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Lagzian A, Ghorbani A, Tabein S, Riseh RS. Genetic variations and gene expression profiles of Rice Black-streaked dwarf virus (RBSDV) in different host plants and insect vectors: insights from RNA-Seq analysis. BMC Genomics 2024; 25:736. [PMID: 39080552 PMCID: PMC11289972 DOI: 10.1186/s12864-024-10649-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) is an etiological agent of a destructive disease infecting some economically important crops from the Gramineae family in Asia. While RBSDV causes high yield losses, genetic characteristics of replicative viral populations have not been investigated within different host plants and insect vectors. Herein, eleven publicly available RNA-Seq datasets from Chinese RBSDV-infected rice, maize, and viruliferous planthopper (Laodelphax striatellus) were obtained from the NCBI database. The patterns of SNP and RNA expression profiles of expected RBSDV populations were analyzed by CLC Workbench 20 and Geneious Prime software. These analyses discovered 2,646 mutations with codon changes in RBSDV whole transcriptome and forty-seven co-mutated hotspots with high variant frequency within the crucial regions of S5-1, S5-2, S6, S7-1, S7-2, S9, and S10 open reading frames (ORFs) which are responsible for some virulence and host range functions. Moreover, three joint mutations are located on the three-dimensional protein of P9-1. The infected RBSDV-susceptible rice cultivar KTWYJ3 and indigenous planthopper datasets showed more co-mutated hotspot numbers than others. Our analyses showed the expression patterns of viral genomic fragments varied depending on the host type. Unlike planthopper, S5-1, S2, S6, and S9-1 ORFs, respectively had the greatest read numbers in host plants; and S5-2, S9-2, and S7-2 were expressed in the lowest level. These findings underscore virus/host complexes are effective in the genetic variations and gene expression profiles of plant viruses. Our analysis revealed no evidence of recombination events. Interestingly, the negative selection was observed at 12 RBSDV ORFs, except for position 1015 in the P1 protein, where a positive selection was detected. The research highlights the potential of SRA datasets for analysis of the virus cycle and enhances our understanding of RBSDV's genetic diversity and host specificity.
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Affiliation(s)
- Arezoo Lagzian
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute, Karaj, Iran.
| | - Saeid Tabein
- Department of Plant Protection, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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Zhang M, Hong Y, Zhu J, Pan Y, Zhou H, Lv C, Guo B, Wang F, Xu R. Molecular insights into the responses of barley to yellow mosaic disease through transcriptome analysis. BMC PLANT BIOLOGY 2023; 23:267. [PMID: 37208619 DOI: 10.1186/s12870-023-04276-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Barley (Hordeum vulgare L.) represents the fourth most essential cereal crop in the world, vulnerable to barley yellow mosaic virus (BaYMV) and/or barley mild mosaic virus (BaMMV), leading to the significant yield reduction. To gain a better understanding of the mechanisms regarding barley crop tolerance to virus infection, we employed a transcriptome sequencing approach and investigated global gene expression among three barley varieties under both infected and control conditions. RESULTS High-throughput sequencing outputs revealed massive genetic responses, reflected by the barley transcriptome after BaYMV and/or BaMMV infection. Significant enrichments in peptidase complex and protein processing in endoplasmic reticulum were clustered through Gene ontology and KEGG analysis. Many genes were identified as transcription factors, antioxidants, disease resistance genes and plant hormones and differentially expressed between infected and uninfected barley varieties. Importantly, general response genes, variety-specific and infection-specific genes were also discovered. Our results provide useful information for future barley breeding to resist BaYMV and BaMMV. CONCLUSIONS Our study elucidates transcriptomic adaptations in barley response to BaYMV/BaMMV infection through high-throughput sequencing technique. The analysis outcome from GO and KEGG pathways suggests that BaYMV disease induced regulations in multiple molecular-biology processes and signalling pathways. Moreover, critical DEGs involved in defence and stress tolerance mechanisms were displayed. Further functional investigations focusing on these DEGs contributes to understanding the molecular mechanisms of plant response to BaYMV disease infection, thereby offering precious genetic resources for breeding barley varieties resistant to BaYMV disease.
