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Sun M, Xiao X, Khan KS, Lyu J, Yu J. Characterization and functions of Myeloblastosis (MYB) transcription factors in cucurbit crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112235. [PMID: 39186952 DOI: 10.1016/j.plantsci.2024.112235] [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: 05/03/2024] [Revised: 07/15/2024] [Accepted: 08/18/2024] [Indexed: 08/28/2024]
Abstract
Myeloblastosis (MYB) is one of the largest family of transcription factors (TFs) in plants. It plays a key role in plant life activities, such as metabolic regulation, stress resistant, as well as helpful for plant growth and development. In China, cucurbit is an important and nutrients rich vegetable crop, which have high medicinal and socio-economic values. In this review, we discussed the structure and characterization of MYB TFs and how do regulate flower development, fruit maturity, fruit quality, and flavonoid biosynthesis. Furthermore, we highlight the effect and contribution of MYB TFs in the regulation of biotic and abiotic stress resistance. This comprehensive review will provide a new reference for the more effective application of MYB TF in quality control, stress resistance research and molecular breeding of cucurbit crops.
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Affiliation(s)
- Mingming Sun
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Xuemei Xiao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Khuram Shehzad Khan
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, PR China; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Jian Lyu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Jihua Yu
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, PR China; State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, PR China.
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2
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Wang D, Chen M, Peng J, Zheng H, Lu Y, Wu G, Wu J, Li J, Chen J, Yan F, Rao S. Transcriptome Analysis of Tomato Leaves Reveals Candidate Genes Responsive to Tomato Brown Rugose Fruit Virus Infection. Int J Mol Sci 2024; 25:4012. [PMID: 38612822 PMCID: PMC11012278 DOI: 10.3390/ijms25074012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) is a newly-emerging tobamovirus which was first reported on tomatoes in Israel and Jordan, and which has now spread rapidly in Asia, Europe, North America, and Africa. ToBRFV can overcome the resistance to other tobamoviruses conferred by tomato Tm-1, Tm-2, and Tm-22 genes, and it has seriously affected global crop production. The rapid and comprehensive transcription reprogramming of host plant cells is the key to resisting virus attack, but there have been no studies of the transcriptome changes induced by ToBRFV in tomatoes. Here, we made a comparative transcriptome analysis between tomato leaves infected with ToBRFV for 21 days and those mock-inoculated as controls. A total of 522 differentially expressed genes were identified after ToBRFV infection, of which 270 were up-regulated and 252 were down-regulated. Functional analysis showed that DEGs were involved in biological processes such as response to wounding, response to stress, protein folding, and defense response. Ten DEGs were selected and verified by qRT-PCR, confirming the reliability of the high-throughput sequencing data. These results provide candidate genes or signal pathways for the response of tomato leaves to ToBRFV infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (D.W.); (H.Z.); (J.L.)
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (D.W.); (H.Z.); (J.L.)
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3
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Li Z, Tang Y, Lan G, Yu L, Ding S, She X, He Z. Transcriptome and Metabolome Analyses Reveal That Jasmonic Acids May Facilitate the Infection of Cucumber Green Mottle Mosaic Virus in Bottle Gourd. Int J Mol Sci 2023; 24:16566. [PMID: 38068889 PMCID: PMC10706418 DOI: 10.3390/ijms242316566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) is a typical seed-borne tobamovirus that mainly infects cucurbit crops. Due to the rapid growth of international trade, CGMMV has spread worldwide and become a significant threat to cucurbit industry. Despite various studies focusing on the interaction between CGMMV and host plants, the molecular mechanism of CGMMV infection is still unclear. In this study, we utilized transcriptome and metabolome analyses to investigate the antiviral response of bottle gourd (Lagenaria siceraria) under CGMMV stress. The transcriptome analysis revealed that in comparison to mock-inoculated bottle gourd, 1929 differently expressed genes (DEGs) were identified in CGMMV-inoculated bottle gourd. Among them, 1397 genes were upregulated while 532 genes were downregulated. KEGG pathway enrichment indicated that the DEGs were mainly involved in pathways including the metabolic pathway, the biosynthesis of secondary metabolites, plant hormone signal transduction, plant-pathogen interaction, and starch and sucrose metabolism. The metabolome result showed that there were 76 differentially accumulated metabolites (DAMs), of which 69 metabolites were up-accumulated, and 7 metabolites were down-accumulated. These DAMs were clustered into several pathways, including biosynthesis of secondary metabolites, tyrosine metabolism, flavonoid biosynthesis, carbon metabolism, and plant hormone signal transduction. Combining the transcriptome and metabolome results, the genes and metabolites involved in the jasmonic acid and its derivatives (JAs) synthesis pathway were significantly induced upon CGMMV infection. The silencing of the allene oxide synthase (AOS) gene, which is the key gene involved in JAs synthesis, reduced CGMMV accumulation. These findings suggest that JAs may facilitate CGMMV infection in bottle gourd.
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Affiliation(s)
| | | | | | | | | | - Xiaoman She
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Z.L.); (Y.T.); (G.L.); (L.Y.); (S.D.)
| | - Zifu He
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (Z.L.); (Y.T.); (G.L.); (L.Y.); (S.D.)
