Molecular Structure to Field Effects. FRONTIERS IN PLANT SCIENCE 2016; 7:1420. [PMID: 27725823 PMCID: PMC5035753 DOI: 10.3389/fpls.2016.01420] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/06/2016] [Indexed: 05/20/2023]
Abstract
We review half a century of research on Cucumis melo resistance to Aphis gossypii from molecular to field levels. The Vat gene is unique in conferring resistance to both A. gossypii and the viruses it transmits. This double phenotype is aphid clone-dependent and has been observed in 25 melon accessions, mostly from Asia. It is controlled by a cluster of genes including CC-NLR, which has been characterized in detail. Copy-number polymorphisms (for the whole gene and for a domain that stands out in the LLR region) and single-nucleotide polymorphisms have been identified in the Vat cluster. The role of these polymorphisms in plant/aphid interactions remains unclear. The Vat gene structure suggests a functioning with separate recognition and response phases. During the recognition phase, the VAT protein is thought to interact (likely indirectly) with an aphid effector introduced during cell puncture by the aphid. A few hours later, several miRNAs are upregulated in Vat plants. Peroxidase activity increases, and callose and lignin are deposited in the walls of the cells adjacent to the stylet path, disturbing aphid behavior. In aphids feeding on Vat plants, Piwi-interacting RNA-like sequences are abundant and the levels of other miRNAs are modified. At the plant level, resistance to aphids is quantitative (aphids escape the plant and display low rates of reproduction). Resistance to viruses is qualitative and local. Durability of NLR genes is highly variable. A. gossypii clones are adapted to Vat resistance, either by introducing a new effector that interferes with the deployment of plant defenses, or by adapting to the defenses it triggered. Viruses transmitted in a non-persistent manner cannot adapt to Vat resistance. At population level, Vat reduces aphid density and genetic diversity. The durability of Vat resistance to A. gossypii populations depends strongly on the agro-ecosystem, including, in particular, the presence of other cucurbit crops serving as alternative hosts for adapted clones in fall and winter. At the crop level, Vat resistance decreases the intensity of virus epidemics when A. gossypii is the main aphid vector in the crop environment.
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Affiliation(s)
- Nathalie Boissot
- Génétique et Amélioration des Fruits et Légumes, INRAMontfavet, France
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Sattar S, Addo-Quaye C, Thompson GA. miRNA-mediated auxin signalling repression during Vat-mediated aphid resistance in Cucumis melo. PLANT, CELL & ENVIRONMENT 2016; 39:1216-27. [PMID: 26437210 DOI: 10.1111/pce.12645] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/12/2015] [Accepted: 09/16/2015] [Indexed: 05/06/2023]
Abstract
Resistance to Aphis gossypii in melon is attributed to the presence of the single dominant R gene virus aphid transmission (Vat), which is biologically expressed as antibiosis, antixenosis and tolerance. However, the mechanism of resistance is poorly understood at the molecular level. Aphid-induced transcriptional changes, including differentially expressed miRNA profiles that correspond to resistance interaction have been reported in melon. The potential regulatory roles of miRNAs in Vat-mediated aphid resistance were further revealed by identifying the specific miRNA degradation targets. A total of 70 miRNA:target pairs, including 28 novel miRNA:target pairs, for the differentially expressed miRNAs were identified: 11 were associated with phytohormone regulation, including six miRNAs that potentially regulate auxin interactions. A model for a redundant regulatory system of miRNA-mediated auxin insensitivity is proposed that incorporates auxin perception, auxin modification and auxin-regulated transcription. Chemically inhibiting the transport inhibitor response-1 (TIR-1) auxin receptor in susceptible melon tissues provides in vivo support for the model of auxin-mediated impacts on A. gossypii resistance.
