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Ahmad N, Hussain H, Naeem M, Rahman SU, Khan KA, Iqbal B, Umar AW. Metabolites-induced co-evolutionary warfare between plants, viruses, and their associated vectors: So close yet so far away. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112165. [PMID: 38925477 DOI: 10.1016/j.plantsci.2024.112165] [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: 03/31/2024] [Revised: 06/11/2024] [Accepted: 06/16/2024] [Indexed: 06/28/2024]
Abstract
Agriculture and global food security encounter significant challenges due to viral threats. In the following decades, several molecular studies have focused on discovering biosynthetic pathways of numerous defensive and signaling compounds, as key regulators of plant interactions, either with viruses or their associated vectors. Nevertheless, the complexities of specialized metabolites mediated plant-virus-vector tripartite viewpoint and the identification of their co-evolutionary crossroads toward antiviral defense system, remain elusive. The current study reviews the various roles of plant-specialized metabolites (PSMs) and how plants use these metabolites to defend against viruses. It discusses recent examples of specialized metabolites that have broad-spectrum antiviral properties. Additionally, the study presents the co-evolutionary basis of metabolite-mediated plant-virus-insect interactions as a potential bioinspired approach to combat viral threats. The prospects also show promising metabolic engineering strategies aimed at discovering a wide range of PSMs that are effective in fending off viruses and their related vectors. These advances in understanding the potential role of PSMs in plant-virus interactions not only serve as a cornerstone for developing plant antiviral systems, but also highlight essential principles of biological control.
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Affiliation(s)
- Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
| | - Hamad Hussain
- Department of Agriculture, Faculty of Chemical and Life Sciences, Abdul Wali Khan University Mardan, Mardan 23390, Pakistan.
| | - Muhammad Naeem
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.
| | - Saeed Ur Rahman
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai 200240, People's Republic of China.
| | - Khalid Ali Khan
- Applied College, Center of Bee Research and its Products (CBRP), and Unit of Bee Research and Honey Production, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.
| | - Babar Iqbal
- School of Environment and Safety Engineering, School of Emergency Management, Jiangsu University, Zhenjiang 212013, People's Republic of China.
| | - Abdul Wakeel Umar
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai (BNUZ), Zhuhai City 519087, People's Republic of China.
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Su CF, Das D, Muhammad Aslam M, Xie JQ, Li XY, Chen MX. Eukaryotic splicing machinery in the plant-virus battleground. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1793. [PMID: 37198737 DOI: 10.1002/wrna.1793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/24/2023] [Accepted: 04/19/2023] [Indexed: 05/19/2023]
Abstract
Plant virual infections are mainly caused by plant-virus parasitism which affects ecological communities. Some viruses are highly pathogen specific that can infect only specific plants, while some can cause widespread harm, such as tobacco mosaic virus (TMV) and cucumber mosaic virus (CMV). After a virus infects the host, undergoes a series of harmful effects, including the destruction of host cell membrane receptors, changes in cell membrane components, cell fusion, and the production of neoantigens on the cell surface. Therefore, competition between the host and the virus arises. The virus starts gaining control of critical cellular functions of the host cells and ultimately affects the fate of the targeted host plants. Among these critical cellular processes, alternative splicing (AS) is an essential posttranscriptional regulation process in RNA maturation, which amplify host protein diversity and manipulates transcript abundance in response to plant pathogens. AS is widespread in nearly all human genes and critical in regulating animal-virus interactions. In particular, an animal virus can hijack the host splicing machinery to re-organize its compartments for propagation. Changes in AS are known to cause human disease, and various AS events have been reported to regulate tissue specificity, development, tumour proliferation, and multi-functionality. However, the mechanisms underlying plant-virus interactions are poorly understood. Here, we summarize the current understanding of how viruses interact with their plant hosts compared with humans, analyze currently used and putative candidate agrochemicals to treat plant-viral infections, and finally discussed the potential research hotspots in the future. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Chang-Feng Su
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Mehtab Muhammad Aslam
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ji-Qin Xie
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
| | - Xiang-Yang Li
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
| | - Mo-Xian Chen
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang, Guizhou Province, China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang, China
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Chaudhary S, Singh RK, Kumar P. Genome-wide identification, characterization and primer designing of simple sequence repeats across Leguminosae family. 3 Biotech 2023; 13:286. [PMID: 37520343 PMCID: PMC10382446 DOI: 10.1007/s13205-023-03706-9] [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: 05/18/2023] [Accepted: 07/16/2023] [Indexed: 08/01/2023] Open
Abstract
Legumes are important clade of commercially important family Leguminosae that mainly include medicinal, flowering and edible plants. Although the genomic sequence of legumes is accessible, only the limited number of effective simple sequence repeat markers has been identified by prior research. Additional polymorphic simple sequence repeats marker discovery will aid in the genetics and breeding of legumes. In this study, 13 complete genome sequences were screened for the identification of chromosome-wise simple sequence repeats (SSRs) and 1,866,861 SSRs were identified. Based on the study, it was observed that the number of SSRs in non-coding region was more as compared to coding region and frequency of mononucleotides was highest followed by di-nucleotides while penta- and hexa-nucleotide repeats were least frequent one. The identified genome-wide SSRs and newly developed SSR markers, primers and their mapping will provide a powerful means for genetic researches across Leguminosae plants, including genetic diversity and evolutionary origin analysis, fingerprinting, QTL mapping and marker-assisted selection for breeding as well as comparative genomic analysis studies.