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4
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Liu M, Kang B, Wu H, Aranda MA, Peng B, Liu L, Fei Z, Hong N, Gu Q. Transcriptomic and metabolic profiling of watermelon uncovers the role of salicylic acid and flavonoids in the resistance to cucumber green mottle mosaic virus. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5218-5235. [PMID: 37235634 DOI: 10.1093/jxb/erad197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/24/2023] [Indexed: 05/28/2023]
Abstract
Understanding the mechanisms underlying plant resistance to virus infections is crucial for viral disease management in agriculture. However, the defense mechanism of watermelon (Citrullus lanatus) against cucumber green mottle mosaic virus (CGMMV) infection remains largely unknown. In this study, we performed transcriptomic, metabolomic, and phytohormone analyses of a CGMMV susceptible watermelon cultivar 'Zhengkang No.2' ('ZK') and a CGMMV resistant wild watermelon accession PI 220778 (PI) to identify the key regulatory genes, metabolites, and phytohormones responsible for CGMMV resistance. We then tested several phytohormones and metabolites for their roles in watermelon CGMMV resistance via foliar application, followed by CGMMV inoculation. Several phenylpropanoid metabolism-associated genes and metabolites, especially those involved in the flavonoid biosynthesis pathway, were found to be significantly enriched in the CGMMV-infected PI plants compared with the CGMMV-infected 'ZK' plants. We also identified a gene encoding UDP-glycosyltransferase (UGT) that is involved in kaempferol-3-O-sophoroside biosynthesis and controls disease resistance, as well as plant height. Additionally, salicylic acid (SA) biogenesis increased in the CGMMV-infected 'ZK' plants, resulting in the activation of a downstream signaling cascade. SA levels in the tested watermelon plants correlated with that of total flavonoids, and SA pre-treatment up-regulated the expression of flavonoid biosynthesis genes, thus increasing the total flavonoid content. Furthermore, application of exogenous SA or flavonoids extracted from watermelon leaves suppressed CGMMV infection. In summary, our study demonstrates the role of SA-induced flavonoid biosynthesis in plant development and CGMMV resistance, which could be used to breed for CGMMV resistance in watermelon.
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Affiliation(s)
- Mei Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Baoshan Kang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Huijie Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)- CSIC, Apdo. correos 164, 30100 Espinardo, Murcia, Spain
| | - Bin Peng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Liming Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Ni Hong
- Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinsheng Gu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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Philosoph AM, Dombrovsky A, Luria N, Sela N, Elad Y, Frenkel O. Rapid defense mechanism suppression during viral- oomycete disease complex formation. FRONTIERS IN PLANT SCIENCE 2023; 14:1124911. [PMID: 37360707 PMCID: PMC10288809 DOI: 10.3389/fpls.2023.1124911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
Combined infection of the host plant with pathogens involving different parasitic lifestyles may result in synergistic effects that intensify disease symptoms. Understanding the molecular dynamics during concurrent infection provides essential insight into the host response. The transcriptomic pattern of cucumber plants infected with a necrotrophic pathogen, Pythium spinosum, and a biotrophic pathogen, Cucumber green mottle mosaic virus (CGMMV) was studied at different time points, under regimes of single and co-infection. Analysis of CGMMV infection alone revealed a mild influence on host gene expression at the stem base, while the infection by P. spinosum is associated with drastic changes in gene expression. Comparing P. spinosum as a single infecting pathogen with a later co-infection by CGMMV revealed a rapid host response as early as 24 hours post-CGMMV inoculation with a sharp downregulation of genes related to the host defense mechanism against the necrotrophic pathogen. Suppression of the defense mechanism of co-infected plants was followed by severe stress, including 30% plants mortality and an increase of the P. spinosum hyphae. The first evidence of defense recovery against the necrotrophic pathogen only occurred 13 days post-viral infection. These results support the hypothesis that the viral infection of the Pythium pre-infected plants subverted the host defense system and changed the equilibrium obtained with P. spinosum. It also implies a time window in which the plants are most susceptible to P. spinosum after CGMMV infection.
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Affiliation(s)
- Amit M. Philosoph
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Aviv Dombrovsky
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
| | - Neta Luria
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
| | - Yigal Elad
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
| | - Omer Frenkel
- Department of Plant Pathology and Weed Science, The Volcani Institute, Agricultural Research Organization, Bet Dagan, Israel
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6
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Viswanath KK, Kuo SY, Tu CW, Hsu YH, Huang YW, Hu CC. The Role of Plant Transcription Factors in the Fight against Plant Viruses. Int J Mol Sci 2023; 24:ijms24098433. [PMID: 37176135 PMCID: PMC10179606 DOI: 10.3390/ijms24098433] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Plants are vulnerable to the challenges of unstable environments and pathogen infections due to their immobility. Among various stress conditions, viral infection is a major threat that causes significant crop loss. In response to viral infection, plants undergo complex molecular and physiological changes, which trigger defense and morphogenic pathways. Transcription factors (TFs), and their interactions with cofactors and cis-regulatory genomic elements, are essential for plant defense mechanisms. The transcriptional regulation by TFs is crucial in establishing plant defense and associated activities during viral infections. Therefore, identifying and characterizing the critical genes involved in the responses of plants against virus stress is essential for the development of transgenic plants that exhibit enhanced tolerance or resistance. This article reviews the current understanding of the transcriptional control of plant defenses, with a special focus on NAC, MYB, WRKY, bZIP, and AP2/ERF TFs. The review provides an update on the latest advances in understanding how plant TFs regulate defense genes expression during viral infection.
