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Aknadibossian V, Huguet-Tapia JC, Golyaev V, Pooggin MM, Folimonova SY. Transcriptomic alterations in the sweet orange vasculature correlate with growth repression induced by a variant of citrus tristeza virus. Front Microbiol 2023; 14:1162613. [PMID: 37138615 PMCID: PMC10150063 DOI: 10.3389/fmicb.2023.1162613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
Citrus tristeza virus (CTV, family Closteroviridae) is an economically important pathogen of citrus. CTV resides in the phloem of the infected plants and induces a range of disease phenotypes, including stem pitting and quick decline as well as a number of other deleterious syndromes. To uncover the biological processes underlying the poorly understood damaging symptoms of CTV, we profiled the transcriptome of sweet orange (Citrus sinensis) phloem-rich bark tissues of non-infected, mock-inoculated trees and trees singly infected with two distinct variants of CTV, T36 or T68-1. The T36 and T68-1 variants accumulated in the infected plants at similar titers. With that, young trees infected with T68-1 were markedly repressed in growth, while the growth rate of the trees infected with T36 was comparable to the mock-inoculated trees. Only a small number of differentially expressed genes (DEGs) were identified in the nearly asymptomatic T36-infected trees, whereas almost fourfold the number of DEGs were identified with the growth-restricting T68-1 infection. DEGs were validated using quantitative reverse transcription-PCR. While T36 did not induce many noteworthy changes, T68-1 altered the expression of numerous host mRNAs encoding proteins within significant biological pathways, including immunity and stress response proteins, papain-like cysteine proteases (PLCPs), cell-wall modifying enzymes, vascular development proteins and others. The transcriptomic alterations in the T68-1-infected trees, in particular, the strong and persistent increase in the expression levels of PLCPs, appear to contribute to the observed stem growth repression. On the other hand, analysis of the viral small interfering RNAs revealed that the host RNA silencing-based response to the infection by T36 and that by T68-1 was comparable, and thus, the induction of this antiviral mechanism may not contribute to the difference in the observed symptoms. The DEGs identified in this study promote our understanding of the underlying mechanisms of the yet unexplained growth repression induced by severe CTV isolates in sweet orange trees.
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Affiliation(s)
- Vicken Aknadibossian
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Jose C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Victor Golyaev
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, IRD, Institute Agro, Montpellier, France
| | - Mikhail M. Pooggin
- PHIM Plant Health Institute, University Montpellier, CIRAD, INRAE, IRD, Institute Agro, Montpellier, France
| | - Svetlana Y. Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
- *Correspondence: Svetlana Y. Folimonova,
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Moreno P, López C, Ruiz-Ruiz S, Peña L, Guerri J. From the smallest to the largest subcellular plant pathogen: Citrus tristeza virus and its unique p23 protein. Virus Res 2022; 314:198755. [PMID: 35341876 DOI: 10.1016/j.virusres.2022.198755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/07/2022] [Accepted: 03/23/2022] [Indexed: 10/18/2022]
Abstract
Knowledge on diseases caused by Citrus tristeza virus (CTV) has greatly increased in last decades after their etiology was demonstrated in the past seventies. Professor Ricardo Flores substantially contributed to these advances in topics like: i) improvement of virus purification to obtain biologically active virions, ii) sequencing mild CTV isolates for genetic comparisons with sequences of moderate or severe isolates and genetic engineering, iii) analysis of genetic variation of both CTV genomic RNA ends and features of the highly variable 5' end that allow accommodating this variation within a conserved secondary structure, iv) studies on the structure, subcellular localization and biological functions of the CTV-unique p23 protein, and v) potential use of p23 and other 3'-proximal regions of the CTV genome to develop transgenic citrus resistant to the virus. Here we review his main achievements on these topics and how they contributed to deeper understanding of CTV biology and to new potential measures for disease control.
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Affiliation(s)
- Pedro Moreno
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113-Valencia, Spain. (Retired).
| | - Carmelo López
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, 46022-Valencia, Spain
| | - Susana Ruiz-Ruiz
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), 46022-Valencia, Spain
| | - Leandro Peña
- Instituto de Biología Molecular y Celular de Plantas (IBMCP). Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), 46022-Valencia, Spain
| | - José Guerri
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113-Valencia, Spain. (Retired)
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Sun Y, Zhang L, Folimonova SY. Citrus miraculin-like protein hijacks a viral movement-related p33 protein and induces cellular oxidative stress in defence against Citrus tristeza virus. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:977-991. [PMID: 33283396 PMCID: PMC8131049 DOI: 10.1111/pbi.13523] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 10/26/2020] [Accepted: 11/30/2020] [Indexed: 05/16/2023]
Abstract
To defend against pathogens, plants have developed a complex immune system, which recognizes the pathogen effectors and mounts defence responses. In this study, the p33 protein of Citrus tristeza virus (CTV), a viral membrane-associated effector, was used as a molecular bait to explore virus interactions with host immunity. We discovered that Citrus macrophylla miraculin-like protein 2 (CmMLP2), a member of the soybean Kunitz-type trypsin inhibitor family, targets the viral p33 protein. The expression of CmMLP2 was up-regulated by p33 in the citrus phloem-associated cells. Knock-down of the MLP2 expression in citrus plants resulted in a higher virus accumulation, while the overexpression of CmMLP2 reduced the infectivity of CTV in the plant hosts. Further investigation revealed that, on the one hand, binding of CmMLP2 interrupts the cellular distribution of p33 whose proper function is necessary for the effective virus movement throughout the host. On the other hand, the ability of CmMLP2 to reorganize the endomembrane system, amalgamating the endoplasmic reticulum and the Golgi apparatus, induces cellular stress and accumulation of the reactive oxygen species, which inhibits the replication of CTV. Altogether, our data suggest that CmMLP2 employs a two-way strategy in defence against CTV infection.
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Affiliation(s)
- Yong‐Duo Sun
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
| | - Lei Zhang
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA
- Present address:
College of Horticulture and Plant ProtectionInner Mongolia Agricultural UniversityHohhot010018China
| | - Svetlana Y. Folimonova
- Department of Plant PathologyUniversity of FloridaGainesvilleFLUSA
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFLUSA
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4
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Nehela Y, Killiny N. The unknown soldier in citrus plants: polyamines-based defensive mechanisms against biotic and abiotic stresses and their relationship with other stress-associated metabolites. PLANT SIGNALING & BEHAVIOR 2020; 15:1761080. [PMID: 32408848 PMCID: PMC8570725 DOI: 10.1080/15592324.2020.1761080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 05/07/2023]
Abstract
Citrus plants are challenged by a broad diversity of abiotic and biotic stresses, which definitely alter their growth, development, and productivity. In order to survive the various stressful conditions, citrus plants relay on multi-layered adaptive strategies, among which is the accumulation of stress-associated metabolites that play vital and complex roles in citrus defensive responses. These metabolites included amino acids, organic acids, fatty acids, phytohormones, polyamines (PAs), and other secondary metabolites. However, the contribution of PAs pathways in citrus defense responses is poorly understood. In this review article, we will discuss the recent metabolic, genetic, and molecular evidence illustrating the potential roles of PAs in citrus defensive responses against biotic and abiotic stressors. We believe that PAs-based defensive role, against biotic and abiotic stress in citrus, is involving the interaction with other stress-associated metabolites, particularly phytohormones. The knowledge gained so far about PAs-based defensive responses in citrus underpins our need for further genetic manipulation of PAs biosynthetic genes to produce transgenic citrus plants with modulated PAs content that may enhance the tolerance of citrus plants against stressful conditions. In addition, it provides valuable information for the potential use of PAs or their synthetic analogs and their emergence as a promising approach to practical applications in citriculture to enhance stress tolerance in citrus plants.