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Affiliation(s)
- Sakshi Chaudhary
- Dr. A. P. J. Abdul Kalam Technical University, Lucknow, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067 India
| | - Ravi Kant Singh
- Amity Institute of Biotechnology, Amity University, Noida, UP 201313 India
| | - Pradeep Kumar
- Department of Botany, University of Lucknow, Lucknow, UP 226007 India
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Wang L, Zhang W, Shen W, Li M, Fu Y, Li Z, Li J, Liu H, Su X, Zhang B, Zhao J. Integrated transcriptome and microRNA sequencing analyses reveal gene responses in poplar leaves infected by the novel pathogen bean common mosaic virus (BCMV). FRONTIERS IN PLANT SCIENCE 2023; 14:1163232. [PMID: 37396641 PMCID: PMC10308444 DOI: 10.3389/fpls.2023.1163232] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Recently, a novel poplar mosaic disease caused by bean common mosaic virus (BCMV) was investigated in Populus alba var. pyramidalis in China. Symptom characteristics, physiological performance of the host, histopathology, genome sequences and vectors, and gene regulation at the transcriptional and posttranscriptional levels were analyzed and RT-qPCR (quantitative reverse transcription PCR) validation of expression was performed in our experiments. In this work, the mechanisms by which the BCMV pathogen impacts physiological performance and the molecular mechanisms of the poplar response to viral infection were reported. The results showed that BCMV infection decreased the chlorophyll content, inhibited the net photosynthesis rate (Pn) and stomatal conductance (Gs), and significantly changed chlorophyll fluorescence parameters in diseased leaves. Transcriptome analysis revealed that the expression of the majority of DEGs (differentially expressed genes) involved in the flavonoid biosynthesis pathway was promoted, but the expression of all or almost all DEGs associated with photosynthesis-antenna proteins and the photosynthesis pathway was inhibited in poplar leaves, suggesting that BCMV infection increased the accumulation of flavonoids but decreased photosynthesis in hosts. Gene set enrichment analysis (GSEA) illustrated that viral infection promoted the expression of genes involved in the defense response or plant-pathogen interaction. MicroRNA-seq analysis illustrated that 10 miRNA families were upregulated while 6 families were downregulated in diseased poplar leaves; moreover, miR156, the largest family with the most miRNA members and target genes, was only differentially upregulated in long-period disease (LD) poplar leaves. Integrated transcriptome and miRNA-seq analyses revealed 29 and 145 candidate miRNA-target gene pairs; however, only 17 and 76 pairs, accounting for 2.2% and 3.2% of all DEGs, were authentically negatively regulated in short-period disease (SD) and LD leaves, respectively. Interestingly, 4 miR156/SPL (squamosa promoter-binding-like protein) miRNA-target gene pairs were identified in LD leaves: the miR156 molecules were upregulated, but SPL genes were downregulated. In conclusion, BCMV infection significantly changed transcriptional and posttranscriptional gene expression in poplar leaves, inhibited photosynthesis, increased the accumulation of flavonoids, induced systematic mosaic symptoms, and decreased physiological performance in diseased poplar leaves. This study elucidated the fine-tuned regulation of poplar gene expression by BCMV; moreover, the results also suggested that miR156/SPL modules played important roles in the virus response and development of viral systematic symptoms in plant virus disease.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wanna Shen
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Min Li
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Yuchen Fu
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Zheng Li
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Jinxin Li
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Taian, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bingyu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jiaping Zhao
- State Key Laboratory of Tree Genetics and Breeding, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, Beijing, China
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Jha UC, Nayyar H, Chattopadhyay A, Beena R, Lone AA, Naik YD, Thudi M, Prasad PVV, Gupta S, Dixit GP, Siddique KHM. Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration. FRONTIERS IN PLANT SCIENCE 2023; 14:1183505. [PMID: 37229109 PMCID: PMC10204772 DOI: 10.3389/fpls.2023.1183505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 05/27/2023]
Abstract
Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Anirudha Chattopadhyay
- Department of Plant Pathology, Pulse Research Station, S.D. Agricultural University SK Nagar, SK Nagar, Gujarat, India
| | - Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University (KAU), Thiruvananthapuram, Kerala, India
| | - Ajaz A. Lone
- Dryland Agriculture Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST)-Kashmir, Srinagar, India
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samatipur, Bihar, India
- Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
- Center for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | | | - Sanjeev Gupta
- Indian Council of Agricultural Research, New Delhi, India
| | - Girish Prasad Dixit
- Indian Institute of Pulses Research (IIPR), Indian Council of Agricultural Research (ICAR), Kanpur, Uttar Pradesh, India
| | - Kadambot H. M. Siddique
- The University of Western Australia (UWA) Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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Zhong X, Yang L, Li J, Tang Z, Wu C, Zhang L, Zhou X, Wang Y, Wang Z. Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B. Virol J 2022; 19:182. [DOI: 10.1186/s12985-022-01890-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Chrysanthemum virus B (CVB), a key member of the genus Carlavirus, family Betaflexiviridae, causes severe viral diseases in chrysanthemum (Chrysanthemum morifolium) plants worldwide. However, information on the mechanisms underlying the response of chrysanthemum plants to CVB is scant.
Methods
Here, an integrated next-generation sequencing and comparative transcriptomic analysis of chrysanthemum leaves was conducted to explore the molecular response mechanisms of plants to a Chinese isolate of CVB (CVB-CN) at the molecular level.