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Affiliation(s)
- Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yuhan Pan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Hui Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Feifei Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/ Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Sharaf A, Nuc P, Ripl J, Alquicer G, Ibrahim E, Wang X, Maruthi MN, Kundu JK. Transcriptome Dynamics in Triticum aestivum Genotypes Associated with Resistance against the Wheat Dwarf Virus. Viruses 2023; 15:v15030689. [PMID: 36992398 PMCID: PMC10054045 DOI: 10.3390/v15030689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Wheat dwarf virus (WDV) is one of the most important pathogens of cereal crops worldwide. To understand the molecular mechanism of resistance, here we investigated the comparative transcriptome of wheat genotypes with different levels of resistance (Svitava and Fengyou 3) and susceptibility (Akteur) to WDV. We found a significantly higher number of differentially expressed transcripts (DETs) in the susceptible genotype than in the resistant one (e.g., Svitava). The number of downregulated transcripts was also higher in the susceptible genotype than in the resistant one (Svitava) and the opposite was true for the upregulated transcripts. Further functional analysis of gene ontology (GO) enrichment identified a total of 114 GO terms for the DETs. Of these, 64 biological processes, 28 cellular components and 22 molecular function GO terms were significantly enriched. A few of these genes appear to have a specific expression pattern related to resistance or susceptibility to WDV infection. Validation of the expression pattern by RT-qPCR showed that glycosyltransferase was significantly downregulated in the susceptible genotype compared to the resistant genotypes after WDV infection, while CYCLIN-T1-3, a regulator of CDK kinases (cyclin-dependent kinase), was upregulated. On the other hand, the expression pattern of the transcription factor (TF) MYB (TraesCS4B02G174600.2; myeloblastosis domain of transcription factor) was downregulated by WDV infection in the resistant genotypes compared to the susceptible genotype, while a large number of TFs belonging to 54 TF families were differentially expressed due to WDV infection. In addition, two transcripts (TraesCS7A02G341400.1 and TraesCS3B02G239900.1) were upregulated with uncharacterised proteins involved in transport and regulation of cell growth, respectively. Altogether, our findings showed a clear gene expression profile associated with resistance or susceptibility of wheat to WDV. In future studies, we will explore the regulatory network within the same experiment context. This knowledge will broaden not only the future for the development of virus-resistant wheat genotypes but also the future of genetic improvement of cereals for resilience and WDV-resistance breeding.
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Affiliation(s)
- Abdoallah Sharaf
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Przemysław Nuc
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Jan Ripl
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Glenda Alquicer
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Emad Ibrahim
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Midatharahally N. Maruthi
- Agriculture, Health and Environment Department, Natural Resources Institute, Medway Campus, University of Greenwich, Chatham, Kent ME4 4TB, UK;
| | - Jiban Kumar Kundu
- Plant Virus and Vector Interactions, Centre for Plant Virus Research, Crop Research Institute, 16106 Prague, Czech Republic; (A.S.); (P.N.); (J.R.); (G.A.); (E.I.)