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Affiliation(s)
- Kotapati Kasi Viswanath
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Song-Yi Kuo
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chin-Wei Tu
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
| | - Ying-Wen Huang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
- Advanced Plant Biotechnology Centre, National Chung Hsing University, Taichung 40227, Taiwan
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Cai L, Liu J, Wang S, Gong Z, Yang S, Xu F, Hu Z, Zhang M, Yang J. The coiled-coil protein gene WPRb confers recessive resistance to Cucumber green mottle mosaic virus. PLANT PHYSIOLOGY 2023; 191:369-381. [PMID: 36179097 PMCID: PMC9806632 DOI: 10.1093/plphys/kiac466] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/11/2022] [Indexed: 06/16/2023]
Abstract
Cucumber green mottle mosaic virus (CGMMV) is one of the major global quarantine viruses and causes severe symptoms in Cucurbit crops, particularly with regard to fruit decay. However, the genetic mechanisms that control plant resistance to CGMMV have yet to be elucidated. Here, we found that WPRb, a weak chloroplast movement under blue light 1 and plastid movement impaired 2-related protein family gene, is recessively associated with CGMMV resistance in watermelon (Citrullus lanatus). We developed a reproducible marker based on a single non-synonymous substitution (G1282A) in WPRb, which can be used for marker-assisted selection for CGMMV resistance in watermelon. Editing of WPRb conferred greater tolerance to CGMMV. We found WPRb targets to the plasmodesmata (PD) and biochemically interacts with the CGMMV movement protein, facilitating viral intercellular movement by affecting the permeability of PD. Our findings enable us to genetically control CGMMV resistance in planta by using precise genome editing techniques targeted to WPRb.
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Affiliation(s)
- Lingmin Cai
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Liu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Weimeng Seed Co. Ltd, Ningbo 315000, China
| | - Shuchang Wang
- Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zihui Gong
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Siyu Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Fengyuan Xu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, Hangzhou 310058, China
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Guo H, Bi X, Wang Z, Jiang D, Cai M, An M, Xia Z, Wu Y. Reactive oxygen species-related genes participate in resistance to cucumber green mottle mosaic virus infection regulated by boron in Nicotiana benthamiana and watermelon. FRONTIERS IN PLANT SCIENCE 2022; 13:1027404. [PMID: 36438146 PMCID: PMC9691971 DOI: 10.3389/fpls.2022.1027404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Cucumber green mottle mosaic virus (CGMMV) infection causes acidification and rot of watermelon flesh, resulting in serious economic losses. It is widely reported the interaction relationship between boron and reactive oxygen species (ROS) in regulating normal growth and disease resistance in plants. Our previous results demonstrated that exogenous boron could improve watermelon resistance to CGMMV infection. However, the roles of ROS-related genes regulated by boron in resistance to CGMMV infection are unclear. Here, we demonstrated that CGMMV symptoms were alleviated, and viral accumulations were decreased by boron application in Nicotiana benthamiana, indicating that boron contributed to inhibiting CGMMV infection. Meanwhile, we found that a number of differentially expressed genes (DEGs) associated with inositol biosynthesis, ethylene synthesis, Ca2+ signaling transduction and ROS scavenging system were up-regulated, while many DEGs involved in ABA catabolism, GA signal transduction and ascorbic acid metabolism were down-regulated by boron application under CGMMV infection. Additionally, we individually silenced nine ROS-related genes to explore their anti-CGMMV roles using a tobacco rattle virus (TRV) vector. The results showed that NbCat1, NbGME1, NbGGP and NbPrx Q were required for CGMMV infection, while NbGST and NbIPS played roles in resistance to CGMMV infection. The similar results were obtained in watermelon by silencing of ClCat, ClPrx or ClGST expression using a pV190 vector. This study proposed a new strategy for improving plant resistance to CGMMV infection by boron-regulated ROS pathway and provided several target genes for watermelon disease resistance breeding.
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Affiliation(s)
- Huiyan Guo
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xinyue Bi
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Zhiping Wang
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Dong Jiang
- Green Agricultural Technology Center of Liaoning Province, Shenyang, China
| | - Ming Cai
- Green Agricultural Technology Center of Liaoning Province, Shenyang, China
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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9
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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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10
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Bi X, Guo H, Li X, Zheng L, An M, Xia Z, Wu Y. A novel strategy for improving watermelon resistance to cucumber green mottle mosaic virus by exogenous boron application. MOLECULAR PLANT PATHOLOGY 2022; 23:1361-1380. [PMID: 35671152 PMCID: PMC9366068 DOI: 10.1111/mpp.13234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
The molecular mode controlling cucumber green mottle mosaic virus (CGMMV)-induced watermelon blood flesh disease (WBFD) is largely unknown. In this study, we have found that application of exogenous boron suppressed CGMMV infection in watermelon fruit and alleviated WBFD symptoms. Our transcriptome analysis showed that the most up-regulated differentially expressed genes (DEGs) were associated with polyamine and auxin biosynthesis, abscisic acid catabolism, defence-related pathways, cell wall modification, and energy and secondary metabolism, while the down-regulated DEGs were mostly involved in ethylene biosynthesis, cell wall catabolism, and plasma membrane functions. Our virus-induced gene silencing results showed that silencing of SPDS expression in watermelon resulted in a higher putrescine content and an inhibited CGMMV infection correlating with no WBFD symptoms. SBT and TUBB1 were also required for CGMMV infection. In contrast, silencing of XTH23 and PE/PEI7 (low-level lignin, cellulose and pectin) and ATPS1 (low-level glutathione) promoted CGMMV accumulation. Furthermore, RAP2-3, MYB6, WRKY12, H2A, and DnaJ11 are likely to participate in host antiviral resistance. In addition, a higher (spermidine + spermine):putrescine ratio, malondialdehyde content, and lactic acid content were responsible for fruit decay and acidification. Our results provide new knowledge on the roles of boron in watermelon resistance to CGMMV-induced WBFD. This new knowledge can be used to design better control methods for CGMMV in the field and to breed CGMMV resistant watermelon and other cucurbit crops.