Results
In total, 4934 significant differentially expressed genes (SDEGs) were identified to respond to CVB-CN, of which 4097 were upregulated and 837 were downregulated. Gene ontology and functional classification showed that the majority of upregulated SDEGs were categorized into gene cohorts involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, and ribosome metabolism. Enrichment analysis demonstrated that ethylene pathway-related genes were significantly upregulated following CVB-CN infection, indicating a strong promotion of ethylene biosynthesis and signaling. Furthermore, disruption of the ethylene pathway in Nicotiana benthamiana, a model plant, using virus-induced gene silencing technology rendered them more susceptible to cysteine-rich protein of CVB-CN induced hypersensitive response, suggesting a crucial role of this pathway in response to CVB-CN infection.
Conclusion
This study provides evidence that ethylene pathway has an essential role of plant in response to CVB and offers valuable insights into the defense mechanisms of chrysanthemum against Carlavirus.
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Cheng SS, Ku YS, Cheung MY, Lam HM. Identification of stably expressed reference genes for expression studies in Arabidopsis thaliana using mass spectrometry-based label-free quantification. FRONTIERS IN PLANT SCIENCE 2022; 13:1001920. [PMID: 36247637 PMCID: PMC9557097 DOI: 10.3389/fpls.2022.1001920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Arabidopsis thaliana has been used regularly as a model plant in gene expression studies on transcriptional reprogramming upon pathogen infection, such as that by Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), or when subjected to stress hormone treatments including jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA). Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has been extensively employed to quantitate these gene expression changes. However, the accuracy of the quantitation is largely dependent on the stability of the expressions of reference genes used for normalization. Recently, RNA sequencing (RNA-seq) has been widely used to mine stably expressed genes for use as references in RT-qPCR. However, the amplification step in RNA-seq creates an intrinsic bias against those genes with relatively low expression levels, and therefore does not provide an accurate quantification of all expressed genes. In this study, we employed mass spectrometry-based label-free quantification (LFQ) in proteomic analyses to identify those proteins with abundances unaffected by Pst DC3000 infection. We verified, using RT-qPCR, that the levels of their corresponding mRNAs were also unaffected by Pst DC3000 infection. Compared to commonly used reference genes for expression studies in A. thaliana upon Pst DC3000 infection, the candidate reference genes reported in this study generally have a higher expression stability. In addition, using RT-qPCR, we verified that the mRNAs of the candidate reference genes were stably expressed upon stress hormone treatments including JA, SA, and ABA. Results indicated that the candidate genes identified here had stable expressions upon these stresses and are suitable to be used as reference genes for RT-qPCR. Among the 18 candidate reference genes reported in this study, many of them had greater expression stability than the commonly used reference genes, such as ACT7, in previous studies. Here, besides proposing more appropriate reference genes for Arabidopsis expression studies, we also demonstrated the capacity of mass spectrometry-based LFQ to quantify protein abundance and the possibility to extend protein expression studies to the transcript level.
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Alvarez-Diaz JC, Laugé R, Delannoy E, Huguet S, Paysant-Le Roux C, Gratias A, Geffroy V. Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean. PLANTS 2022; 11:plants11151995. [PMID: 35956473 PMCID: PMC9370732 DOI: 10.3390/plants11151995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022]
Abstract
Bean anthracnose caused by the hemibiotrophic fungus Colletotrichum lindemuthianum is one of the most important diseases of common bean (Phaseolus vulgaris) in the world. In the present study, the whole transcriptome of common bean infected with C. lindemuthianum during compatible and incompatible interactions was characterized at 48 and 72 hpi, corresponding to the biotrophy phase of the infection cycle. Our results highlight the prominent role of pathogenesis-related (PR) genes from the PR10/Bet vI family as well as a complex interplay of different plant hormone pathways including Ethylene, Salicylic acid (SA) and Jasmonic acid pathways. Gene Ontology enrichment analysis reveals that infected common bean seedlings responded by down-regulation of photosynthesis, ubiquitination-mediated proteolysis and cell wall modifications. In infected common bean, SA biosynthesis seems to be based on the PAL pathway instead of the ICS pathway, contrarily to what is described in Arabidopsis. Interestingly, ~30 NLR were up-regulated in both contexts. Overall, our results suggest that the difference between the compatible and incompatible reaction is more a question of timing and strength, than a massive difference in differentially expressed genes between these two contexts. Finally, we used RT-qPCR to validate the expression patterns of several genes, and the results showed an excellent agreement with deep sequencing.
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Affiliation(s)
- Juan C. Alvarez-Diaz
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Richard Laugé
- Université Paris-Saclay, INRAE UR 1290 BIOGER, Av. Lucien Bretignières, BP 01, 78850 Thiverval Grignon, France;
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Christine Paysant-Le Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France; (J.C.A.-D.); (E.D.); (S.H.); (C.P.-L.R.); (A.G.)
- Université Paris-Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Correspondence: ; Tel.: +33-1-69-15-33-65
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Du K, Jiang T, Chen H, Murphy AM, Carr JP, Du Z, Li X, Fan Z, Zhou T. Viral Perturbation of Alternative Splicing of a Host Transcript Benefits Infection. PLANT PHYSIOLOGY 2020; 184:1514-1531. [PMID: 32958561 PMCID: PMC7608148 DOI: 10.1104/pp.20.00903] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Pathogens disturb alternative splicing patterns of infected eukaryotic hosts. However, in plants it is unknown if this is incidental to infection or represents a pathogen-induced remodeling of host gene expression needed to support infection. Here, we compared changes in transcription and protein accumulation with changes in transcript splicing patterns in maize (Zea mays) infected with the globally important pathogen sugarcane mosaic virus (SCMV). Our results suggested that changes in alternative splicing play a major role in determining virus-induced proteomic changes. Focusing on maize phytoene synthase1 (ZmPSY1), which encodes the key regulatory enzyme in carotenoid biosynthesis, we found that although SCMV infection decreases total ZmPSY1 transcript accumulation, the proportion of splice variant T001 increases by later infection stages so that ZmPSY1 protein levels are maintained. We determined that ZmPSY1 has two leaf-specific transcripts, T001 and T003, distinguished by differences between the respective 3'-untranslated regions (UTRs). The shorter 3'-UTR of T001 makes it the more efficient mRNA. Nonsense ZmPSY1 mutants or virus-induced silencing of ZmPSY1 expression suppressed SCMV accumulation, attenuated symptoms, and decreased chloroplast damage. Thus, ZmPSY1 acts as a proviral host factor that is required for virus accumulation and pathogenesis. Taken together, our findings reveal that SCMV infection-modulated alternative splicing ensures that ZmPSY1 synthesis is sustained during infection, which supports efficient virus infection.