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Affiliation(s)
- Sampurna Sattar
- College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Charles Addo-Quaye
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Gary A Thompson
- College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Boissot N, Thomas S, Chovelon V, Lecoq H. NBS-LRR-mediated resistance triggered by aphids: viruses do not adapt; aphids adapt via different mechanisms. BMC PLANT BIOLOGY 2016; 16:25. [PMID: 26801763 PMCID: PMC4722753 DOI: 10.1186/s12870-016-0708-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 01/11/2016] [Indexed: 05/06/2023]
Abstract
BACKGROUND Aphids are serious pest on crops. By probing with their stylets, they interact with the plant, they vector viruses and when they reach the phloem they start a continuous ingestion. Many plant resistances to aphids have been identified, several have been deployed. However, some resistances breaking down have been observed. In the melon, a gene that confers resistance to aphids has been deployed in some melon-producing areas, and aphid colony development on Vat-carrying plants has been observed in certain agrosystems. The Vat gene is a NBS-LRR gene that confers resistance to the aphid species Aphis gossypii and exhibits the unusual characteristic of also conferring resistance to non-persistently transmitted viruses when they are inoculated by the aphid. Thus, we characterized patterns of resistance to aphid and virus using the aphid diversity and we investigated the mechanisms by which aphids and viruses may adapt to the Vat gene. RESULTS Using a Vat-transgenic line built in a susceptible background, we described the Vat- spectrum of resistance to aphids, and resistance to viruses triggered by aphids using a set of six A. gossypii biotypes. Discrepancies between both resistance phenotypes revealed that aphid adaptation to Vat-mediated resistance does not occur only via avirulence factor alterations but also via adaptation to elicited defenses. In experiments conducted with three virus species serially inoculated by aphids from and to Vat plants, the viruses did not evolve to circumvent Vat-mediated resistance. We confirmed discrepancies between both resistance phenotypes by testing each aphid biotype with a set of thirteen melon accessions chosen to reflect the natural diversity of the melon. Inheritance studies revealed that patterns of resistance to virus triggered by aphids are controlled by different alleles at the Vat locus and at least another locus located at a short genetic distance. Therefore, resistance to viruses triggered by aphids is controlled by a gene cluster. CONCLUSIONS Under the Flor model, changes in the avirulence gene determine the ability of the pathogen to overcome the resistance conferred by a plant gene. The Vat gene belongs to a resistance gene family that fits this pest/pathogen-plant interaction, and we revealed an additional mechanism of aphid adaptation that potentially exists in other interactions between plants and pests or pathogens.
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Affiliation(s)
- Nathalie Boissot
- Institut National de la Recherche Agronomique (INRA), UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - Allée des chênes, CS 60094, F-84143, Montfavet cedex, France.
| | - Sophie Thomas
- Institut National de la Recherche Agronomique (INRA), UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - Allée des chênes, CS 60094, F-84143, Montfavet cedex, France.
| | - Véronique Chovelon
- Institut National de la Recherche Agronomique (INRA), UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - Allée des chênes, CS 60094, F-84143, Montfavet cedex, France.
| | - Hervé Lecoq
- Institut National de la Recherche Agronomique (INRA), UR452, Unité de Pathologie Végétale, Domaine St Maurice - Allée des chênes, CS 60094, F-84143, Montfavet cedex, France.
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Sattar S, Thompson GA. Small RNA Regulators of Plant-Hemipteran Interactions: Micromanagers with Versatile Roles. FRONTIERS IN PLANT SCIENCE 2016; 7:1241. [PMID: 27625654 PMCID: PMC5003895 DOI: 10.3389/fpls.2016.01241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/04/2016] [Indexed: 05/13/2023]
Abstract
Non-coding small RNAs (sRNAs) in plants have important roles in regulating biological processes, including development, reproduction, and stress responses. Recent research indicates significant roles for sRNA-mediated gene silencing during plant-hemipteran interactions that involve all three of these biological processes. Plant responses to hemipteran feeding are determined by changes in the host transcriptome that appear to be fine-tuned by sRNAs. The role of sRNA in plant defense responses is complex. Different forms of sRNAs, with specific modes of action, regulate changes in the host transcriptome primarily through post-transcriptional gene silencing and occasionally through translational repression. Plant genetic resistance against hemipterans provides a model to explore the regulatory roles of sRNAs in plant defense. Aphid-induced sRNA expression in resistance genotypes delivers a new paradigm in understanding the regulation of R gene-mediated resistance in host plants. Unique sRNA profiles, including changes in sRNA biogenesis and expression can also provide insights into susceptibility to insect herbivores. Activation of phytohormone-mediated defense responses against insect herbivory is another hallmark of this interaction, and recent studies have shown that regulation of phytohormone signaling is under the control of sRNAs. Hemipterans feeding on resistant plants also show changes in insect sRNA profiles, possibly influencing insect development and reproduction. Changes in insect traits such as fecundity, host range, and resistance to insecticides are impacted by sRNAs and can directly contribute to the success of certain insect biotypes. In addition to causing direct damage to the host plant, hemipteran insects are often vectors of viral pathogens. Insect anti-viral RNAi machinery is activated to limit virus accumulation, suggesting a role in insect immunity. Virus-derived long sRNAs strongly resemble insect piRNAs, leading to the speculation that the piRNA pathway is induced in response to viral infection. Evidence for robust insect RNAi machinery in several hemipteran species is of immense interest and is being actively pursued as a possible tool for insect control. RNAi-induced gene silencing following uptake of exogenous dsRNA was successfully demonstrated in several hemipterans and the presence of sid-1 like genes support the concept of a systemic response in some species.