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Affiliation(s)
- Xinyue Bi
- Liaoning Key Laboratory of Plant Pathology, College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
| | - Huiyan Guo
- Liaoning Key Laboratory of Plant Pathology, College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
| | - Xiaodong Li
- Liaoning Key Laboratory of Plant Pathology, College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
- Centre for Biological Disaster Prevention and ControlNational Forestry and Grassland AdministrationShenyangChina
| | - Lijiao Zheng
- Xinmin City Agricultural Technology Extension CentreShenyangChina
| | - Mengnan An
- Liaoning Key Laboratory of Plant Pathology, College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
| | - Zihao Xia
- Liaoning Key Laboratory of Plant Pathology, College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
| | - Yuanhua Wu
- Liaoning Key Laboratory of Plant Pathology, College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
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11
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Valmonte-Cortes GR, Lilly ST, Pearson MN, Higgins CM, MacDiarmid RM. The Potential of Molecular Indicators of Plant Virus Infection: Are Plants Able to Tell Us They Are Infected? PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020188. [PMID: 35050076 PMCID: PMC8777591 DOI: 10.3390/plants11020188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/21/2021] [Accepted: 01/06/2022] [Indexed: 05/06/2023]
Abstract
To our knowledge, there are no reports that demonstrate the use of host molecular markers for the purpose of detecting generic plant virus infection. Two approaches involving molecular indicators of virus infection in the model plant Arabidopsis thaliana were examined: the accumulation of small RNAs (sRNAs) using a microfluidics-based method (Bioanalyzer); and the transcript accumulation of virus-response related host plant genes, suppressor of gene silencing 3 (AtSGS3) and calcium-dependent protein kinase 3 (AtCPK3) by reverse transcriptase-quantitative PCR (RT-qPCR). The microfluidics approach using sRNA chips has previously demonstrated good linearity and good reproducibility, both within and between chips. Good limits of detection have been demonstrated from two-fold 10-point serial dilution regression to 0.1 ng of RNA. The ratio of small RNA (sRNA) to ribosomal RNA (rRNA), as a proportion of averaged mock-inoculation, correlated with known virus infection to a high degree of certainty. AtSGS3 transcript decreased between 14- and 28-days post inoculation (dpi) for all viruses investigated, while AtCPK3 transcript increased between 14 and 28 dpi for all viruses. A combination of these two molecular approaches may be useful for assessment of virus-infection of samples without the need for diagnosis of specific virus infection.
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Affiliation(s)
- Gardette R. Valmonte-Cortes
- School of Science, AUT City Campus, Auckland University of Technology, Auckland 1142, New Zealand;
- The New Zealand Institute for Plant & Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand; (S.T.L.); (R.M.M.)
- Correspondence:
| | - Sonia T. Lilly
- The New Zealand Institute for Plant & Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand; (S.T.L.); (R.M.M.)
- School of Biological Sciences, The University of Auckland, Thomas Building, 3a Symonds Street, Auckland 1010, New Zealand;
| | - Michael N. Pearson
- School of Biological Sciences, The University of Auckland, Thomas Building, 3a Symonds Street, Auckland 1010, New Zealand;
| | - Colleen M. Higgins
- School of Science, AUT City Campus, Auckland University of Technology, Auckland 1142, New Zealand;
| | - Robin M. MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand; (S.T.L.); (R.M.M.)
- School of Biological Sciences, The University of Auckland, Thomas Building, 3a Symonds Street, Auckland 1010, New Zealand;
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12
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He Y, Li L, Yao Y, Li Y, Zhang H, Fan M. Transcriptome-wide N6-methyladenosine (m 6A) methylation in watermelon under CGMMV infection. BMC PLANT BIOLOGY 2021; 21:516. [PMID: 34749644 PMCID: PMC8574010 DOI: 10.1186/s12870-021-03289-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 10/22/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cucumber green mottle mosaic virus (CGMMV) causes substantial global losses in cucurbit crops, especially watermelon. N6-methyladenosine (m6A) methylation in RNA is one of the most important post-transcriptional modification mechanisms in eukaryotes. It has been shown to have important regulatory functions in some model plants, but there has been no research regarding m6A modifications in watermelon. RESULTS We measured the global m6A level in resistant watermelon after CGMMV infection using a colorimetric method. And the results found that the global m6A level significantly decreased in resistant watermelon after CGMMV infection. Specifically, m6A libraries were constructed for the resistant watermelon leaves collected 48 h after CGMMV infection and the whole-genome m6A-seq were carried out. Numerous m6A modified peaks were identified from CGMMV-infected and control (uninfected) samples. The modification distributions and motifs of these m6A peaks were highly conserved in watermelon transcripts but the modification was more abundant than in other reported crop plants. In early response to CGMMV infection, 422 differentially methylated genes (DMGs) were identified, most of which were hypomethylated, and probably associated with the increased expression of watermelon m6A demethylase gene ClALKBH4B. Gene Ontology (GO) analysis indicated quite a few DMGs were involved in RNA biology and stress responsive pathways. Combined with RNA-seq analysis, there was generally a negative correlation between m6A RNA methylation and transcript level in the watermelon transcriptome. Both the m6A methylation and transcript levels of 59 modified genes significantly changed in response to CGMMV infection and some were involved in plant immunity. CONCLUSIONS Our study represents the first comprehensive characterization of m6A patterns in the watermelon transcriptome and helps to clarify the roles and regulatory mechanisms of m6A modification in watermelon in early responses to CGMMV.