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Affiliation(s)
- Yasser Nehela
- Citrus Research and Education Center and Department of Plant Pathology, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Nabil Killiny
- Citrus Research and Education Center and Department of Plant Pathology, IFAS, University of Florida, Lake Alfred, FL, USA
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5
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Pérez-Clemente RM, Montoliu A, Vives-Peris V, Arbona V, Gómez-Cadenas A. Hormonal and metabolic responses of Mexican lime plants to CTV infection. JOURNAL OF PLANT PHYSIOLOGY 2019; 238:40-52. [PMID: 31129470 DOI: 10.1016/j.jplph.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 05/20/2023]
Abstract
Plant viral infections alter gene expression and metabolism in infected host. To study the molecular responses of Mexican lime to CTV infection, an analysis of plant metabolome in response to infection with severe (T318) or mild (T385) isolates of CTV was performed. Healthy plants and those infected with any of the two virus strains showed different metabolite profiles, at different stages of new sprout development. Proline content increased in plants infected with CTV, proportionally to the virulence of the virus strain. Abscisic acid content decreased after virus infection whereas jasmonic and salicylic acid levels increased. CTV infection had an impact on plant secondary metabolism, by stimulating the synthesis of different metabolites such as l-methylhistidine, phenylpropanoid derivatives. These metabolites are common responses of different organisms, including higher mammals, to viral diseases, and its presence in this system points to the existence of universal responses to virus infection among different kingdoms.
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Affiliation(s)
- Rosa María Pérez-Clemente
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón de la Plana, Spain
| | - Almudena Montoliu
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón de la Plana, Spain
| | - Vicente Vives-Peris
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón de la Plana, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón de la Plana, Spain
| | - Aurelio Gómez-Cadenas
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, Avda. Sos Baynat s/n, 12071, Castellón de la Plana, Spain.
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6
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Sun YD, Folimonova SY. The p33 protein of Citrus tristeza virus affects viral pathogenicity by modulating a host immune response. THE NEW PHYTOLOGIST 2019; 221:2039-2053. [PMID: 30220089 DOI: 10.1111/nph.15482] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/10/2018] [Indexed: 06/08/2023]
Abstract
Accumulation of reactive oxygen species (ROS) is a general plant basal defense strategy against viruses. In this study, we show that infection by Citrus tristeza virus (CTV) triggered ROS burst in Nicotiana benthamiana and in the natural citrus host, the extent of which was virus-dose dependent. Using Agrobacterium-mediated expression of CTV-encoded proteins in N. benthamiana, we found that p33, a unique viral protein, contributed to the induction of ROS accumulation and programmed cell death. The role of p33 in CTV pathogenicity was assessed based on gene knockout and complementation in N. benthamiana. In the citrus-CTV pathosystem, deletion of the p33 open reading frame in a CTV variant resulted in a significant decrease in ROS production, compared to that of the wild type CTV, which correlated with invasion of the mutant virus into the immature xylem tracheid cells and abnormal differentiation of the vascular system. By contrast, the wild type CTV exhibited phloem-limited distribution with a minor effect on the vasculature. We conclude that the p33 protein is a CTV effector that negatively affects virus pathogenicity and suggest that N. benthamiana recognizes p33 to activate the host immune response to restrict CTV into the phloem tissue and minimize the disease syndrome.
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Affiliation(s)
- Yong-Duo Sun
- Plant Pathology Department, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32611, USA
| | - Svetlana Y Folimonova
- Plant Pathology Department, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32611, USA
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Gómez‐Muñoz N, Velázquez K, Vives MC, Ruiz‐Ruiz S, Pina JA, Flores R, Moreno P, Guerri J. The resistance of sour orange to Citrus tristeza virus is mediated by both the salicylic acid and RNA silencing defence pathways. MOLECULAR PLANT PATHOLOGY 2017; 18:1253-1266. [PMID: 27588892 PMCID: PMC6638288 DOI: 10.1111/mpp.12488] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/26/2016] [Accepted: 08/30/2016] [Indexed: 05/08/2023]
Abstract
Citrus tristeza virus (CTV) induces in the field the decline and death of citrus varieties grafted on sour orange (SO) rootstock, which has forced the use of alternative decline-tolerant rootstocks in affected countries, despite the highly desirable agronomic features of the SO rootstock. Declining citrus plants display phloem necrosis below the bud union. In addition, SO is minimally susceptible to CTV compared with other citrus varieties, suggesting partial resistance of SO to CTV. Here, by silencing different citrus genes with a Citrus leaf blotch virus-based vector, we have examined the implication of the RNA silencing and salicylic acid (SA) defence pathways in the resistance of SO to CTV. Silencing of the genes RDR1, NPR1 and DCL2/DCL4, associated with these defence pathways, enhanced virus spread and accumulation in SO plants in comparison with non-silenced controls, whereas silencing of the genes NPR3/NPR4, associated with the hypersensitive response, produced a slight decrease in CTV accumulation and reduced stunting of SO grafted on CTV-infected rough lemon plants. We also found that the CTV RNA silencing suppressors p20 and p23 also suppress the SA signalling defence, with the suppressor activity being higher in the most virulent isolates.
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Affiliation(s)
- Neus Gómez‐Muñoz
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - Karelia Velázquez
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - María Carmen Vives
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - Susana Ruiz‐Ruiz
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - José Antonio Pina
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas (UPV‐CSIC), Universidad Politécnica de Valencia, Avenida de los NaranjosValencia46022Spain
| | - Pedro Moreno
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
| | - José Guerri
- Instituto Valenciano de Investigaciones Agrarias (IVIA)Centro de Protección Vegetal y BiotecnologíaMoncada, Valencia46113Spain
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8
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Bruckner FP, Xavier ADS, Cascardo RDS, Otoni WC, Zerbini FM, Alfenas‐Zerbini P. Translationally controlled tumour protein (TCTP) from tomato and Nicotiana benthamiana is necessary for successful infection by a potyvirus. MOLECULAR PLANT PATHOLOGY 2017; 18:672-683. [PMID: 27159273 PMCID: PMC6638207 DOI: 10.1111/mpp.12426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/02/2016] [Accepted: 05/05/2016] [Indexed: 05/20/2023]
Abstract
Translationally controlled tumour protein (TCTP) is a ubiquitously distributed protein in eukaryotes, involved in the regulation of several processes, including cell cycle progression, cell growth, stress protection, apoptosis and maintenance of genomic integrity. Its expression is induced during the early stages of tomato (Solanum lycopersicum) infection by the potyvirus Pepper yellow mosaic virus (PepYMV, a close relative of Potato virus Y). Tomato TCTP is a protein of 168 amino acids, which contains all the conserved domains of the TCTP family. To study the effects of TCTP silencing in PepYMV infection, Nicotiana benthamiana plants were silenced by virus-induced gene silencing (VIGS) and transgenic tomato plants silenced for TCTP were obtained. In the early stages of infection, both tomato and N. benthamiana silenced plants accumulated less virus than control plants. Transgenic tomato plants showed a drastic reduction in symptoms and no viral accumulation at 14 days post-inoculation. Subcellular localization of TCTP was determined in healthy and systemically infected N. benthamiana leaves. TCTP was observed in both the nuclei and cytoplasm of non-infected cells, but only in the cytoplasm of infected cells. Our results indicate that TCTP is a growth regulator necessary for successful PepYMV infection and that its localization is altered by the virus, probably to favour the establishment of virus infection. A network with putative interactions that may occur between TCTP and Arabidopsis thaliana proteins was built. This network brings together experimental data of interactions that occur in other eukaryotes and helps us to discuss the possibilities of TCTP involvement in viral infection.