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Affiliation(s)
- Kaitong Du
- State Key Laboratory for Agro-Biotechnology, and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Tong Jiang
- State Key Laboratory for Agro-Biotechnology, and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Hui Chen
- State Key Laboratory for Agro-Biotechnology, and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Alex M Murphy
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - John P Carr
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Zhiyou Du
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Xiangdong Li
- College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology, and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Tao Zhou
- State Key Laboratory for Agro-Biotechnology, and Key Laboratory for Pest Monitoring and Green Management-Ministry of Agriculture and Rural Affairs, Department of Plant Pathology, China Agricultural University, Beijing 100193, China
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10
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Wilker J, Humphries S, Rosas-Sotomayor JC, Gómez Cerna M, Torkamaneh D, Edwards M, Navabi A, Pauls KP. Genetic Diversity, Nitrogen Fixation, and Water Use Efficiency in a Panel of Honduran Common Bean ( Phaseolus vulgaris L.) Landraces and Modern Genotypes. PLANTS 2020; 9:plants9091238. [PMID: 32961677 PMCID: PMC7569834 DOI: 10.3390/plants9091238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 01/09/2023]
Abstract
Common bean (Phaseolus vulgaris L.) provides critical nutrition and a livelihood for millions of smallholder farmers worldwide. Beans engage in symbiotic nitrogen fixation (SNF) with Rhizobia. Honduran hillside farmers farm marginal land and utilize few production inputs; therefore, bean varieties with high SNF capacity and environmental resiliency would be of benefit to them. We explored the diversity for SNF, agronomic traits, and water use efficiency (WUE) among 70 Honduran landrace, participatory bred (PPB), and conventionally bred bean varieties (HON panel) and 6 North American check varieties in 3 low-N field trials in Ontario, Canada and Honduras. Genetic diversity was measured with a 6K single nucleotide polymorphism (SNP) array, and phenotyping for agronomic, SNF, and WUE traits was carried out. STRUCTURE analysis revealed two subpopulations with admixture between the subpopulations. Nucleotide diversity was greater in the landraces than the PPB varieties across the genome, and multiple genomic regions were identified where population genetic differentiation between the landraces and PPB varieties was evident. Significant differences were found between varieties and breeding categories for agronomic traits, SNF, and WUE. Landraces had above average SNF capacity, conventional varieties showed higher yields, and PPB varieties performed well for WUE. Varieties with the best SNF capacity could be used in further participatory breeding efforts.
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Affiliation(s)
- Jennifer Wilker
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Sally Humphries
- Department of Sociology and Anthropology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Juan Carlos Rosas-Sotomayor
- Departamento de Ciencia y Producción Agropecuaria, Escuela Agrícola Panamericana, Zamorano, Tegucigalpa 11101, Honduras;
| | - Marvin Gómez Cerna
- Fundación para la Investigación Participativa con Agricultores de Honduras, La Ceiba, Atlántida 561, Honduras;
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Michelle Edwards
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
| | - K. Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (J.W.); (D.T.); (M.E.)
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 54136)
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11
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Pasin F, Shan H, García B, Müller M, San León D, Ludman M, Fresno DH, Fátyol K, Munné-Bosch S, Rodrigo G, García JA. Abscisic Acid Connects Phytohormone Signaling with RNA Metabolic Pathways and Promotes an Antiviral Response that Is Evaded by a Self-Controlled RNA Virus. PLANT COMMUNICATIONS 2020; 1:100099. [PMID: 32984814 PMCID: PMC7518510 DOI: 10.1016/j.xplc.2020.100099] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 05/13/2023]
Abstract
A complex network of cellular receptors, RNA targeting pathways, and small-molecule signaling provides robust plant immunity and tolerance to viruses. To maximize their fitness, viruses must evolve control mechanisms to balance host immune evasion and plant-damaging effects. The genus Potyvirus comprises plant viruses characterized by RNA genomes that encode large polyproteins led by the P1 protease. A P1 autoinhibitory domain controls polyprotein processing, the release of a downstream functional RNA-silencing suppressor, and viral replication. Here, we show that P1Pro, a plum pox virus clone that lacks the P1 autoinhibitory domain, triggers complex reprogramming of the host transcriptome and high levels of abscisic acid (ABA) accumulation. A meta-analysis highlighted ABA connections with host pathways known to control RNA stability, turnover, maturation, and translation. Transcriptomic changes triggered by P1Pro infection or ABA showed similarities in host RNA abundance and diversity. Genetic and hormone treatment assays showed that ABA promotes plant resistance to potyviral infection. Finally, quantitative mathematical modeling of viral replication in the presence of defense pathways supported self-control of polyprotein processing kinetics as a viral mechanism that attenuates the magnitude of the host antiviral response. Overall, our findings indicate that ABA is an active player in plant antiviral immunity, which is nonetheless evaded by a self-controlled RNA virus.