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Affiliation(s)
- Yanjun He
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Lili Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Yixiu Yao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Yulin Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Huiqing Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Min Fan
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China.
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Transcriptomic Analysis of Genes Involved in Plant Defense Response to the Cucumber Green Mottle Mosaic Virus Infection. Life (Basel) 2021; 11:life11101064. [PMID: 34685435 PMCID: PMC8541684 DOI: 10.3390/life11101064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 11/17/2022] Open
Abstract
Plants have evolved a complex multilayered defense system to counteract various invading pathogens during their life cycle. In addition to silencing, considered to be a major molecular defense response against viruses, different signaling pathways activated by phytohormones trigger the expression of secondary metabolites and proteins preventing virus entry and propagation. In this study, we explored the response of cucumber plants to one of the global pathogens, cucumber green mottle mosaic virus (CGMMV), which causes severe symptoms on leaves and fruits. The inbred line of Cucumis sativus L., which is highly susceptible to CGMMV, was chosen for inoculation. Transcriptomes of infected plants at the early and late stages of infection were analyzed in comparison with the corresponding transcriptomes of healthy plants using RNA-seq. The changes in the signaling pathways of ethylene and salicylic and jasmonic acids, as well as the differences in silencing response and expression of pathogenesis-related proteins and transcription factors, were revealed. The results show that silencing was strongly suppressed in infected plants, while the salicylic acid and ethylene signaling pathways were induced. The genes encoding pathogenesis-related proteins and the genes involved in the jasmonic acid pathway changed their expression insignificantly. It was also found that WRKY and NAC were the most sensitive to CGMMV infection among the transcription factors detected.
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Kaur K, Awasthi P, Tiwari S. Comparative transcriptome analysis of unripe and ripe banana (cv. Nendran) unraveling genes involved in ripening and other related processes. PLoS One 2021; 16:e0254709. [PMID: 34314413 PMCID: PMC8315498 DOI: 10.1371/journal.pone.0254709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/02/2021] [Indexed: 11/21/2022] Open
Abstract
Banana is one of the most important fruit crops consumed globally owing to its high nutritional value. Previously, we demonstrated that the ripe pulp of the banana cultivar (cv.) Nendran (AAB) contained a high amount of pro-vitamin A carotenoids. However, the molecular factors involved in the ripening process in Nendran fruit are unexplored. Hence, we commenced a transcriptome study by using the Illumina HiSeq 2500 at two stages i.e. unripe and ripe fruit-pulp of Nendran. Overall, 3474 up and 4727 down-regulated genes were obtained. A large number of identified transcripts were related to genes involved in ripening, cell wall degradation and aroma formation. Gene ontology analysis highlighted differentially expressed genes that play a key role in various pathways. These pathways were mainly linked to cellular, molecular and biological processes. The present transcriptome study also reveals a crucial role of up-regulated carotenoid biosynthesis pathway genes namely, lycopene beta cyclase and geranylgeranyl pyrophosphate synthase at the ripening stage. Genes related to the ripening and other processes like aroma and flavor were highly expressed in the ripe pulp. Expression of numerous transcription factor family genes was also identified. This study lays a path towards understanding the ripening, carotenoid accumulation and other related processes in banana.
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Affiliation(s)
- Karambir Kaur
- Department of Biotechnology, Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Ministry of Science and Technology (Government of India), Mohali, Punjab, India
| | - Praveen Awasthi
- Department of Biotechnology, Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Ministry of Science and Technology (Government of India), Mohali, Punjab, India
| | - Siddharth Tiwari
- Department of Biotechnology, Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Ministry of Science and Technology (Government of India), Mohali, Punjab, India
- * E-mail: ,
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15
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Yue H, Huang LP, Lu DYH, Zhang ZH, Zhang Z, Zhang DY, Zheng LM, Gao Y, Tan XQ, Zhou XG, Shi XB, Liu Y. Integrated Analysis of microRNA and mRNA Transcriptome Reveals the Molecular Mechanism of Solanum lycopersicum Response to Bemisia tabaci and Tomato chlorosis virus. Front Microbiol 2021; 12:693574. [PMID: 34239512 PMCID: PMC8258350 DOI: 10.3389/fmicb.2021.693574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Tomato chlorosis virus (ToCV), is one of the most devastating cultivated tomato viruses, seriously threatened the growth of crops worldwide. As the vector of ToCV, the whitefly Bemisia tabaci Mediterranean (MED) is mainly responsible for the rapid spread of ToCV. The current understanding of tomato plant responses to this virus and B. tabaci is very limited. To understand the molecular mechanism of the interaction between tomato, ToCV and B. tabaci, we adopted a next-generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed under the infection of B. tabaci and ToCV in tomato plants. Our data revealed that 6199 mRNAs were significantly regulated, and the differentially expressed genes were most significantly associated with the plant-pathogen interaction, the MAPK signaling pathway, the glyoxylate, and the carbon fixation in photosynthetic organisms and photosynthesis related proteins. Concomitantly, 242 differentially expressed miRNAs were detected, including novel putative miRNAs. Sly-miR159, sly-miR9471b-3p, and sly-miR162 were the most expressed miRNAs in each sample compare to control group. Moreover, we compared the similarities and differences of gene expression in tomato plant caused by infection or co-infection of B. tabaci and ToCV. Taken together, the analysis reported in this article lays a solid foundation for further research on the interaction between tomato, ToCV and B. tabaci, and provide evidence for the identification of potential key genes that influences virus transmission in tomato plants.