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Affiliation(s)
- Fernanda Prieto Bruckner
- Departamento de Microbiologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - André Da Silva Xavier
- Departamento de Fitopatologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - Renan De Souza Cascardo
- Departamento de Microbiologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - Wagner Campos Otoni
- Departamento de Biologia Vegetal/BIOAGROUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
| | - Poliane Alfenas‐Zerbini
- Departamento de Microbiologia/BIOAGRO/National Institute of Science and Technology in Plant‐Pest InteractionsUniversidade Federal de ViçosaViçosaMG36570‐900Brazil
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Liu XY, Li J, Liu MM, Yao Q, Chen JZ. Transcriptome Profiling to Understand the Effect of Citrus Rootstocks on the Growth of 'Shatangju' Mandarin. PLoS One 2017; 12:e0169897. [PMID: 28081213 PMCID: PMC5231354 DOI: 10.1371/journal.pone.0169897] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 12/24/2016] [Indexed: 01/01/2023] Open
Abstract
To obtain insight into potential mechanisms underlying the influence of rootstock on scion growth, we performed a comparative analysis of 'Shatangju' mandarin grafted onto 5 rootstocks: Fragrant orange (Citrus junons Sieb. ex. Tanaka), Red tangerine (Citrus reticulata Blanco), 'Shatangju' mandarin (Citrus reticulata Blanco), Rough lemon (Citrus jambhiri Lush) and Canton lemon (Citrus limonia Osbeck). The tree size of 'Shatangju' mandarin grafted onto Canton lemon and Rough lemon were the largest, followed by self-rooted rootstock trees, and the lowest tree sizes correspond to ones grafted on Red tangerine and Fragrant orange rootstocks. The levels of indoleacetic acid (IAA) and gibberellin (GA) were significantly and positively related to growth vigor. The differences of gene expression in leaves of trees grafted onto Red tangerine, Canton lemon and 'Shatangju' mandarin were analyzed by RNA-Seq. Results showed that more differentially expressed genes involved in oxidoreductase function, hormonal signal transduction and the glycolytic pathway were enriched in 'Red tangerine vs Canton lemon'. qRT-PCR analysis showed that expression levels of ARF1, ARF8, GH3 and IAA4 were negatively correlated with the growth vigor and IAA content. The metabolism of GA was influenced by the differential expression of KO1 and GA2OX1 in grafted trees. In addition, most of antioxidant enzyme genes were up-regulated in leaves of trees grafted onto Red tangerine, resulting in a higher peroxidase activity. We concluded that different rootstocks significantly affected the expression of genes involved in auxin signal transduction pathway and GA biosynthesis pathway in the grafted plants, and then regulated the hormone levels and their signal pathways.
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Affiliation(s)
- Xiang-Yu Liu
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
- Qingdao Agricultural University, Qingdao, Shandong, China
| | - Juan Li
- Department of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Meng-Meng Liu
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jie-Zhong Chen
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
- * E-mail:
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10
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Fu S, Shao J, Zhou C, Hartung JS. Co-infection of Sweet Orange with Severe and Mild Strains of Citrus tristeza virus Is Overwhelmingly Dominated by the Severe Strain on Both the Transcriptional and Biological Levels. FRONTIERS IN PLANT SCIENCE 2017; 8:1419. [PMID: 28912786 PMCID: PMC5583216 DOI: 10.3389/fpls.2017.01419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/31/2017] [Indexed: 05/18/2023]
Abstract
Citrus tristeza is one of the most destructive citrus diseases and is caused by the phloem-restricted Closterovirus, Citrus tristeza virus. Mild strain CTV-B2 does not cause obvious symptoms on indicators whereas severe strain CTV-B6 causes symptoms, including stem pitting, cupping, yellowing, and stiffening of leaves, and vein corking. Our laboratory has previously characterized changes in transcription in sweet orange separately infected with CTV-B2 and CTV-B6. In the present study, transcriptome analysis of Citrus sinensis in response to double infection by CTV-B2 and CTV-B6 was carried out. Four hundred and eleven transcripts were up-regulated and 356 transcripts were down-regulated prior to the onset of symptoms. Repressed genes were overwhelmingly associated with photosynthesis, and carbon and nucleic acid metabolism. Expression of genes related to the glycolytic, oxidative pentose phosphate (OPP), tricarboxylic acid cycle (TCA) pathways, tetrapyrrole synthesis, redox homeostasis, nucleotide metabolism, protein synthesis and post translational protein modification and folding, and cell organization were all reduced. Ribosomal composition was also greatly altered in response to infection by CTV-B2/CTV-B6. Genes that were induced were related to cell wall structure, secondary and hormone metabolism, responses to biotic stress, regulation of transcription, signaling, and secondary metabolism. Transport systems dedicated to metal ions were especially disturbed and ZIPs (Zinc Transporter Precursors) showed different expression patterns in response to co-infection by CTV-B2/CTV-B6 and single infection by CTV-B2. Host plants experienced root decline that may have contributed to Zn, Fe, and other nutrient deficiencies. Though defense responses, such as, strengthening of the cell wall, alteration of hormone metabolism, secondary metabolites, and signaling pathways, were activated, these defense responses did not suppress the spread of the pathogens and the development of symptoms. The mild strain CTV-B2 did not provide a useful level of cross-protection to citrus against the severe strain CTV-B6.
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Affiliation(s)
- Shimin Fu
- Citrus Research Institute, Southwest UniversityChongqing, China
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
| | - Jonathan Shao
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
| | - Changyong Zhou
- Citrus Research Institute, Southwest UniversityChongqing, China
| | - John S. Hartung
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research ServiceBeltsville, MD, United States
- *Correspondence: John S. Hartung
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Nwugo CC, Doud MS, Duan YP, Lin H. Proteomics analysis reveals novel host molecular mechanisms associated with thermotherapy of 'Ca. Liberibacter asiaticus'-infected citrus plants. BMC PLANT BIOLOGY 2016; 16:253. [PMID: 27842496 PMCID: PMC5109811 DOI: 10.1186/s12870-016-0942-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/02/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Citrus Huanglongbing (HLB), which is linked to the bacterial pathogen 'Ca. Liberibacter asiaticus' (Las), is the most devastating disease of citrus plants, and longer-term control measures via breeding or genetic engineering have been unwieldy because all cultivated citrus species are susceptible to the disease. However, the degree of susceptibility varies among citrus species, which has prompted efforts to identify potential Las resistance/tolerance-related genes in citrus plants for application in breeding or genetic engineering programs. Plant exposure to one form of stress has been shown to serendipitously induce innate resistance to other forms of stress and a recent study showed that continuous heat treatment (40 to 42 °C) reduced Las titer and HLB-associated symptoms in citrus seedlings. The goal of the present study was to apply comparative proteomics analysis via 2-DE and mass spectrometry to elucidate the molecular processes associated with heat-induced mitigation of HLB in citrus plants. Healthy or Las-infected citrus grapefruit plants were exposed to room temperature or to continuous heat treatment of 40 °C for 6 days. RESULTS An exhaustive total protein extraction process facilitated the identification of 107 differentially-expressed proteins in response to Las and/or heat treatment, which included a strong up-regulation of chaperones including small (23.6, 18.5 and 17.9 kDa) heat shock proteins, a HSP70-like protein and a ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO)-binding 60 kDa chaperonin, particularly in response to heat treatment. Other proteins that were generally down-regulated due to Las infection but up-regulated in response to heat treatment include RuBisCO activase, chlorophyll a/b binding protein, glucosidase II beta subunit-like protein, a putative lipoxygenase protein, a ferritin-like protein, and a glutathione S-transferase. CONCLUSIONS The differentially-expressed proteins identified in this study highlights a premier characterization of the molecular mechanisms potentially involved in the reversal of Las-induced pathogenicity processes in citrus plants and are hence proposed targets for application towards the development of cisgenic Las-resistant/tolerant citrus plants.