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Affiliation(s)
- Fabio Pasin
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
- Agricultural Biotechnology Research Center, Academia Sinica, 11529 Taipei, Taiwan
| | - Hongying Shan
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Beatriz García
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Maren Müller
- Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Facultad de Biología, Universidad de Barcelona, 08028 Barcelona, Spain
| | - David San León
- Centro Nacional de Biotecnología (CNB-CSIC), 28049 Madrid, Spain
| | - Márta Ludman
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, 2100 Gödöllő, Hungary
| | - David H. Fresno
- Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Facultad de Biología, Universidad de Barcelona, 08028 Barcelona, Spain
| | - Károly Fátyol
- Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, 2100 Gödöllő, Hungary
| | - Sergi Munné-Bosch
- Departamento de Biología Evolutiva, Ecología y Ciencias Ambientales, Facultad de Biología, Universidad de Barcelona, 08028 Barcelona, Spain
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, 46980 Paterna, Spain
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12
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Likhanov AF, Antipov IA, Hrynchuk KV, Dragovoz IV. Formation of Cell and Tissue Barriers in Phaseolus vulgaris L. Ovules in a System of Antiviral Resistance. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Kumar S, Dhembla C, P H, Sundd M, Patel AK. Differential expression of structural and functional proteins during bean common mosaic virus-host plant interaction. Microb Pathog 2019; 138:103812. [PMID: 31669830 DOI: 10.1016/j.micpath.2019.103812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/15/2019] [Accepted: 10/18/2019] [Indexed: 12/17/2022]
Abstract
Bean common mosaic virus (BCMV), the most common seed-borne pathogen in Phaseolus vulgaris L. is known to cause severe loss in productivity across the globe. In the present study, proteomic analyses were performed for leaf samples from control (healthy) and susceptible BCMV infected plants. The differential expression of proteins was evaluated using two-dimensional gel electrophoresis (2-DE). Approximately, 1098 proteins were spotted, amongst which 107 proteins were observed to be statistically significant with differential expression. The functional categorization of the differential proteins illustrated that they were involved in biotic/abiotic stress (18%), energy and carbon metabolism (11%), photosynthesis (46%), protein biosynthesis (10%), chaperoning (5%), chlorophyll (5%) and polyunsaturated fatty acid biosynthesis (5%). This is the first report on the comparative proteome study of compatible plant-BCMV interactions in P. vulgaris which contributes largely to the understanding of protein-mediated disease resistance/susceptible mechanisms.
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Affiliation(s)
- Sunil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Chetna Dhembla
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Hariprasad P
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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14
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Kankanala P, Nandety RS, Mysore KS. Genomics of Plant Disease Resistance in Legumes. FRONTIERS IN PLANT SCIENCE 2019; 10:1345. [PMID: 31749817 PMCID: PMC6842968 DOI: 10.3389/fpls.2019.01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/27/2019] [Indexed: 05/15/2023]
Abstract
The constant interactions between plants and pathogens in the environment and the resulting outcomes are of significant importance for agriculture and agricultural scientists. Disease resistance genes in plant cultivars can break down in the field due to the evolution of pathogens under high selection pressure. Thus, the protection of crop plants against pathogens is a continuous arms race. Like any other type of crop plant, legumes are susceptible to many pathogens. The dawn of the genomic era, in which high-throughput and cost-effective genomic tools have become available, has revolutionized our understanding of the complex interactions between legumes and pathogens. Genomic tools have enabled a global view of transcriptome changes during these interactions, from which several key players in both the resistant and susceptible interactions have been identified. This review summarizes some of the large-scale genomic studies that have clarified the host transcriptional changes during interactions between legumes and their plant pathogens while highlighting some of the molecular breeding tools that are available to introgress the traits into breeding programs. These studies provide valuable insights into the molecular basis of different levels of host defenses in resistant and susceptible interactions.
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15
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Zhang L, Shang J, Wang W, Du J, Li K, Wu X, Yu L, Liu C, Khaskheli MI, Yang W. Comparison of Transcriptome Differences in Soybean Response to Soybean Mosaic Virus under Normal Light and in the Shade. Viruses 2019; 11:E793. [PMID: 31470502 PMCID: PMC6784153 DOI: 10.3390/v11090793] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 01/02/2023] Open
Abstract
Shading in the intercropping system is a major abiotic factor which influences soybean growth and development, while soybean mosaic virus (SMV) is a biotic factor that limits the yield and quality of soybean. However, little is known about the defense response of soybean to SMV in the shade. Thus, in the current study, both intensity and quality (red:far-red, R:FR) of the light were changed to simulate the shaded environment and comparative transcriptome analysis was performed. Morphologically, plant growth was inhibited by SMV, which decreased 35.93% of plant height and 8.97% of stem diameter in the shade. A total of 3548 and 4319 differentially expressed genes (DEGs) were identified in soybean plants infected with SMV under normal light and in the shade. Enrichment analysis showed that the plant defense-related genes were upregulated under normal light but downregulated in the shade. Pathways that were repressed include plant-pathogen interaction, secondary metabolism, sugar metabolism, and vitamin metabolism. In addition, genes associated with signaling pathways such as salicylic acid (SA), jasmonic acid (JA), and ethylene (ETH) were also downregulated in the shade. A qRT-PCR assay of 15 DEGs was performed to confirm transcriptome results. According to our knowledge, this is the first report on soybean response to dual stress factors. These results provide insights into the molecular mechanisms in which soybean plants were infected with SMV in the shade.