- Correspondence: ; Tel.: +420-233-022-410
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Wu G, Zhang Y, Wang B, Li K, Lou Y, Zhao Y, Liu F. Proteomic and Transcriptomic Analyses Provide Novel Insights into the Crucial Roles of Host-Induced Carbohydrate Metabolism Enzymes in Xanthomonas oryzae pv. oryzae Virulence and Rice-Xoo Interaction. RICE (NEW YORK, N.Y.) 2021; 14:57. [PMID: 34176023 PMCID: PMC8236019 DOI: 10.1186/s12284-021-00503-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/11/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial leaf blight, a devastating rice disease. The Xoo-rice interaction, wherein wide ranging host- and pathogen-derived proteins and genes wage molecular arms race, is a research hotspot. Hence, the identification of novel rice-induced Xoo virulence factors and characterization of their roles affecting rice global gene expression profiles will provide an integrated and better understanding of Xoo-rice interactions from the molecular perspective. RESULTS Using comparative proteomics and an in vitro interaction system, we revealed that 5 protein spots from Xoo exhibited significantly different expression patterns (|fold change| > 1.5) at 3, 6, 12 h after susceptible rice leaf extract (RLX) treatment. MALDI-TOF MS analysis and pathogenicity tests showed that 4 host-induced proteins, including phosphohexose mutase, inositol monophosphatase, arginase and septum site-determining protein, affected Xoo virulence. Among them, mutants of two host-induced carbohydrate metabolism enzyme-encoding genes, ΔxanA and Δimp, elicited enhanced defense responses and nearly abolished Xoo virulence in rice. To decipher rice differentially expressed genes (DEGs) associated with xanA and imp, transcriptomic responses of ΔxanA-treated and Δimp-treated susceptible rice were compared to those in rice treated with PXO99A at 1 and 3 dpi. A total of 1521 and 227 DEGs were identified for PXO99A vs Δimp at 1 and 3 dpi, while for PXO99A vs ΔxanA, there were 131 and 106 DEGs, respectively. GO, KEGG and MapMan analyses revealed that the DEGs for PXO99A vs Δimp were mainly involved in photosynthesis, signal transduction, transcription, oxidation-reduction, hydrogen peroxide catabolism, ion transport, phenylpropanoid biosynthesis and metabolism of carbohydrates, lipids, amino acids, secondary metabolites, hormones, and nucleotides, while the DEGs from PXO99A vs ΔxanA were predominantly associated with photosynthesis, signal transduction, oxidation-reduction, phenylpropanoid biosynthesis, cytochrome P450 and metabolism of carbohydrates, lipids, amino acids, secondary metabolites and hormones. Although most pathways were associated with both the Δimp and ΔxanA treatments, the underlying genes were not the same. CONCLUSION Our study identified two novel host-induced virulence factors XanA and Imp in Xoo, and revealed their roles in global gene expression in susceptible rice. These results provide valuable insights into the molecular mechanisms of pathogen infection strategies and plant immunity.
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Affiliation(s)
- Guichun Wu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Yuqiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, P. R. China
| | - Bo Wang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Kaihuai Li
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Yuanlai Lou
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China
| | - Yancun Zhao
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China.
| | - Fengquan Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, No. 50 Zhongling Street, Nanjing, Jiangsu, 210014, P. R. China.
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Zhang T, Liang Q, Li C, Fu S, Kundu JK, Zhou X, Wu J. Transcriptome Analysis of Rice Reveals the lncRNA-mRNA Regulatory Network in Response to Rice Black-Streaked Dwarf Virus Infection. Viruses 2020; 12:v12090951. [PMID: 32867233 PMCID: PMC7552052 DOI: 10.3390/v12090951] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 01/05/2023] Open
Abstract
The plant genome can produce long non-coding RNAs (lncRNAs), some of which have been identified as important regulators of gene expression. To better understand the response mechanism of rice plants to Rice black-streaked dwarf virus (RBSDV) infection, we performed a comparative transcriptome analysis between the RBSDV-infected and non-infected rice plants. A total of 1342 mRNAs and 22 lncRNAs were identified to be differentially expressed after RBSDV infection. Most differentially expressed transcripts involved in the plant–pathogen interaction pathway were upregulated after RBSDV infection, indicating the activation of rice defense response by RBSDV. A network of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) was then constructed. In this network, there are 56 plant–pathogen interaction-related DEmRNAs co-expressing with 20 DElncRNAs, suggesting these DElncRNAs and DEmRNAs may play essential roles in rice innate immunity against RBSDV. Moreover, some of the lncRNA–mRNA regulatory relationships were experimentally verified in rice calli by a quick and effective method established in this study. Three DElncRNAs were selected to be tested, and the results indicated that five mRNAs were found to be regulated by them. Together, we give a whole landscape of rice mRNAs and lncRNAs in response to RBSDV infection, and a feasible method to rapidly verify the lncRNA–mRNA regulatory relationship in rice.