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Affiliation(s)
- Chika C. Nwugo
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, 93648 CA USA
| | - Melissa S. Doud
- USDA, Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, 34945 FL USA
| | - Yong-ping Duan
- USDA, Agricultural Research Service, U.S. Horticultural Research Laboratory, Fort Pierce, 34945 FL USA
| | - Hong Lin
- USDA, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, 93648 CA USA
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12
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Fu S, Shao J, Zhou C, Hartung JS. Transcriptome analysis of sweet orange trees infected with 'Candidatus Liberibacter asiaticus' and two strains of Citrus Tristeza Virus. BMC Genomics 2016; 17:349. [PMID: 27169471 PMCID: PMC4865098 DOI: 10.1186/s12864-016-2663-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 04/26/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Huanglongbing (HLB) and tristeza, are diseases of citrus caused by a member of the α-proteobacteria, 'Candidatus Liberibacter asiaticus' (CaLas), and Citrus tristeza virus (CTV) respectively. HLB is a devastating disease, but CTV strains vary from very severe to very mild. Both CaLas and CTV are phloem-restricted. The CaLas-B232 strain and CTV-B6 cause a wide range of severe and similar symptoms. The mild strain CTV-B2 doesn't induce significant symptoms or damage to plants. RESULTS Transcriptome profiles obtained through RNA-seq revealed 611, 404 and 285 differentially expressed transcripts (DETs) after infection with CaLas-B232, CTV-B6 and CTV-B2. These DETs were components of a wide range of pathways involved in circadian rhythm, cell wall modification and cell organization, as well as transcription factors, transport, hormone response and secondary metabolism, signaling and stress response. The number of transcripts that responded to both CTV-B6 and CaLas-B232 was much larger than the number of transcripts that responded to both strains of CTV or to both CTV-B2 and CaLas-B232. A total of 38 genes were assayed by RT-qPCR and the correlation coefficients between Gfold and RT-qPCR were 0.82, 0.69, 0.81 for sweet orange plants infected with CTV-B2, CTV-B6 and CaLas-B232, respectively. CONCLUSIONS The number and composition of DETs reflected the complexity of symptoms caused by the pathogens in established infections, although the leaf tissues sampled were asymptomatic. There were greater similarities between the sweet orange in response to CTV-B6 and CaLas-B232 than between the two CTV strains, reflecting the similar physiological changes caused by both CTV-B6 and CaLas-B232. The circadian rhythm system of plants was perturbed by all three pathogens, especially by CTV-B6, and the ion balance was also disrupted by all three pathogens, especially by CaLas-B232. Defense responses related to cell wall modification, transcriptional regulation, hormones, secondary metabolites, kinases and stress were activated by all three pathogens but with different patterns. The transcriptome profiles of Citrus sinensis identified host genes whose expression is affected by the presence of a pathogen in the phloem without producing symptoms (CTV-B2), and host genes whose expression leads to induction of symptoms in the plant (CTV-B6, CaLas-B232).
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Affiliation(s)
- Shimin Fu
- College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing, China
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA
- Lingnan Normal University, Zhanjian, China
| | - Jonathan Shao
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA
| | - Changyong Zhou
- College of Plant Protection/Citrus Research Institute, Southwest University, Chongqing, China.
| | - John S Hartung
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA.
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13
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Laino P, Russo MP, Guardo M, Reforgiato-Recupero G, Valè G, Cattivelli L, Moliterni VMC. Rootstock-scion interaction affecting citrus response to CTV infection: a proteomic view. PHYSIOLOGIA PLANTARUM 2016; 156:444-67. [PMID: 26459956 DOI: 10.1111/ppl.12395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 08/28/2015] [Accepted: 09/12/2015] [Indexed: 05/19/2023]
Abstract
Citrus tristeza virus (CTV) is the causal agent of various diseases with dramatic effects on citrus crops worldwide. Most Citrus species, grown on their own roots, are symptomless hosts for many CTV isolates. However, depending on different scion-rootstock combination, CTV infection should result in distinct syndromes, being 'tristeza' the more severe one, leading to a complete decline of the susceptible plants in a few weeks. Transcriptomic analyses revealed several genes involved either in defense response, or systemic acquired resistance, as well as transcription factors and components of the phosphorylation cascades, to be differentially regulated during CTV infection in Citrus aurantifolia species. To date little is known about the molecular mechanism of this host-pathogen interaction, and about the rootstock effect on citrus response to CTV infection. In this work, the response to CTV infection has been investigated in tolerant and susceptible scion-rootstock combinations by two-dimensional gel electrophoresis (2DE). A total of 125 protein spots have been found to be differently accumulated and/or phosphorylated between the two rootstock combinations. Downregulation in tolerant plants upon CTV infection was detected for proteins involved in reactive oxygen species (ROS) scavenging and defense response, suggesting a probable acclimation response able to minimize the systemic effects of virus infection. Some of these proteins resulted to be modulated also in absence of virus infection, revealing a rootstock effect on scion proteome modulation. Moreover, the phospho-modulation of proteins involved in ROS scavenging and defense response, further supports their involvement either in scion-rootstock crosstalk or in the establishment of tolerance/susceptibility to CTV infection.