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Affiliation(s)
- Lei Zhang
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Shang
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China.
| | - Wenming Wang
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Junbo Du
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Li
- National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Xiaoling Wu
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Liang Yu
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunyan Liu
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
| | - Muhammad Ibrahim Khaskheli
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
- Department of Plant Protection, Sindh Agriculture University, Tandojam 70060, Pakistan
| | - Wenyu Yang
- Sichuan Engineering Research Center for Crop Strip Intercropping System, College of Agronomy and Key Laboratory for Major Crop Diseases, Sichuan Agricultural University, Chengdu 611130, China
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16
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Padmanabhan C, Ma Q, Shekasteband R, Stewart KS, Hutton SF, Scott JW, Fei Z, Ling KS. Comprehensive transcriptome analysis and functional characterization of PR-5 for its involvement in tomato Sw-7 resistance to tomato spotted wilt tospovirus. Sci Rep 2019; 9:7673. [PMID: 31114006 PMCID: PMC6529424 DOI: 10.1038/s41598-019-44100-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/08/2019] [Indexed: 02/06/2023] Open
Abstract
Tomato spotted wilt tospovirus (TSWV), one of the most important plant viruses, causes yield losses to many crops including tomato. The current disease management for TSWV is based mainly on breeding tomato cultivars containing the Sw-5 locus. Unfortunately, several Sw-5 resistance-breaking strains of TSWV have been identified. Sw-7 is an alternative locus conferring resistance to a broad range of TSWV strains. In an effort to uncover gene networks that are associated with the Sw-7 resistance, we performed a comparative transcriptome profiling and gene expression analysis between a nearly-isogenic Sw-7 line and its susceptible recurrent parent (Fla. 8059) upon infection by TSWV. A total of 1,244 differentially expressed genes were identified throughout a disease progression process involving networks of host resistance genes, RNA silencing/antiviral defense genes, and crucial transcriptional and translational regulators. Notable induced genes in Sw-7 include those involved in callose accumulation, lignin deposition, proteolysis process, transcriptional activation/repression, and phosphorylation. Finally, we investigated potential involvement of PR-5 in the Sw-7 resistance. Interestingly, PR-5 overexpressed plants conferred enhanced resistance, resulting in delay in virus accumulation and symptom expression. These findings will facilitate breeding and genetic engineering efforts to incorporate this new source of resistance in tomato for protection against TSWV.
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Affiliation(s)
- Chellappan Padmanabhan
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - Qiyue Ma
- Boyce Thompson Institute, Cornell University, Ithaca, New York, USA
| | - Reza Shekasteband
- University of Florida, IFAS, Gulf Coast Research and Education Center, Wimauma, FL, USA
| | - Kevin S Stewart
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - Samuel F Hutton
- University of Florida, IFAS, Gulf Coast Research and Education Center, Wimauma, FL, USA
| | - John W Scott
- University of Florida, IFAS, Gulf Coast Research and Education Center, Wimauma, FL, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York, USA.
- USDA-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA.
| | - Kai-Shu Ling
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, South Carolina, USA.
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17
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Boudreault S, Roy P, Lemay G, Bisaillon M. Viral modulation of cellular RNA alternative splicing: A new key player in virus-host interactions? WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1543. [PMID: 31034770 PMCID: PMC6767064 DOI: 10.1002/wrna.1543] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
Abstract
Upon viral infection, a tug of war is triggered between host cells and viruses to maintain/gain control of vital cellular functions, the result of which will ultimately dictate the fate of the host cell. Among these essential cellular functions, alternative splicing (AS) is an important RNA maturation step that allows exons, or parts of exons, and introns to be retained in mature transcripts, thereby expanding proteome diversity and function. AS is widespread in higher eukaryotes, as it is estimated that nearly all genes in humans are alternatively spliced. Recent evidence has shown that upon infection by numerous viruses, the AS landscape of host‐cells is affected. In this review, we summarize recent advances in our understanding of how virus infection impacts the AS of cellular transcripts. We also present various molecular mechanisms allowing viruses to modulate cellular AS. Finally, the functional consequences of these changes in the RNA splicing signatures during virus–host interactions are discussed. This article is categorized under:RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing
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Affiliation(s)
- Simon Boudreault
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Patricia Roy
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Guy Lemay
- Département de microbiologie, infectiologie et immunologie, Faculté de médecine, Université de Montréal, Montréal, Québec, Canada
| | - Martin Bisaillon
- Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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18
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Silva KJP, Singh J, Bednarek R, Fei Z, Khan A. Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple ( Malus × domestica). HORTICULTURE RESEARCH 2019; 6:35. [PMID: 30962933 PMCID: PMC6441656 DOI: 10.1038/s41438-019-0120-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/06/2018] [Accepted: 12/30/2018] [Indexed: 05/25/2023]
Abstract
Apple cultivars with durable resistance are needed for sustainable management of fire blight, the most destructive bacterial disease of apples. Although studies have identified genetic resistance to fire blight in both wild species and cultivated apples, more research is needed to understand the molecular mechanisms underlying host-pathogen interaction and differential genotypic responses to fire blight infection. We have analyzed phenotypic and transcriptional responses of 'Empire' and 'Gala' apple cultivars to fire blight by infecting them with a highly aggressive E. amylovora strain. Disease progress, based on the percentage of visual shoot necrosis, started showing significant (p < 0.001) differences between 'Empire' and 'Gala' 4 days after infection (dai). 'Empire' seems to slow down bacterial progress more rapidly after this point. We further compared transcriptome profiles of 'Empire' and 'Gala' at three different time points after fire blight infection. More genes showed differential expression in 'Gala' at earlier stages, but the number of differentially expressed genes increased in 'Empire' at 3 dai. Functional classes related to defense, cell cycle, response to stress, and biotic stress were identified and a few co-expression gene networks showed particular enrichment for plant defense and abiotic stress response genes. Several of these genes also co-localized in previously identified quantitative trait locus regions for fire blight resistance on linkage groups 7 and 12, and can serve as functional candidates for future research. These results highlight different molecular mechanisms for pathogen perception and control in two apple cultivars and will contribute toward better understanding of E. amylovora-Malus pathosystem.