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Xia X, Shao Y, Jiang J, Du X, Sheng L, Chen F, Fang W, Guan Z, Chen S. MicroRNA Expression Profile during Aphid Feeding in Chrysanthemum (Chrysanthemum morifolium). PLoS One 2015; 10:e0143720. [PMID: 26650759 PMCID: PMC4674109 DOI: 10.1371/journal.pone.0143720] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 11/09/2015] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression, affecting many biological processes. As yet, their roles in the response of chrysanthemum to aphid feeding have not been explored. Here, the identity and abundance of miRNAs induced by aphid infestation have been obtained using high-throughput Illumina sequencing platform. Three leaf small RNA libraries were generated, one from plants infested with the aphid Macrosiphoniella sanbourni (library A), one from plants with mock puncture treatment (library M), and the third from untreated control plants (library CK). A total of 7,944,797, 7,605,251 and 9,244,002 clean unique reads, ranging from 18 to 30 nucleotides (nt) in length, were obtained from library CK, A and M, respectively. As a result, 303 conserved miRNAs belonging to 276 miRNAs families and 234 potential novel miRNAs were detected in chrysanthemum leaf, out of which 80, 100 and 79 significantly differentially expressed miRNAs were identified in the comparison of CK-VS-A, CK-VS-M and M-VS-A, respectively. Several of the differentially abundant miRNAs (in particular miR159a, miR160a, miR393a) may be associated with the plant's response to aphid infestation.
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Affiliation(s)
- Xiaolong Xia
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yafeng Shao
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xinping Du
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Liping Sheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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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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Bruce TJA. Interplay between insects and plants: dynamic and complex interactions that have coevolved over millions of years but act in milliseconds. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:455-65. [PMID: 25271259 DOI: 10.1093/jxb/eru391] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In an environment with changing availability and quality of host plants, phytophagous insects are under selection pressure to find quality hosts. They need to maximize their fitness by locating suitable plants and avoiding unsuitable ones. Thus, they have evolved a finely tuned sensory system, for detection of host cues, and a nervous system, capable of integrating inputs from sensory neurons with a high level of spatio-temporal resolution. Insect responses to cues are not fixed but depend on the context in which they are perceived, the physiological state of the insect, and prior learning experiences. However, there are examples of insects making 'mistakes' and being attracted to poor quality hosts. While insects have evolved ways of finding hosts, plants have been under selection pressure to do precisely the opposite and evade detection or defend themselves when attacked. Once on the plant, insect-associated molecules may trigger or suppress defence depending on whether the plant or the insect is ahead in evolutionary terms. Plant volatile emission is influenced by defence responses induced by insect feeding or oviposition which can attract natural enemies but repel herbivores. Conversely, plant reproductive fitness is increased by attraction of pollinators. Interactions can be altered by other organisms associated with the plant such as other insects, plant pathogens, or mycorrhizal fungi. Plant phenotype is plastic and can be changed by epigenetic factors in adaptation to periods of biotic stress. Space and time play crucial roles in influencing the outcome of interactions between insects and plants.
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Zhang B, Wang Q. MicroRNA-based biotechnology for plant improvement. J Cell Physiol 2015; 230:1-15. [PMID: 24909308 DOI: 10.1002/jcp.24685] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/21/2014] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are an extensive class of newly discovered endogenous small RNAs, which negatively regulate gene expression at the post-transcription levels. As the application of next-generation deep sequencing and advanced bioinformatics, the miRNA-related study has been expended to non-model plant species and the number of identified miRNAs has dramatically increased in the past years. miRNAs play a critical role in almost all biological and metabolic processes, and provide a unique strategy for plant improvement. Here, we first briefly review the discovery, history, and biogenesis of miRNAs, then focus more on the application of miRNAs on plant breeding and the future directions. Increased plant biomass through controlling plant development and phase change has been one achievement for miRNA-based biotechnology; plant tolerance to abiotic and biotic stress was also significantly enhanced by regulating the expression of an individual miRNA. Both endogenous and artificial miRNAs may serve as important tools for plant improvement.