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Affiliation(s)
- Paolo Laino
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Genomics Research Centre, Fiorenzuola d'Arda (PC), Italy
| | - Maria P Russo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, Acireale (CT), Italy
| | - Maria Guardo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, Acireale (CT), Italy
| | - Giuseppe Reforgiato-Recupero
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca per l'Agrumicoltura e le Colture Mediterranee, Acireale (CT), Italy
| | - Giampiero Valè
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Rice Research Unit, Vercelli, Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Genomics Research Centre, Fiorenzuola d'Arda (PC), Italy
| | - Vita M C Moliterni
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Genomics Research Centre, Fiorenzuola d'Arda (PC), Italy
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14
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Alam SB, Rochon D. Cucumber Necrosis Virus Recruits Cellular Heat Shock Protein 70 Homologs at Several Stages of Infection. J Virol 2015; 90:3302-17. [PMID: 26719261 PMCID: PMC4794660 DOI: 10.1128/jvi.02833-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/16/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED RNA viruses often depend on host factors for multiplication inside cells due to the constraints of their small genome size and limited coding capacity. One such factor that has been exploited by several plant and animal viruses is heat shock protein 70 (HSP70) family homologs which have been shown to play roles for different viruses in viral RNA replication, viral assembly, disassembly, and cell-to-cell movement. Using next generation sequence analysis, we reveal that several isoforms of Hsp70 and Hsc70 transcripts are induced to very high levels during cucumber necrosis virus (CNV) infection of Nicotiana benthamiana and that HSP70 proteins are also induced by at least 10-fold. We show that HSP70 family protein homologs are co-opted by CNV at several stages of infection. We have found that overexpression of Hsp70 or Hsc70 leads to enhanced CNV genomic RNA, coat protein (CP), and virion accumulation, whereas downregulation leads to a corresponding decrease. Hsc70-2 was found to increase solubility of CNV CP in vitro and to increase accumulation of CNV CP independently of viral RNA replication during coagroinfiltration in N. benthamiana. In addition, virus particle assembly into virus-like particles in CP agroinfiltrated plants was increased in the presence of Hsc70-2. HSP70 was found to increase the targeting of CNV CP to chloroplasts during infection, reinforcing the role of HSP70 in chloroplast targeting of host proteins. Hence, our findings have led to the discovery of a highly induced host factor that has been co-opted to play multiple roles during several stages of the CNV infection cycle. IMPORTANCE Because of the small size of its RNA genome, CNV is dependent on interaction with host cellular components to successfully complete its multiplication cycle. We have found that CNV induces HSP70 family homologs to a high level during infection, possibly as a result of the host response to the high levels of CNV proteins that accumulate during infection. Moreover, we have found that CNV co-opts HSP70 family homologs to facilitate several aspects of the infection process such as viral RNA, coat protein and virus accumulation. Chloroplast targeting of the CNV CP is also facilitated, which may aid in CNV suppression of host defense responses. Several viruses have been shown to induce HSP70 during infection and others to utilize HSP70 for specific aspects of infection such as replication, assembly, and disassembly. We speculate that HSP70 may play multiple roles in the infection processes of many viruses.
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Affiliation(s)
- Syed Benazir Alam
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - D'Ann Rochon
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
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15
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Soler N, Fagoaga C, López C, Moreno P, Navarro L, Flores R, Peña L. Symptoms induced by transgenic expression of p23 from Citrus tristeza virus in phloem-associated cells of Mexican lime mimic virus infection without the aberrations accompanying constitutive expression. MOLECULAR PLANT PATHOLOGY 2015; 16:388-99. [PMID: 25171669 PMCID: PMC6638416 DOI: 10.1111/mpp.12188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Citrus tristeza virus (CTV) is phloem restricted in natural citrus hosts. The 23-kDa protein (p23) encoded by the virus is an RNA silencing suppressor and a pathogenicity determinant. The expression of p23, or its N-terminal 157-amino-acid fragment comprising the zinc finger and flanking basic motifs, driven by the constitutive 35S promoter of cauliflower mosaic virus, induces CTV-like symptoms and other aberrations in transgenic citrus. To better define the role of p23 in CTV pathogenesis, we compared the phenotypes of Mexican lime transformed with p23-derived transgenes from the severe T36 and mild T317 CTV isolates under the control of the phloem-specific promoter from Commelina yellow mottle virus (CoYMV) or the 35S promoter. Expression of the constructs restricted to the phloem induced a phenotype resembling CTV-specific symptoms (vein clearing and necrosis, and stem pitting), but not the non-specific aberrations (such as mature leaf epinasty and yellow pinpoints, growth cessation and apical necrosis) observed when p23 was ectopically expressed. Furthermore, vein necrosis and stem pitting in Mexican lime appeared to be specifically associated with p23 from T36. Phloem-specific accumulation of the p23Δ158-209(T36) fragment was sufficient to induce the same anomalies, indicating that the region comprising the N-terminal 157 amino acids of p23 is responsible (at least in part) for the vein clearing, stem pitting and, possibly, vein corking in this host.
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Affiliation(s)
- Nuria Soler
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apdo. Oficial, Moncada, Valencia, 46113, Spain
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16
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Dawson WO, Bar-Joseph M, Garnsey SM, Moreno P. Citrus tristeza virus: making an ally from an enemy. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:137-55. [PMID: 25973695 DOI: 10.1146/annurev-phyto-080614-120012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Virus diseases of perennial trees and vines have characteristics not amenable to study using small model annual plants. Unique disease symptoms such as graft incompatibilities and stem pitting cause considerable crop losses. Also, viruses in these long-living plants tend to accumulate complex populations of viruses and strains. Considerable progress has been made in understanding the biology and genetics of Citrus tristeza virus (CTV) and in developing it into a tool for crop protection and improvement. The diseases in tree and vine crops have commonalities for which CTV can be used to develop a baseline. The purpose of this review is to provide a necessary background of systems and reagents developed for CTV that can be used for continued progress in this area and to point out the value of the CTV-citrus system in answering important questions on plant-virus interactions and developing new methods for controlling plant diseases.
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Affiliation(s)
- William O Dawson
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, Lake Alfred, Florida 33850; ,
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17
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Agüero J, Vives MDC, Velázquez K, Pina JA, Navarro L, Moreno P, Guerri J. Effectiveness of gene silencing induced by viral vectors based on Citrus leaf blotch virus is different in Nicotiana benthamiana and citrus plants. Virology 2014; 460-461:154-64. [PMID: 25010281 DOI: 10.1016/j.virol.2014.04.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 02/12/2014] [Accepted: 04/12/2014] [Indexed: 11/23/2022]
Abstract
Virus induced gene silencing (VIGS) is an effective technology for gene function analysis in plants. We assessed the VIGS effectiveness in Nicotiana benthamiana and citrus plants of different Citrus leaf blotch virus (CLBV)-based vectors, using insets of the phytoene desaturase (pds) gene. While in N. benthamiana the silencing phenotype was induced only by the construct carrying a 58-nt pds hairpin, in citrus plants all the constructs induced the silencing phenotype. Differences in the generation of secondary small interfering RNAs in both species are believed to be responsible for differential host-species effects. The ability of CLBV-based vectors to silence different endogenous citrus genes was further confirmed. Since CLBV-based vectors are known to be stable and induce VIGS in successive flushes for several months, these vectors provide an important genomic tool and it is expected that they will be useful to analyze gene function by reverse genetics in the long-lived citrus plants.
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Affiliation(s)
- Jesus Agüero
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km. 4.5, Moncada, 46113 Valencia, Spain
| | - María del Carmen Vives
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km. 4.5, Moncada, 46113 Valencia, Spain
| | - Karelia Velázquez
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km. 4.5, Moncada, 46113 Valencia, Spain
| | - José Antonio Pina
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km. 4.5, Moncada, 46113 Valencia, Spain
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km. 4.5, Moncada, 46113 Valencia, Spain
| | - Pedro Moreno
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km. 4.5, Moncada, 46113 Valencia, Spain
| | - Jose Guerri
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera Km. 4.5, Moncada, 46113 Valencia, Spain.