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Affiliation(s)
- Tianze Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | - Qian Liang
- Key Laboratory of microorganism technology and bioinformatics research of Zhejiang Province, NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang TianKe High-Technology Development Co. Ltd., Hangzhou 310023, China;
| | - Chenyang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | | | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
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Correr FH, Hosaka GK, Gómez SGP, Cia MC, Vitorello CBM, Camargo LEA, Massola NS, Carneiro MS, Margarido GRA. Time-series expression profiling of sugarcane leaves infected with Puccinia kuehnii reveals an ineffective defense system leading to susceptibility. PLANT CELL REPORTS 2020; 39:873-889. [PMID: 32314046 DOI: 10.1007/s00299-020-02536-w] [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: 12/20/2019] [Accepted: 03/30/2020] [Indexed: 05/02/2023]
Abstract
Successful orange rust development on sugarcane can potentially be explained as suppression of the plant immune system by the pathogen or delayed plant signaling to trigger defense responses. Puccinia kuehnii is an obligate biotrophic fungus that infects sugarcane leaves causing a disease called orange rust. It spread out to other countries resulting in reduction of crop yield since its first outbreak. One of the knowledge gaps of that pathosystem is to understand the molecular mechanisms altered in susceptible plants by this biotic stress. Here, we investigated the changes in temporal expression of transcripts in pathways associated with the immune system. To achieve this purpose, we used RNA-Seq to analyze infected leaf samples collected at five time points after inoculation. Differential expression analyses of adjacent time points revealed substantial changes at 12, 48 h after inoculation and 12 days after inoculation, coinciding with the events of spore germination, haustoria post-penetration and post-sporulation, respectively. During the first 24 h, a lack of transcripts involved with resistance mechanisms was revealed by underrepresentation of hypersensitive and defense response related genes. However, two days after inoculation, upregulation of genes involved with immune response regulation provided evidence of some potential defense response. Events related to biotic stress responses were predominantly downregulated in the initial time points, but expression was later restored to basal levels. Genes involved in carbohydrate metabolism showed evidence of repression followed by upregulation, possibly to ensure the pathogen nutritional requirements were met. Our results support the hypothesis that P. kuehnii initially suppressed sugarcane genes involved in plant defense systems. Late overexpression of specific regulatory pathways also suggests the possibility of an inefficient recognition system by a susceptible sugarcane genotype.
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Affiliation(s)
- Fernando Henrique Correr
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Guilherme Kenichi Hosaka
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Sergio Gregorio Pérez Gómez
- Departamento de Fitopatologia, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Mariana Cicarelli Cia
- Departamento de Fitopatologia, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Claudia Barros Monteiro Vitorello
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Luis Eduardo Aranha Camargo
- Departamento de Fitopatologia, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Nelson Sidnei Massola
- Departamento de Fitopatologia, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil
| | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Universidade Federal de São Carlos, Centro de Ciências Agrárias, Araras, São Paulo, Brazil
| | - Gabriel Rodrigues Alves Margarido
- Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Piracicaba, São Paulo, Brazil.