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Affiliation(s)
- Hao Yue
- Subcollege of Longping, Graduate School of Hunan University, Changsha, China
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - Li-Ping Huang
- Subcollege of Longping, Graduate School of Hunan University, Changsha, China
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - Ding-Yi-Hui Lu
- Subcollege of Longping, Graduate School of Hunan University, Changsha, China
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - Zhan-Hong Zhang
- Institute of Vegetable, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhuo Zhang
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - De-Yong Zhang
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - Li-Min Zheng
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - Yang Gao
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - Xin-Qiu Tan
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - Xu-Guo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY, United States
| | - Xiao-Bin Shi
- Subcollege of Longping, Graduate School of Hunan University, Changsha, China
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
| | - Yong Liu
- Subcollege of Longping, Graduate School of Hunan University, Changsha, China
- Hunan Academy of Agricultural Sciences, Institute of Plant Protection, Changsha, China
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Sáez C, Flores-León A, Montero-Pau J, Sifres A, Dhillon NPS, López C, Picó B. RNA-Seq Transcriptome Analysis Provides Candidate Genes for Resistance to Tomato Leaf Curl New Delhi Virus in Melon. FRONTIERS IN PLANT SCIENCE 2021; 12:798858. [PMID: 35116050 PMCID: PMC8805612 DOI: 10.3389/fpls.2021.798858] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 05/10/2023]
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) emerged in the Mediterranean Basin in 2012 as the first DNA bipartite begomovirus (Geminiviridae family), causing severe yield and economic losses in cucurbit crops. A major resistance locus was identified in the wild melon accession WM-7 (Cucumis melo kachri group), but the mechanisms involved in the resistant response remained unknown. In this work, we used RNA-sequencing to identify disease-associated genes that are differentially expressed in the course of ToLCNDV infection and could contribute to resistance. Transcriptomes of the resistant WM-7 genotype and the susceptible cultivar Piñonet Piel de Sapo (PS) (C. melo ibericus group) in ToLCNDV and mock inoculated plants were compared at four time points during infection (0, 3, 6, and 12 days post inoculation). Different gene expression patterns were observed over time in the resistant and susceptible genotypes in comparison to their respective controls. Differentially expressed genes (DEGs) in ToLCNDV-infected plants were classified using gene ontology (GO) terms, and genes of the categories transcription, DNA replication, and helicase activity were downregulated in WM-7 but upregulated in PS, suggesting that reduced activity of these functions reduces ToLCNDV replication and intercellular spread and thereby contributes to resistance. DEGs involved in the jasmonic acid signaling pathway, photosynthesis, RNA silencing, transmembrane, and sugar transporters entail adverse consequences for systemic infection in the resistant genotype, and lead to susceptibility in PS. The expression levels of selected candidate genes were validated by qRT-PCR to corroborate their differential expression upon ToLCNDV infection in resistant and susceptible melon. Furthermore, single nucleotide polymorphism (SNPs) with an effect on structural functionality of DEGs linked to the main QTLs for ToLCNDV resistance have been identified. The obtained results pinpoint cellular functions and candidate genes that are differentially expressed in a resistant and susceptible melon line in response to ToLCNDV, an information of great relevance for breeding ToLCNDV-resistant melon cultivars.
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Affiliation(s)
- Cristina Sáez
- Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València, Valencia, Spain
- *Correspondence: Cristina Sáez,
| | - Alejandro Flores-León
- Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València, Valencia, Spain
| | - Javier Montero-Pau
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
| | - Alicia Sifres
- Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València, Valencia, Spain
| | - Narinder P. S. Dhillon
- World Vegetable Center, East and Southeast Asia, Research and Training Station, Kasetsart University, Nakhon Pathom, Thailand
| | - Carmelo López
- Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València, Valencia, Spain
- Carmelo López,
| | - Belén Picó
- Institute for the Conservation and Breeding of Agricultural Biodiversity, Universitat Politècnica de València, Valencia, Spain
- Belén Picó,
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Xu L, Zong X, Wang J, Wei H, Chen X, Liu Q. Transcriptomic analysis reveals insights into the response to Hop stunt viroid (HSVd) in sweet cherry ( Prunus avium L.) fruits. PeerJ 2020; 8:e10005. [PMID: 33005494 PMCID: PMC7513744 DOI: 10.7717/peerj.10005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Hop stunt viroid (HSVd) is a member of the genus Hostuviroid of the family Pospiviroidae and has been found in a wide range of herbaceous and woody hosts. It causes serious dapple fruit symptoms on infected sweet cherry, notably inducing cherry tree decay. In order to better understand the molecular mechanisms of HSVd infection in sweet cherry fruit, transcriptome analysis of HSVd-infected and healthy sweet cherry fruits was carried out. A total of 1,572 differentially expressed genes (DEGs) were identified, involving 961 upregulated DEGs and 611 downregulated DEGs. Functional analysis indicated that the DEGs were mainly involved in plant hormone signal transduction, plant-pathogen interactions, secondary metabolism, and the MAPK signaling pathway. In addition, C2H2 zinc finger, MYB, bHLH, AP2/ERF, C2C2-dof, NAC and WRKY transcription factors can respond to HSVd infection. In order to confirm the high-throughput sequencing results, 16 DEGs were verified by RT-qPCR analysis. The results provided insight into the pathways and genes of sweet cherry fruit in response to HSVd infection.