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18
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Miozzi L, Napoli C, Sardo L, Accotto GP. Transcriptomics of the interaction between the monopartite phloem-limited geminivirus tomato yellow leaf curl Sardinia virus and Solanum lycopersicum highlights a role for plant hormones, autophagy and plant immune system fine tuning during infection. PLoS One 2014; 9:e89951. [PMID: 24587146 PMCID: PMC3938563 DOI: 10.1371/journal.pone.0089951] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/25/2014] [Indexed: 12/13/2022] Open
Abstract
Tomato yellow leaf curl Sardinia virus (TYLCSV), a DNA virus belonging to the genus Begomovirus, causes severe losses in tomato crops. It infects only a limited number of cells in the vascular tissues, making difficult to detect changes in host gene expression linked to its presence. Here we present the first microarray study of transcriptional changes induced by the phloem-limited geminivirus TYLCSV infecting tomato, its natural host. The analysis was performed on the midrib of mature leaves, a material naturally enriched in vascular tissues. A total of 2206 genes were up-regulated and 1398 were down-regulated in infected plants, with an overrepresentation of genes involved in hormone metabolism and responses, nucleic acid metabolism, regulation of transcription, ubiquitin-proteasome pathway and autophagy among those up-regulated, and in primary and secondary metabolism, phosphorylation, transcription and methylation-dependent chromatin silencing among those down-regulated. Our analysis showed a series of responses, such as the induction of GA- and ABA-responsive genes, the activation of the autophagic process and the fine tuning of the plant immune system, observed only in TYLCSV-tomato compatible interaction so far. On the other hand, comparisons with transcriptional changes observed in other geminivirus-plant interactions highlighted common host responses consisting in the deregulation of biotic stress responsive genes, key enzymes in the ethylene biosynthesis and methylation cycle, components of the ubiquitin proteasome system and DNA polymerases II. The involvement of conserved miRNAs and of solanaceous- and tomato-specific miRNAs in geminivirus infection, investigated by integrating differential gene expression data with miRNA targeting data, is discussed.
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Affiliation(s)
- Laura Miozzi
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
| | - Chiara Napoli
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
| | - Luca Sardo
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
- Viral Recombination Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Gian Paolo Accotto
- Istituto di Virologia Vegetale, (National Research Council) CNR, Torino, Italy
- * E-mail:
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19
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Martinelli F, Reagan RL, Uratsu SL, Phu ML, Albrecht U, Zhao W, Davis CE, Bowman KD, Dandekar AM. Gene regulatory networks elucidating huanglongbing disease mechanisms. PLoS One 2013; 8:e74256. [PMID: 24086326 PMCID: PMC3783430 DOI: 10.1371/journal.pone.0074256] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/29/2013] [Indexed: 12/02/2022] Open
Abstract
Next-generation sequencing was exploited to gain deeper insight into the response to infection by Candidatus liberibacter asiaticus (CaLas), especially the immune disregulation and metabolic dysfunction caused by source-sink disruption. Previous fruit transcriptome data were compared with additional RNA-Seq data in three tissues: immature fruit, and young and mature leaves. Four categories of orchard trees were studied: symptomatic, asymptomatic, apparently healthy, and healthy. Principal component analysis found distinct expression patterns between immature and mature fruits and leaf samples for all four categories of trees. A predicted protein - protein interaction network identified HLB-regulated genes for sugar transporters playing key roles in the overall plant responses. Gene set and pathway enrichment analyses highlight the role of sucrose and starch metabolism in disease symptom development in all tissues. HLB-regulated genes (glucose-phosphate-transporter, invertase, starch-related genes) would likely determine the source-sink relationship disruption. In infected leaves, transcriptomic changes were observed for light reactions genes (downregulation), sucrose metabolism (upregulation), and starch biosynthesis (upregulation). In parallel, symptomatic fruits over-expressed genes involved in photosynthesis, sucrose and raffinose metabolism, and downregulated starch biosynthesis. We visualized gene networks between tissues inducing a source-sink shift. CaLas alters the hormone crosstalk, resulting in weak and ineffective tissue-specific plant immune responses necessary for bacterial clearance. Accordingly, expression of WRKYs (including WRKY70) was higher in fruits than in leaves. Systemic acquired responses were inadequately activated in young leaves, generally considered the sites where most new infections occur.
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Affiliation(s)
- Federico Martinelli
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
- Dipartimento di Sistemi Agro-ambientali, Università degli Studi di Palermo, Palermo, Italy
| | - Russell L. Reagan
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Sandra L. Uratsu
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - My L. Phu
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Ute Albrecht
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, United States of America
| | - Weixiang Zhao
- Department of Mechanical and Aerospace Engineering, University of California Davis, Davis, California, United States of America
| | - Cristina E. Davis
- Department of Mechanical and Aerospace Engineering, University of California Davis, Davis, California, United States of America
| | - Kim D. Bowman
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, United States of America
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
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20
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Daurelio LD, Romero MS, Petrocelli S, Merelo P, Cortadi AA, Talón M, Tadeo FR, Orellano EG. Characterization of Citrus sinensis transcription factors closely associated with the non-host response to Xanthomonas campestris pv. vesicatoria. JOURNAL OF PLANT PHYSIOLOGY 2013; 170:934-942. [PMID: 23453188 DOI: 10.1016/j.jplph.2013.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 01/29/2013] [Accepted: 01/29/2013] [Indexed: 05/28/2023]
Abstract
Plants, when exposed to certain pathogens, may display a form of genotype-independent resistance, known as non-host response. In this study, the response of Citrus sinensis (sweet orange) leaves to Xanthomonas campestris pv. vesicatoria (Xcv), a pepper and tomato pathogenic bacterium, was analyzed through biochemical assays and cDNA microarray hybridization and compared with Asiatic citrus canker infection caused by Xanthomonas citri subsp. citri. Citrus leaves exposed to the non-host bacterium Xcv showed hypersensitive response (HR) symptoms (cell death), a defense mechanism common in plants but poorly understood in citrus. The HR response was accompanied by differentially expressed genes that are associated with biotic stress and cell death. Moreover, 58 transcription factors (TFs) were differentially regulated by Xcv in citrus leaves, including 26 TFs from the stress-associated families AP2-EREBP, bZip, Myb and WRKY. Remarkably, in silico analysis of the distribution of expressed sequence tags revealed that 10 of the 58 TFs, belonging to C2C2-GATA, C2H2, CCAAT, HSF, NAC and WRKY gene families, were specifically over-represented in citrus stress cDNA libraries. This study identified candidate TF genes for the regulation of key steps during the citrus non-host HR. Furthermore, these TFs might be useful in future strategies of molecular breeding for citrus disease resistance.