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Pesti R, Kontra L, Paul K, Vass I, Csorba T, Havelda Z, Várallyay É. Differential gene expression and physiological changes during acute or persistent plant virus interactions may contribute to viral symptom differences. PLoS One 2019; 14:e0216618. [PMID: 31051010 PMCID: PMC6499435 DOI: 10.1371/journal.pone.0216618] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/24/2019] [Indexed: 01/01/2023] Open
Abstract
Viruses have different strategies for infecting their hosts. Fast and acute infections result in the development of severe symptoms and may cause the death of the plant. By contrast, in a persistent interaction, the virus can survive within its host for a long time, inducing only mild symptoms. In this study, we investigated the gene expression changes induced in CymRSV-, crTMV-, and TCV-infected Nicotiana benthamiana and in PVX- and TMV-U1-infected Solanum lycopersicum plants after the systemic spread of the virus by two different high-throughput methods: microarray hybridization or RNA sequencing. Using these techniques, we were able to clearly differentiate between acute and persistent infections. We validated the gene expression changes of selected genes by Northern blot hybridization or by qRT-PCR. We show that, in contrast to persistent infections, the drastic shut-off of housekeeping genes, downregulation of photosynthesis-related transcripts and induction of stress genes are specific outcomes with acute infections. We also show that these changes are not a consequence of host necrosis or the presence of a viral silencing suppressor. Thermal imaging data and chlorophyll fluorescence measurements correlated very well with the molecular changes. We believe that the molecular and physiological changes detected during acute infections mostly contribute to virus symptom development. The observed characteristic physiological changes associated with economically more dangerous acute infections could serve as a basis for the elaboration of remote monitoring systems suitable for detecting developing virus infections in crops. Moreover, as molecular and physiological changes are characteristics of different types of virus lifestyles, this knowledge can support risk assessments of recently described novel viruses.
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Affiliation(s)
- Réka Pesti
- Diagnostic Group, Department of Genomics, Agricultural Biotechnology Research Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary
| | - Levente Kontra
- Diagnostic Group, Department of Genomics, Agricultural Biotechnology Research Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary
| | - Kenny Paul
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Imre Vass
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | - Tibor Csorba
- Virology Group, Department of Plant Biotechnology, Agricultural Biotechnology Research Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary
| | - Zoltán Havelda
- Plant Developmental Biology Group, Department of Plant Biotechnology, Agricultural Biotechnology Research Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary
| | - Éva Várallyay
- Diagnostic Group, Department of Genomics, Agricultural Biotechnology Research Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary
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Yue R, Lu C, Han X, Guo S, Yan S, Liu L, Fu X, Chen N, Guo X, Chi H, Tie S. Comparative proteomic analysis of maize (Zea mays L.) seedlings under rice black-streaked dwarf virus infection. BMC PLANT BIOLOGY 2018; 18:191. [PMID: 30208842 PMCID: PMC6136180 DOI: 10.1186/s12870-018-1419-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/06/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Maize rough dwarf disease (MRDD) is a severe disease that has been occurring frequently in southern China and many other Asian countries. MRDD is caused by the infection of Rice black streaked dwarf virus (RBSDV) and leads to significant economic losses in maize production. To well understand the destructive effects of RBSDV infection on maize growth, comparative proteomic analyses of maize seedlings under RBSDV infection was performed using an integrated approach involving LC-MS/MS and Tandem Mass Tag (TMT) labeling. RESULTS In total, 7615 maize proteins, 6319 of which were quantified. A total of 116 differentially accumulated proteins (DAPs) were identified, including 35 up- and 81 down-regulated proteins under the RBSDV infection. Enrichment analysis showed that the DAPs were most strongly associated with cyanoamino acid metabolism, protein processing in ER, and ribosome-related pathways. Two sulfur metabolism-related proteins were significantly reduced, indicating that sulfur may participate in the resistance against RBSDV infection. Furthermore, 15 DAPs involved in six metabolic pathways were identified in maize under the RBSDV infection. CONCLUSIONS Our data revealed that the responses of maize to RBSDV infection were controlled by various metabolic pathways.
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Affiliation(s)
- Runqing Yue
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Caixia Lu
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Xiaohua Han
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Shulei Guo
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Shufeng Yan
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Lu Liu
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Xiaolei Fu
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Nana Chen
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Xinhai Guo
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Haifeng Chi
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| | - Shuanggui Tie
- Henan Academy of Agricultural Sciences, Zhengzhou, China
- The Henan Provincial Key Laboratory of Maize Biology, Zhengzhou, China
| |
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