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Affiliation(s)
- Li Xu
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Xiaojuan Zong
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Jiawei Wang
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Hairong Wei
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Xin Chen
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
| | - Qingzhong Liu
- Key Laboratory for Fruit Biotechnology Breeding of Shandong Province, Shandong Institute of Pomology, Taian, Shandong, People's Republic of China
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iTRAQ-Based Proteomic Analysis of Watermelon Fruits in Response to Cucumber green mottle mosaic virus Infection. Int J Mol Sci 2020; 21:ijms21072541. [PMID: 32268502 PMCID: PMC7178218 DOI: 10.3390/ijms21072541] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 01/07/2023] Open
Abstract
Cucumber green mottle mosaic virus (CGMMV) is an important viral pathogen on cucurbit plants worldwide, which can cause severe fruit decay symptoms on infected watermelon (usually called “watermelon blood flesh”). However, the molecular mechanism of this disease has not been well understood. In this study, we employed the isobaric tags for relative and absolute quantitation (iTRAQ) technique to analyze the proteomic profiles of watermelon fruits in response to CGMMV infection. A total of 595 differentially accumulated proteins (DAPs) were identified, of which 404 were upregulated and 191 were downregulated. Functional annotation analysis showed that these DAPs were mainly involved in photosynthesis, carbohydrate metabolism, secondary metabolite biosynthesis, plant–pathogen interaction, and protein synthesis and turnover. The accumulation levels of several proteins related to chlorophyll metabolism, pyruvate metabolism, TCA cycle, heat shock proteins, thioredoxins, ribosomal proteins, translation initiation factors, and elongation factors were strongly affected by CGMMV infection. Furthermore, a correlation analysis was performed between CGMMV-responsive proteome and transcriptome data of watermelon fruits obtained in our previous study, which could contribute to comprehensively elucidating the molecular mechanism of “watermelon blood flesh”. To confirm the iTRAQ-based proteome data, the corresponding transcripts of ten DAPs were validated by determining their abundance via quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). These results could provide a scientific basis for in-depth understanding of the pathogenic mechanisms underlying CGMMV-induced “watermelon blood flesh”, and lay the foundation for further functional exploration and verification of related genes and proteins.
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19
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Sun Y, Zhang H, Fan M, He Y, Guo P. Genome-wide identification of long non-coding RNAs and circular RNAs reveal their ceRNA networks in response to cucumber green mottle mosaic virus infection in watermelon. Arch Virol 2020; 165:1177-1190. [PMID: 32232674 DOI: 10.1007/s00705-020-04589-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/11/2020] [Indexed: 01/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play vital roles in plant defense responses against viral infections. However, there is no systematic understanding of lncRNAs and circRNAs and their competing endogenous RNA (ceRNA) networks in watermelon under cucumber green mottle mosaic virus (CGMMV) stress. Here, we present the characterization and expression profiles of lncRNAs and circRNAs in watermelon leaves 48-h post-inoculation (48 hpi) with CGMMV, with mock inoculation as a control. Deep sequencing analysis revealed 2373 lncRNAs and 606 circRNAs in the two libraries. Among them, 67 lncRNAs (40 upregulated and 27 downregulated) and 548 circRNAs (277 upregulated and 271 downregulated) were differentially expressed (DE) in the 48 hpi library compared with the control library. Furthermore, 263 cis-acting matched lncRNA-mRNA pairs were detected for 49 of the DE-lncRNAs. KEGG pathway analysis of the cis target genes of the DE-lncRNAs revealed significant associations with phenylalanine metabolism, the citrate cycle (TCA cycle), and endocytosis. Additionally, 30 DE-lncRNAs were identified as putative target mimics of 33 microRNAs (miRNAs), and 153 DE-circRNAs were identified as putative target mimics of 88 miRNAs. Furthermore, ceRNA networks of lncRNA/circRNA-miRNA-mRNA in response to CGMMV infection are described, with 12 DE-lncRNAs and 65 DE-circRNAs combining with 22 miRNAs and competing for the miRNA binding sites on 29 mRNAs. The qRT-PCR validation of selected lncRNAs and circRNAs showed a general correlation with the high-throughput sequencing results. This study provides a valuable resource of lncRNAs and circRNAs involved in the response to CGMMV infection in watermelon.