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Affiliation(s)
- Lucas D Daurelio
- Área de Biología Molecular, Instituto de Biología Molecular y Celular de Rosario IBR, Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario UNR, Suipacha 531 S2002LRK, Rosario, Santa Fe, Argentina
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21
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Agüero J, Ruiz-Ruiz S, Del Carmen Vives M, Velázquez K, Navarro L, Peña L, Moreno P, Guerri J. Development of viral vectors based on Citrus leaf blotch virus to express foreign proteins or analyze gene function in citrus plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1326-37. [PMID: 22670755 DOI: 10.1094/mpmi-02-12-0048-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Viral vectors have been used to express foreign proteins in plants or to silence endogenous genes. This methodology could be appropriate for citrus plants that have long juvenile periods and adult plants that are difficult to transform. We developed viral vectors based on Citrus leaf blotch virus (CLBV) by duplicating a minimum promoter (92 bp) either at the 3' untranslated region (clbv3'pr vector) or at the intergenic region between the movement and coat protein (CP) genes (clbvINpr vector). The duplicated fragment (-42/+50) around the transcription start site of the CP subgenomic RNA (sgRNA) had the full promoter activity and induced synthesis of a new sgRNA in infected plants. Agroinoculation with these vectors resulted in systemic infection of Nicotiana benthamiana and the resulting virions systemically infected citrus plants. A clbvINpr vector carrying the green fluorescent protein (GFP) gene expressed GFP in citrus plants and triggered gfp silencing in gfp-transgenic citrus plants, and vectors carrying fragments of the phytoene desaturase or the magnesium chelatase genes incited a silencing phenotype in citrus plants. These silenced phenotypes persisted in successive flushes. Because CLBV infections are symptomless in most citrus species, the effective silencing induced by CLBV-derived vectors will be helpful to analyze citrus gene function.
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Affiliation(s)
- Jesús Agüero
- Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
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22
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Fu XZ, Gong XQ, Zhang YX, Wang Y, Liu JH. Different transcriptional response to Xanthomonas citri subsp. citri between kumquat and sweet orange with contrasting canker tolerance. PLoS One 2012; 7:e41790. [PMID: 22848606 PMCID: PMC3406098 DOI: 10.1371/journal.pone.0041790] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 06/25/2012] [Indexed: 01/25/2023] Open
Abstract
Citrus canker disease caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating biotic stresses affecting the citrus industry. Meiwa kumquat (Fortunella crassifolia) is canker-resistant, while Newhall navel orange (Citrus sinensis Osbeck) is canker-sensitive. To understand the molecular mechanisms underlying the differences in responses to Xcc, transcriptomic profiles of these two genotypes following Xcc attack were compared by using the Affymetrix citrus genome GeneChip. A total of 794 and 1324 differentially expressed genes (DEGs) were identified as canker-responsive genes in Meiwa and Newhall, respectively. Of these, 230 genes were expressed in common between both genotypes, while 564 and 1094 genes were only significantly expressed in either Meiwa or Newhall. Gene ontology (GO) annotation and Singular Enrichment Analysis (SEA) of the DEGs showed that genes related to the cell wall and polysaccharide metabolism were induced for basic defense in both Meiwa and Newhall, such as chitinase, glucanase and thaumatin-like protein. Moreover, apart from inducing basic defense, Meiwa showed specially upregulated expression of several genes involved in the response to biotic stimulus, defense response, and cation binding as comparing with Newhall. And in Newhall, abundant photosynthesis-related genes were significantly down-regulated, which may be in order to ensure the basic defense. This study revealed different molecular responses to canker disease in Meiwa and Newhall, affording insight into the response to canker and providing valuable information for the identification of potential genes for engineering canker tolerance in the future.
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Affiliation(s)
- Xing-Zheng Fu
- Key Laboratory of Horticultural Plant Biology (MOE), National Key Laboratory of Crop Genetic Improvement, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
- Citrus Research Institute, Chinese Academy of Agricultural Sciences, Chongqing, China
| | - Xiao-Qing Gong
- Key Laboratory of Horticultural Plant Biology (MOE), National Key Laboratory of Crop Genetic Improvement, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Yue-Xin Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), National Key Laboratory of Crop Genetic Improvement, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Yin Wang
- Key Laboratory of Horticultural Plant Biology (MOE), National Key Laboratory of Crop Genetic Improvement, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology (MOE), National Key Laboratory of Crop Genetic Improvement, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
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Albrecht U, Bowman KD. Transcriptional response of susceptible and tolerant citrus to infection with Candidatus Liberibacter asiaticus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 185-186:118-30. [PMID: 22325873 DOI: 10.1016/j.plantsci.2011.09.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/26/2011] [Accepted: 09/27/2011] [Indexed: 05/06/2023]
Abstract
Candidatus Liberibacter asiaticus (Las), a non-culturable phloem-limited bacterium, is the suspected causal agent of huanglongbing (HLB) in Florida. HLB is one of the most devastating diseases of citrus and no resistant cultivars have been identified to date, though tolerance has been observed in the genus Poncirus and some of its hybrids. This study compares transcriptional changes in tolerant US-897 (Citrus reticulata Blanco×Poncirus trifoliata L. Raf.) and susceptible 'Cleopatra' mandarin (C. reticulata) seedlings in response to infection with Las using the Affymetrix GeneChip citrus array, with the main objective of identifying genes associated with tolerance to HLB. Microarray analysis identified 326 genes which were significantly upregulated by at least 4-fold in the susceptible genotype, compared with only 17 genes in US-897. Exclusively upregulated in US-897 was a gene for a 2-oxoglutarate (2OG) and Fe(II)-dependant oxygenase, an important enzyme involved in the biosynthesis of plant secondary metabolites. More than eight hundred genes were expressed at much higher levels in US-897 independent of infection with Las. Among these, genes for a constitutive disease resistance protein (CDR1) were notable. The possible involvement of these and other detected genes in tolerance to HLB and their possible use for biotechnology are discussed.
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Affiliation(s)
- Ute Albrecht
- US Horticultural Research Laboratory, US Department of Agriculture, Agricultural Research Service, Fort Pierce, FL 34945, USA.
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24
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Romero P, Rodrigo MJ, Alférez F, Ballester AR, González-Candelas L, Zacarías L, Lafuente MT. Unravelling molecular responses to moderate dehydration in harvested fruit of sweet orange (Citrus sinensis L. Osbeck) using a fruit-specific ABA-deficient mutant. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2753-67. [PMID: 22315241 PMCID: PMC3346234 DOI: 10.1093/jxb/err461] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 12/22/2011] [Accepted: 12/22/2011] [Indexed: 05/23/2023]
Abstract
Water stress affects many agronomic traits that may be regulated by the phytohormone abscisic acid (ABA). Within these traits, loss of fruit quality becomes important in many citrus cultivars that develop peel damage in response to dehydration. To study peel dehydration transcriptional responsiveness in harvested citrus fruit and the putative role of ABA in this process, this study performed a comparative large-scale transcriptional analysis of water-stressed fruits of the wild-type Navelate orange (Citrus sinesis L. Osbeck) and its spontaneous ABA-deficient mutant Pinalate, which is more prone to dehydration and to developing peel damage. Major changes in gene expression occurring in the wild-type line were impaired in the mutant fruit. Gene ontology analysis revealed the ability of Navelate fruits to induce the response to water deprivation and di-, tri-valent inorganic cation transport biological processes, as well as repression of the carbohydrate biosynthesis process in the mutant. Exogenous ABA triggered relevant transcriptional changes and repressed the protein ubiquitination process, although it could not fully rescue the physiological behaviour of the mutant. Overall, the results indicated that dehydration responsiveness requires ABA-dependent and -independent signals, and highlight that the ability of citrus fruits to trigger molecular responses against dehydration is an important factor in reducing their susceptibility to developing peel damage.