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Affiliation(s)
- Baohong Zhang
- Department of Biology, East Carolina University, Greenville, North Carolina; Henan Institute of Sciences and Technology, Xinxiang, Henan, China
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30
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Molecular Adaptations of Aphid Biotypes in Overcoming Host-Plant Resistance. SHORT VIEWS ON INSECT GENOMICS AND PROTEOMICS 2015. [DOI: 10.1007/978-3-319-24235-4_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Bansal R, Mian MAR, Mittapalli O, Michel AP. RNA-Seq reveals a xenobiotic stress response in the soybean aphid, Aphis glycines, when fed aphid-resistant soybean. BMC Genomics 2014; 15:972. [PMID: 25399334 PMCID: PMC4289043 DOI: 10.1186/1471-2164-15-972] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While much recent research has expanded our understanding of the molecular interactions between aphids and their host plants, it is lacking for the soybean aphid, Aphis glycines. Since its North American invasion, A. glycines has become one of the most damaging insect pests on this important crop. Five soybean genes for host plant resistance to A. glycines have been identified, but populations of A. glycines have already adapted to overcome these resistance genes. Understanding the molecular interactions between resistant soybean and A. glycines can provide clues to its adaptation mechanisms. Here, we used RNA-Sequencing to compare and contrast A. glycines gene expression when fed resistant (Rag1) and susceptible soybean. RESULTS Combining results from a previous A. glycines transcriptome, we generated 64,860 high quality transcripts, totaling 41,151,086 bases. Statistical analysis revealed 914 genes with significant differential expression. Most genes with higher expression in A. glycines on resistant plants (N = 352) were related to stress and detoxification such as cytochrome P450s, glutathione-S-transferases, carboxyesterases, and ABC transporters. A total of 562 genes showed lower transcript abundance in A. glycines on resistant plants. From our extensive transcriptome data, we also identified genes encoding for putative salivary effector proteins (N = 73). Among these, 6 effector genes have lower transcript abundance in A. glycines feeding on resistant soybean. CONCLUSIONS Overall, A. glycines exhibited a pattern typical of xenobiotic challenge, thereby validating antibiosis in Rag1, presumably mediated through toxic secondary metabolites. Additionally, this study identified many A. glycines genes and gene families at the forefront of its molecular interaction with soybean. Further investigation of these genes in other biotypes may reveal adaptation mechanisms to resistant plants.
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Affiliation(s)
- Raman Bansal
- />Department of Entomology, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
| | - MAR Mian
- />Department of Entomology, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
- />USDA-ARS Corn and Soybean Research Unit, and the Department of Horticulture and Crop Sciences, OARDC, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
| | - Omprakash Mittapalli
- />Department of Entomology, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
| | - Andy P Michel
- />Department of Entomology, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691 USA
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Prasath D, Karthika R, Habeeba NT, Suraby EJ, Rosana OB, Shaji A, Eapen SJ, Deshpande U, Anandaraj M. Comparison of the transcriptomes of ginger (Zingiber officinale Rosc.) and mango ginger (Curcuma amada Roxb.) in response to the bacterial wilt infection. PLoS One 2014; 9:e99731. [PMID: 24940878 PMCID: PMC4062433 DOI: 10.1371/journal.pone.0099731] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/16/2014] [Indexed: 01/17/2023] Open
Abstract
Bacterial wilt in ginger (Zingiber officinale Rosc.) caused by Ralstonia solanacearum is one of the most important production constraints in tropical, sub-tropical and warm temperature regions of the world. Lack of resistant genotype adds constraints to the crop management. However, mango ginger (Curcuma amada Roxb.), which is resistant to R. solanacearum, is a potential donor, if the exact mechanism of resistance is understood. To identify genes involved in resistance to R. solanacearum, we have sequenced the transcriptome from wilt-sensitive ginger and wilt-resistant mango ginger using Illumina sequencing technology. A total of 26387032 and 22268804 paired-end reads were obtained after quality filtering for C. amada and Z. officinale, respectively. A total of 36359 and 32312 assembled transcript sequences were obtained from both the species. The functions of the unigenes cover a diverse set of molecular functions and biological processes, among which we identified a large number of genes associated with resistance to stresses and response to biotic stimuli. Large scale expression profiling showed that many of the disease resistance related genes were expressed more in C. amada. Comparative analysis also identified genes belonging to different pathways of plant defense against biotic stresses that are differentially expressed in either ginger or mango ginger. The identification of many defense related genes differentially expressed provides many insights to the resistance mechanism to R. solanacearum and for studying potential pathways involved in responses to pathogen. Also, several candidate genes that may underline the difference in resistance to R. solanacearum between ginger and mango ginger were identified. Finally, we have developed a web resource, ginger transcriptome database, which provides public access to the data. Our study is among the first to demonstrate the use of Illumina short read sequencing for de novo transcriptome assembly and comparison in non-model species of Zingiberaceae.