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Affiliation(s)
- Yuyan Sun
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Huiqing Zhang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, 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
| | - Pingan Guo
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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20
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Wang L, Poque S, Valkonen JPT. Phenotyping viral infection in sweetpotato using a high-throughput chlorophyll fluorescence and thermal imaging platform. PLANT METHODS 2019; 15:116. [PMID: 31649744 PMCID: PMC6805361 DOI: 10.1186/s13007-019-0501-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/10/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Virus diseases caused by co-infection with Sweet potato feathery mottle virus (SPFMV) and Sweetpotato chlorotic stunt virus (SPCSV) are a severe problem in the production of sweetpotato (Ipomoea batatas L.). Traditional molecular virus detection methods include nucleic acid-based and serological tests. In this study, we aimed to validate the use of a non-destructive imaging-based plant phenotype platform to study plant-virus synergism in sweetpotato by comparing four virus treatments with two healthy controls. RESULTS By monitoring physiological and morphological effects of viral infection in sweetpotato over 29 days, we quantified photosynthetic performance from chlorophyll fluorescence (ChlF) imaging and leaf thermography from thermal infrared (TIR) imaging among sweetpotatoes. Moreover, the differences among different treatments observed from ChlF and TIR imaging were related to virus accumulation and distribution in sweetpotato. These findings were further validated at the molecular level by related gene expression in both photosynthesis and carbon fixation pathways. CONCLUSION Our study validated for the first time the use of ChlF- and TIR-based imaging systems to distinguish the severity of virus diseases related to SPFMV and SPCSV in sweetpotato. In addition, we demonstrated that the operating efficiency of PSII and photochemical quenching were the most sensitive parameters for the quantification of virus effects compared with maximum quantum efficiency, non-photochemical quenching, and leaf temperature.
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Affiliation(s)
- Linping Wang
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
| | - Sylvain Poque
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
| | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, P.O. Box 27, 00014 Helsinki, Finland
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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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Štajner N, Radišek S, Mishra AK, Nath VS, Matoušek J, Jakše J. Evaluation of Disease Severity and Global Transcriptome Response Induced by Citrus bark cracking viroid, Hop latent viroid, and Their Co-Infection in Hop ( Humulus lupulus L.). Int J Mol Sci 2019; 20:E3154. [PMID: 31261625 PMCID: PMC6651264 DOI: 10.3390/ijms20133154] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 01/10/2023] Open
Abstract
Viroids are small non-capsidated, single-stranded, covalently-closed circular noncoding RNA replicons of 239-401 nucleotides that exploit host factors for their replication, and some cause disease in several economically important crop plants, while others appear to be benign. The proposed mechanisms of viroid pathogenesis include direct interaction of the genomic viroid RNA with host factors and post-transcriptional or transcriptional gene silencing via viroid-derived small RNAs (vd-sRNAs) generated by the host defensive machinery. Humulus lupulus (hop) plants are hosts to several viroids among which Hop latent viroid (HLVd) and Citrus bark cracking viroid (CBCVd) are attractive model systems for the study of viroid-host interactions due to the symptomless infection of the former and severe symptoms induced by the latter in this indicator host. To better understand their interactions with hop plant, a comparative transcriptomic analysis based on RNA sequencing (RNA-seq) was performed to reveal the transcriptional alterations induced as a result of single HLVd and CBCVd infection in hop. Additionally, the effect of HLVd on the aggressiveness of CBCVd that underlies severe stunting in hop in a mixed infection was studied by transcriptomic analysis. Our analysis revealed that CBCVd infection resulted in dynamic changes in the activity of genes as compared to single HLVd infection and their mixed infection. The differentially expressed genes that are involved in defense, phytohormone signaling, photosynthesis and chloroplasts, RNA regulation, processing and binding; protein metabolism and modification; and other mechanisms were more modulated in the CBCVd infection of hop. Nevertheless, Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in the proteolysis mechanism is more active in a mixed infection as compared to a single one, suggesting co-infecting viroids may result in interference with host factors more prominently. Collectively, our results provide a deep transcriptome of hop and insight into complex single HLVd, CBCVd, and their coinfection in hop-plant interactions.
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Affiliation(s)
- Nataša Štajner
- University of Ljubljana, Biotechnical Faculty, Department of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sebastjan Radišek
- Slovenian Institute of Hop Research and Brewing, Plant Protection Department, Cesta Žalskega tabora 2, SI-3310 Žalec, Slovenia
| | - Ajay Kumar Mishra
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Vishnu Sukumari Nath
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, Department of Molecular Genetics, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jernej Jakše
- University of Ljubljana, Biotechnical Faculty, Department of Agronomy, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia.
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23
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DNA Methylation Analysis of the Citrullus lanatus Response to Cucumber Green Mottle Mosaic Virus Infection by Whole-Genome Bisulfite Sequencing. Genes (Basel) 2019; 10:genes10050344. [PMID: 31067797 PMCID: PMC6562589 DOI: 10.3390/genes10050344] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/01/2019] [Accepted: 05/02/2019] [Indexed: 01/11/2023] Open
Abstract
DNA methylation is an important epigenetic mark associated with plant immunity, butlittle is known about its roles in viral infection of watermelon. We carried out whole-genomebisulfite sequencing of watermelon leaves at 0 h (ck), 48 h, and 25 days post-inoculation withCucumber green mottle mosaic virus (CGMMV). The number of differentially methylated regions(DMRs) increased during CGMMV infection and 2788 DMR-associated genes (DMGs) werescreened out among three libraries. Most DMRs and DMGs were obtained under the CHH context.These DMGs were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG)pathways of secondary biosynthesis and metabolism, plant-pathogen interactions, Toll-likereceptor signaling, and ABC transporters. Additionally, DMGs encoding PR1a, CaMs, calciumbindingprotein, RIN4, BAK1, WRKYs, RBOHs, STKs, and RLPs/RLKs were involved in thewatermelon-CGMMV interaction and signaling. The association between DNA methylation andgene expression was analyzed by RNA-seq and no clear relationship was detected. Moreover,downregulation of genes in the RdDM pathway suggested the reduced RdDM-directed CHHmethylation plays an important role in antiviral defense in watermelon. Our findings providegenome-wide DNA methylation profiles of watermelon and will aid in revealing the molecularmechanism in response to CGMMV infection at the methylation level.
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