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Affiliation(s)
| | - Jugpreet Singh
- 1Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456 USA
| | - Ryland Bednarek
- 1Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456 USA
- 2Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Zhangjun Fei
- 2Boyce Thompson Institute, Cornell University, Ithaca, NY 14853 USA
| | - Awais Khan
- 1Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, NY 14456 USA
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19
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Kanwar P, Jha G. Alterations in plant sugar metabolism: signatory of pathogen attack. PLANTA 2019; 249:305-318. [PMID: 30267150 DOI: 10.1007/s00425-018-3018-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/23/2018] [Indexed: 05/03/2023]
Abstract
This review summarizes the current understanding, future challenges and ongoing quest on sugar metabolic alterations that influence the outcome of plant-pathogen interactions. Intricate cellular and molecular events occur during plant-pathogen interactions. They cause major metabolic perturbations in the host and alterations in sugar metabolism play a pivotal role in governing the outcome of various kinds of plant-pathogen interactions. Sugar metabolizing enzymes and transporters of both host and pathogen origin get differentially regulated during the interactions. Both plant and pathogen compete for utilizing the host sugar metabolic machinery and in turn promote resistant or susceptible responses. However, the kind of sugar metabolism alteration that is beneficial for the host or pathogen is yet to be properly understood. Recently developed tools and methodologies are facilitating research to understand the intricate dynamics of sugar metabolism during the interactions. The present review elaborates current understanding, future challenges and ongoing quest on sugar metabolism, mobilization and regulation during various plant-pathogen interactions.
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Affiliation(s)
- Poonam Kanwar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Gopaljee Jha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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20
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Sun Y, Fan M, He Y. Transcriptome Analysis of Watermelon Leaves Reveals Candidate Genes Responsive to Cucumber green mottle mosaic virus Infection. Int J Mol Sci 2019; 20:ijms20030610. [PMID: 30708960 PMCID: PMC6387395 DOI: 10.3390/ijms20030610] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 01/02/2023] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) is a member of the genus Tobamovirus, which cause diseases in cucurbits, especially watermelon. In watermelon, symptoms develop on the whole plant, including leaves, stems, peduncles, and fruit. To better understand the molecular mechanisms of watermelon early responses to CGMMV infection, a comparative transcriptome analysis of 24 h CGMMV-infected and mock-inoculated watermelon leaves was performed. A total of 1641 differently expressed genes (DEGs) were identified, with 886 DEGs upregulated and 755 DEGs downregulated after CGMMV infection. A functional analysis indicated that the DEGs were involved in photosynthesis, plant⁻pathogen interactions, secondary metabolism, and plant hormone signal transduction. In addition, a few transcription factor families, including WRKY, MYB, HLH, bZIP and NAC, were responsive to the CGMMV-induced stress. To confirm the high-throughput sequencing results, 15 DEGs were validated by qRT-PCR analysis. The results provide insights into the identification of candidate genes or pathways involved in the responses of watermelon leaves to CGMMV infection.
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Affiliation(s)
- Yuyan Sun
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Beijing 100081, China.
| | - Min Fan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Yanjun He
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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21
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Hou H, Hu Y, Wang Q, Xu X, Qian Y, Zhou X. Gene Expression Profiling Shows That NbFDN1 Is Involved in Modulating the Hypersensitive Response-Like Cell Death Induced by the Oat dwarf virus RepA Protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1006-1020. [PMID: 29649964 DOI: 10.1094/mpmi-12-17-0291-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, we used high-throughput deep nucleotide sequencing to characterize the global transcriptional response of Nicotiana benthamiana plants to transient expression of the RepA protein from Oat dwarf virus (ODV). We identified 7,878 significantly differentially expressed genes (DEG) that mapped to 125 pathways, suggesting that comprehensive networks are involved in regulation of RepA-induced cell death. Of the 202 DEG associated with photosynthesis, expression of 195 was found to be downregulated, indicating a significant inhibition of photosynthesis in response to RepA expression, which is associated with chloroplast disruption and physiological changes. We focused our analysis on NbFDN1, a member of the ferredoxin protein family that participates in the chloroplast electron transport chain performing oxygenic photosynthesis, which was identified to directly interact with NbTsip1. We separately knocked down the expression of NbFDN1 and NbTsip1 using virus-induced gene silencing, and found that NbFDN1 silencing speeded up the development of RepA-induced cell death, unlike NbTsip1 silencing, which showed an opposite effect on RepA-induced response. Further study showed increased H2O2 accumulation and a negative correlation between the transcripts of NbFDN1 and NbTsip1 in NbFDN1-silenced plants. Hence, we speculate that NbFDN1 has an effect on RepA-induced hypersensitive response-like response by modulating NbTsip1 transcription as well as H2O2 production.