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Affiliation(s)
- Duraisamy Prasath
- Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India
| | | | | | | | | | - Avaroth Shaji
- Indian Institute of Spices Research, Kozhikode (Calicut), Kerala, India
| | | | - Uday Deshpande
- Labindia-GPOD Research and Training Division, Thane, Maharashtra, India
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Kamphuis LG, Zulak K, Gao LL, Anderson J, Singh KB. Plant-aphid interactions with a focus on legumes. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1271-1284. [PMID: 32481194 DOI: 10.1071/fp13090] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/29/2013] [Indexed: 06/11/2023]
Abstract
Sap-sucking insects such as aphids cause substantial yield losses in agriculture by draining plant nutrients as well as vectoring viruses. The main method of control in agriculture is through the application of insecticides. However, aphids rapidly evolve mechanisms to detoxify these, so there is a need to develop durable plant resistance to these damaging insect pests. The focus of this review is on aphid interactions with legumes, but work on aphid interactions with other plants, particularly Arabidopsis and tomato is also discussed. This review covers advances on the plant side of the interaction, including the identification of major resistance genes and quantitative trait loci conferring aphid resistance in legumes, basal and resistance gene mediated defence signalling following aphid infestation and the role of specialised metabolites. On the aphid side of the interaction, this review covers what is known about aphid effector proteins and aphid detoxification enzymes. Recent advances in these areas have provided insight into mechanisms underlying resistance to aphids and the strategies used by aphids for successful infestations and have significant impacts for the delivery of durable resistance to aphids in legume crops.
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Affiliation(s)
- Lars G Kamphuis
- CSIRO Plant Industry, Private Bag 5, Wembley, WA 6913, Australia
| | - Katherine Zulak
- CSIRO Plant Industry, Private Bag 5, Wembley, WA 6913, Australia
| | - Ling-Ling Gao
- CSIRO Plant Industry, Private Bag 5, Wembley, WA 6913, Australia
| | | | - Karam B Singh
- CSIRO Plant Industry, Private Bag 5, Wembley, WA 6913, Australia
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Shelby KS. Functional Immunomics of the Squash Bug, Anasa tristis (De Geer) (Heteroptera: Coreidae). INSECTS 2013; 4:712-30. [PMID: 26462532 PMCID: PMC4553512 DOI: 10.3390/insects4040712] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/07/2013] [Accepted: 11/13/2013] [Indexed: 02/06/2023]
Abstract
The Squash bug, Anasa tristis (De Geer), is a major piercing/sucking pest of cucurbits, causing extensive damage to plants and fruits, and transmitting phytopathogens. No genomic resources to facilitate field and laboratory studies of this pest were available; therefore the first de novo exome for this destructive pest was assembled. RNA was extracted from insects challenged with bacterial and fungal immunoelicitors, insects fed on different cucurbit species, and insects from all life stages from egg to adult. All treatments and replicates were separately barcoded for subsequent analyses, then pooled for sequencing in a single lane using the Illumina HiSeq2000 platform. Over 211 million 100-base tags generated in this manner were trimmed, filtered, and cleaned, then assembled into a de novo reference transcriptome using the Broad Institute Trinity assembly algorithm. The assembly was annotated using NCBIx NR, BLAST2GO, KEGG and other databases. Of the >130,000 total assemblies 37,327 were annotated identifying the sequences of candidate gene silencing targets from immune, endocrine, reproductive, cuticle, and other physiological systems. Expression profiling of the adult immune response was accomplished by aligning the 100-base tags from each biological replicate from each treatment and controls to the annotated reference assembly of the A. tristis transcriptome.
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Affiliation(s)
- Kent S Shelby
- Biological Control of Insects Research Laboratory, United States Department of Agriculture, Agricultural Research Service, 1503 S. Providence Road, Columbia, MO 65203, USA.
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Hicks J, Liu HC. Involvement of eukaryotic small RNA pathways in host defense and viral pathogenesis. Viruses 2013; 5:2659-78. [PMID: 24178713 PMCID: PMC3856408 DOI: 10.3390/v5112659] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 10/18/2013] [Accepted: 10/21/2013] [Indexed: 12/19/2022] Open
Abstract
Post-transcriptional gene regulation by small RNAs is now established as an important branch of the gene regulatory system. Many different classes of small RNAs have been discovered; among these are short interfering RNAs (siRNAs) and microRNA (miRNAs). Though differences in the processing and function of small RNAs exist between plants and animals, both groups utilize small RNA-mediated gene regulation in response to pathogens. Host encoded miRNAs and siRNAs are generated from viral RNA function in host defense and pathogenic resistance in plants. In animals, miRNAs are key regulators in both immune system development and in immune function. Pathogens, in particular viruses, have evolved mechanisms to usurp the host’s small RNA-mediated regulatory system. Overall, small RNAs are a major component of host defense and immunity in eukaryotes. The goal of this review is to summarize our current knowledge of the involvement of eukaryotic small RNA pathways in host defense and viral pathogenesis.
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Affiliation(s)
- Julie Hicks
- Department of Animal Science, North Carolina State University, Raleigh, NC 27695, USA.
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Kettles GJ, Drurey C, Schoonbeek HJ, Maule AJ, Hogenhout SA. Resistance of Arabidopsis thaliana to the green peach aphid, Myzus persicae, involves camalexin and is regulated by microRNAs. THE NEW PHYTOLOGIST 2013; 198:1178-1190. [PMID: 23528052 PMCID: PMC3666093 DOI: 10.1111/nph.12218] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 01/31/2013] [Indexed: 05/18/2023]
Abstract
· Small RNAs play important roles in resistance to plant viruses and the complex responses against pathogens and leaf-chewing insects. · We investigated whether small RNA pathways are involved in Arabidopsis resistance against a phloem-feeding insect, the green peach aphid (Myzus persicae). We used a 2-wk fecundity assay to assess aphid performance on Arabidopsis RNA silencing and defence pathway mutants. Quantitative real-time polymerase chain reaction was used to monitor the transcriptional activity of defence-related genes in plants of varying aphid susceptibility. High-performance liquid chromatography-mass spectrometry was employed to measure the accumulation of the antimicrobial compound camalexin. Artificial diet assays allowed the assessment of the effect of camalexin on aphid performance. · Myzus persicae produces significantly less progeny on Arabidopsis microRNA (miRNA) pathway mutants. Plants unable to process miRNAs respond to aphid infestation with increased induction of PHYTOALEXIN DEFICIENT3 (PAD3) and production of camalexin. Aphids ingest camalexin when feeding on Arabidopsis and are more successful on pad3 and cyp79b2/cyp79b3 mutants defective in camalexin production. Aphids produce less progeny on artificial diets containing camalexin. · Our data indicate that camalexin functions beyond antimicrobial defence to also include hemipteran insects. This work also highlights the extensive role of the miRNA-mediated regulation of secondary metabolic defence pathways with relevance to resistance against a hemipteran pest.