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Affiliation(s)
- Huwei Hou
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Ya Hu
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Qian Wang
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Xiongbiao Xu
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Yajuan Qian
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
| | - Xueping Zhou
- 1 State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People's Republic of China; and
- 2 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
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Obrępalska-Stęplowska A, Zmienko A, Wrzesińska B, Goralski M, Figlerowicz M, Zyprych-Walczak J, Siatkowski I, Pospieszny H. The Defense Response of Nicotiana benthamiana to Peanut Stunt Virus Infection in the Presence of Symptom Exacerbating Satellite RNA. Viruses 2018; 10:E449. [PMID: 30142955 PMCID: PMC6165542 DOI: 10.3390/v10090449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/02/2018] [Accepted: 08/22/2018] [Indexed: 01/22/2023] Open
Abstract
Peanut stunt virus (PSV) is a widespread disease infecting legumes. The PSV strains are classified into four subgroups and some are defined by the association of satellite RNAs (satRNAs). In the case of PSV, the presence of satRNAs alters the symptoms of disease in infected plants. In this study, we elucidated the plant response to PSV-G strain, which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA, which exacerbated pathogenesis in Nicotiana benthamiana. To explain the mechanisms underlying PSV infection and symptoms exacerbation caused by satRNA, we carried out transcriptome profiling of N. benthamiana challenged by PSV-G and satRNA using species-specific microarrays. Co-infection of plants with PSV-G + satRNA increased the number of identified differentially expressed genes (DEGs) compared with the number identified in PSV-G-infected plants. In both treatments, the majority of up-regulated DEGs were engaged in translation, ribosome biogenesis, RNA metabolism, and response to stimuli, while the down-regulated DEGs were required for photosynthesis. The presence of satRNA in PSV-G-infected plants caused different trends in expression of DEGs associated with phosphorylation, ATP binding, and plasma membrane.
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Affiliation(s)
- Aleksandra Obrępalska-Stęplowska
- Department of Entomology, Animal Pests and Biotechnology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
- Institute of Computing Science, Faculty of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965 Poznań, Poland.
| | - Barbara Wrzesińska
- Department of Entomology, Animal Pests and Biotechnology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
| | - Michal Goralski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 12/14 Noskowskiego Street, 61-704 Poznań, Poland.
- Institute of Computing Science, Faculty of Computing Science, Poznań University of Technology, 2 Piotrowo Street, 60-965 Poznań, Poland.
| | - Joanna Zyprych-Walczak
- Department of Mathematical and Statistical Methods, University of Life Sciences in Poznań, Wojska Polskiego 28 Street, 60-637 Poznań, Poland.
| | - Idzi Siatkowski
- Department of Mathematical and Statistical Methods, University of Life Sciences in Poznań, Wojska Polskiego 28 Street, 60-637 Poznań, Poland.
| | - Henryk Pospieszny
- Department of Virology, Institute of Plant Protection-National Research Institute, 20 Władysława Węgorka Street, 60-318 Poznań, Poland.
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Meziadi C, Blanchet S, Geffroy V, Pflieger S. Genetic resistance against viruses in Phaseolus vulgaris L.: State of the art and future prospects. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:39-50. [PMID: 29223341 DOI: 10.1016/j.plantsci.2017.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/24/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Viruses are obligate parasites that replicate intracellularly in many living organisms, including plants. Consequently, no chemicals are available that target only the virus without impacting host cells or vector organisms. The use of natural resistant varieties appears as the most reliable control strategy and remains the best and cheapest option in managing virus diseases, especially in the current ecological context of preserving biodiversity and environment in which the use of phytosanitary products becomes limited. Common bean is a grain legume cultivated mainly in Africa and Central-South America. Virus diseases of common bean have been extensively studied both by breeders to identify natural resistance genes in existing germplasms and by pathologists to understand the molecular bases of plant-virus interactions. Here we present a critical review in which we synthesize previous and recent information concerning 1) main viruses causing diseases in common bean, 2) genetic resistance to viruses in common bean, 3) the different resistance phenotypes observed and more particularly the effect of temperature, 4) the molecular bases of resistance genes to viruses in common bean, and 5) future prospects using transgenic-engineered resistant lines.
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Affiliation(s)
- Chouaïb Meziadi
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France
| | - Sophie Blanchet
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, rue Noetzlin, CS 80004, 91192 Gif sur Yvette cedex, France.
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Zheng Y, Ding B, Fei Z, Wang Y. Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors. Sci Rep 2017; 7:9771. [PMID: 28852064 PMCID: PMC5575331 DOI: 10.1038/s41598-017-10143-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/20/2017] [Indexed: 11/09/2022] Open
Abstract
In plants, virus-induced gene silencing (VIGS) is a popular tool for functional genomic studies or rapidly assessing individual gene functions. However, molecular details regarding plant responses to viral vectors remain elusive, which may complicate experimental designs and data interpretation. To this end, we documented whole transcriptome changes of tomato elicited by the application of the most widely used tobacco rattle virus (TRV)-based vectors, using comprehensive genome-wide analyses. Our data illustrated multiple biological processes with functional implications, including (1) the enhanced activity of miR167 in guiding the cleavage of an auxin response factor; (2) reduced accumulation of phased secondary small interfering RNAs from two genomic loci; (3) altered expression of ~500 protein-coding transcripts; and (4) twenty long noncoding RNAs specifically responsive to TRV vectors. Importantly, we unraveled large-scale changes in mRNA alternative splicing patterns. These observations will facilitate future application of VIGS vectors for functional studies benefiting the plant research community and help deepen the understanding of plant-virus interactions.
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Affiliation(s)
- Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Biao Ding
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA.
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA.
| | - Ying Wang
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39759, USA.
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