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Affiliation(s)
- Graeme J Kettles
- Department of Cell and Developmental Biology, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Claire Drurey
- Department of Cell and Developmental Biology, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Henk-Jan Schoonbeek
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Andy J Maule
- Department of Cell and Developmental Biology, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Saskia A Hogenhout
- Department of Cell and Developmental Biology, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
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Cheng X, Zhu L, He G. Towards understanding of molecular interactions between rice and the brown planthopper. MOLECULAR PLANT 2013; 6:621-34. [PMID: 23396040 DOI: 10.1093/mp/sst030] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The brown planthopper (BPH) is the most notorious pest of rice (Oryza sativa). Studies of rice-BPH interaction have contributed to development of new rice varieties, offering an effective means for long-lasting control of BPH. Here, we review the status of knowledge of the molecular basis of rice-BPH interaction, from the perspective of immunity. The BPH has complicated feeding behaviors on rice, which are mainly related to host resistance. Now, 24 resistance genes have been detected in rice, indicating gene-for-gene relationships with biotypes of the BPH. However, only one BPH resistance gene (Bph14) was identified and characterized using map-based cloning. Bph14 encodes an immune receptor of NB-LRR family, providing a means for studying the molecular mechanisms of rice resistance to BPH. Plant hormones (e.g. salicylic acid and jasmonate/ethylene), Ca(2+), mitogen-activated protein kinases (MAPKs), and OsRac1 play important roles in the immune response of rice to BPH. Signal transduction leads to modifying expression of defense-related genes and defense mechanisms against BPH, including sieve tube sealing, production of secondary metabolites, and induction of proteinase inhibitor. A model for the molecular interactions between rice and the BPH is proposed, although many details remain to be investigated that are valuable for molecular design of BPH-resistant rice varieties.
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Affiliation(s)
- Xiaoyan Cheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China.
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Expression of small RNA in Aphis gossypii and its potential role in the resistance interaction with melon. PLoS One 2012; 7:e48579. [PMID: 23173035 PMCID: PMC3500242 DOI: 10.1371/journal.pone.0048579] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/03/2012] [Indexed: 02/05/2023] Open
Abstract
Background The regulatory role of small RNAs (sRNAs) in various biological processes is an active area of investigation; however, there has been limited information available on the role of sRNAs in plant-insect interactions. This study was designed to identify sRNAs in cotton-melon aphid (Aphis gossypii) during the Vat-mediated resistance interaction with melon (Cucumis melo). Methodology/Principal Findings The role of miRNAs was investigated in response to aphid herbivory, during both resistant and susceptible interactions. sRNA libraries made from A. gossypii tissues feeding on Vat+ and Vat− plants revealed an unexpected abundance of 27 nt long sRNA sequences in the aphids feeding on Vat+ plants. Eighty-one conserved microRNAs (miRNAs), twelve aphid-specific miRNAs, and nine novel candidate miRNAs were also identified. Plant miRNAs found in the aphid libraries were most likely ingested during phloem feeding. The presence of novel miRNAs was verified by qPCR experiments in both resistant Vat+ and susceptible Vat− interactions. The comparative analyses revealed that novel miRNAs were differentially regulated during the resistant and susceptible interactions. Gene targets predicted for the miRNAs identified in this study by in silico analyses revealed their involvement in morphogenesis and anatomical structure determination, signal transduction pathways, cell differentiation and catabolic processes. Conclusion/Significance In this study, conserved and novel miRNAs were reported in A. gossypii. Deep sequencing data showed differences in the abundance of miRNAs and piRNA-like sequences in A. gossypii. Quantitative RT-PCR revealed that A. gossypii miRNAs were differentially regulated during resistant and susceptible interactions. Aphids can also ingest plant miRNAs during phloem feeding that are stable in the insect.
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Louis J, Singh V, Shah J. Arabidopsis thaliana-Aphid Interaction. THE ARABIDOPSIS BOOK 2012; 10:e0159. [PMID: 22666177 PMCID: PMC3365623 DOI: 10.1199/tab.0159] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Aphids are important pests of plants that use their stylets to tap into the sieve elements to consume phloem sap. Besides the removal of photosynthates, aphid infestation also alters source-sink patterns. Most aphids also vector viral diseases. In this chapter, we will summarize on recent significant findings in plant-aphid interaction, and how studies involving Arabidopsis thaliana and Myzus persicae (Sülzer), more commonly known as the green peach aphid (GPA), are beginning to provide important insights into the molecular basis of plant defense and susceptibility to aphids. The recent demonstration that expression of dsRNA in Arabidopsis can be used to silence expression of genes in GPA has further expanded the utility of Arabidopsis for evaluating the contribution of the aphid genome-encoded proteins to this interaction.
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Affiliation(s)
- Joe Louis
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
- Current address: Department of Entomology and Center for Chemical Ecology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Vijay Singh
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Jyoti Shah
- Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
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