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25
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Gonzalez-Ibeas D, Cañizares J, Aranda MA. Microarray analysis shows that recessive resistance to Watermelon mosaic virus in melon is associated with the induction of defense response genes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:107-18. [PMID: 21970693 DOI: 10.1094/mpmi-07-11-0193] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Resistance to Watermelon mosaic virus (WMV) in melon (Cucumis melo L.) accession TGR-1551 is characterized by a significant reduction in virus titer, and is inherited as a recessive, loss-of-susceptibility allele. We measured virus RNA accumulation in TGR-1551 plants and a susceptible control ('Tendral') by real-time quantitative polymerase chain reaction, and also profiled the expression of 17,443 unigenes represented on a melon microarray over a 15-day time course. The virus accumulated to higher levels in cotyledons of the resistant variety up to 9 days postinoculation (dpi) but, thereafter, levels increased in the susceptible variety while those in the resistant variety declined. Microarray experiments looking at the early response to infection (1 and 3 dpi), as well as responses after 7 and 15 dpi, revealed more profound transcriptomic changes in resistant plants than susceptible ones. The gene expression profiles revealed deep and extensive transcriptome remodeling in TGR-1551 plants, often involving genes with pathogen response functions. Overall, our data suggested that resistance to WMV in TGR-1551 melon plants is associated with a defense response, which contrasts with the recessive nature of the resistance trait.
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Affiliation(s)
- Daniel Gonzalez-Ibeas
- Departamento de Biologia del Estres y Patologia Vegetal, Centro de Edafologia y Biologia Aplicada de Segura, Spain
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26
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Ballester AR, Lafuente MT, Forment J, Gadea J, De Vos RCH, Bovy AG, González-Candelas L. Transcriptomic profiling of citrus fruit peel tissues reveals fundamental effects of phenylpropanoids and ethylene on induced resistance. MOLECULAR PLANT PATHOLOGY 2011; 12:879-97. [PMID: 21726388 PMCID: PMC6640524 DOI: 10.1111/j.1364-3703.2011.00721.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Penicillium spp. are the major postharvest pathogens of citrus fruit in Mediterranean climatic regions. The induction of natural resistance constitutes one of the most promising alternatives to avoid the environmental contamination and health problems caused by chemical fungicides. To understand the bases of the induction of resistance in citrus fruit against Penicillium digitatum, we have used a 12k citrus cDNA microarray to study transcriptional changes in the outer and inner parts of the peel (flavedo and albedo, respectively) of elicited fruits. The elicitor treatment led to an over-representation of biological processes associated with secondary metabolism, mainly phenylpropanoids and cellular amino acid biosynthesis and methionine metabolism, and the down-regulation of genes related to biotic and abiotic stresses. Among phenylpropanoids, we detected the over-expression of a large subset of genes important for the synthesis of flavonoids, coumarins and lignin, especially in the internal tissue. Furthermore, these genes and those of ethylene biosynthesis showed the highest induction. The involvement of both phenylpropanoid and ethylene pathways was confirmed by examining changes in gene expression and ethylene production in elicited citrus fruit. Therefore, global results indicate that secondary metabolism, mainly phenylpropanoids, and ethylene play important roles in the induction of resistance in citrus fruit.
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Affiliation(s)
- Ana-Rosa Ballester
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Valencia, Spain
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27
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Enrique R, Siciliano F, Favaro MA, Gerhardt N, Roeschlin R, Rigano L, Sendin L, Castagnaro A, Vojnov A, Marano MR. Novel demonstration of RNAi in citrus reveals importance of citrus callose synthase in defence against Xanthomonas citri subsp. citri. PLANT BIOTECHNOLOGY JOURNAL 2011; 9:394-407. [PMID: 20809929 DOI: 10.1111/j.1467-7652.2010.00555.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Citrus is an economically important fruit crop that is severely afflicted by citrus canker, a disease caused by the bacterial phytopathogen, Xanthomonas citri subsp. citri (Xcc). GenBank houses a large collection of Expressed Sequence Tags (ESTs) enriched with transcripts generated during the defence response against this pathogen; however, there are currently no strategies in citrus to assess the function of candidate genes. This has greatly limited research as defence signalling genes are often involved in multiple pathways. In this study, we demonstrate the efficacy of RNA interference (RNAi) as a functional genomics tool to assess the function of candidate genes involved in the defence response of Citrus limon against the citrus canker pathogen. Double-stranded RNA expression vectors, encoding hairpin RNAs for citrus host genes, were delivered to lemon leaves by transient infiltration with transformed Agrobacterium. As proof of principle, we have established silencing of citrus phytoene desaturase (PDS) and callose synthase (CalS1) genes. Phenotypic and molecular analyses showed that silencing vectors were functional not only in lemon plants but also in other species of the Rutaceae family. Using silencing of CalS1, we have demonstrated that plant cell wall-associated defence is the principal initial barrier against Xanthomonas infection in citrus plants. Additionally, we present here results that suggest that H₂O₂ accumulation, which is suppressed by xanthan from Xcc during pathogenesis, contributes to inhibition of xanthan-deficient Xcc mutant growth either in wild-type or CalS1-silenced plants. With this work, we have demonstrated that high-throughput reverse genetic analysis is feasible in citrus.
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Affiliation(s)
- Ramón Enrique
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha, Rosario, Argentina
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28
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Maserti BE, Del Carratore R, Croce CMD, Podda A, Migheli Q, Froelicher Y, Luro F, Morillon R, Ollitrault P, Talon M, Rossignol M. Comparative analysis of proteome changes induced by the two spotted spider mite Tetranychus urticae and methyl jasmonate in citrus leaves. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:392-402. [PMID: 20926159 DOI: 10.1016/j.jplph.2010.07.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 07/29/2010] [Accepted: 07/30/2010] [Indexed: 05/24/2023]
Abstract
Citrus plants are currently facing biotic and abiotic stresses. Therefore, the characterization of molecular traits involved in the response mechanisms to stress could facilitate selection of resistant varieties. Although large cDNA microarray profiling has been generated in citrus tissues, the available protein expression data are scarce. In this study, to identify differentially expressed proteins in Citrus clementina leaves after infestation by the two-spotted spider mite Tetranychus urticae, a proteome comparison was undertaken using two-dimensional gel electrophoresis. The citrus leaf proteome profile was also compared with that of leaves treated over 0-72h with methyl jasmonate, a compound playing a key role in the defense mechanisms of plants to insect/arthropod attack. Significant variations were observed for 110 protein spots after spider mite infestation and 67 protein spots after MeJA treatments. Of these, 50 proteins were successfully identified by liquid chromatography-mass spectrometry-tandem mass spectrometry. The majority constituted photosynthesis- and metabolism-related proteins. Five were oxidative stress associated enzymes, including phospholipid glutathione peroxidase, a salt stressed associated protein, ascorbate peroxidase and Mn-superoxide dismutase. Seven were defense-related proteins, such as the pathogenesis-related acidic chitinase, the protease inhibitor miraculin-like protein, and a lectin-like protein. This is the first report of differentially regulated proteins after T. urticae attack and exogenous MeJA application in citrus leaves.
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Affiliation(s)
- B E Maserti
- CNR-IBF, Istituto di BioFisica, Area della Ricerca, Via Moruzzi 1, Pisa, Italy
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29
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Catoni M, Miozzi L, Fiorilli V, Lanfranco L, Accotto GP. Comparative analysis of expression profiles in shoots and roots of tomato systemically infected by Tomato spotted wilt virus reveals organ-specific transcriptional responses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:1504-13. [PMID: 19888816 DOI: 10.1094/mpmi-22-12-1504] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Tomato (Solanum lycopersicon), a model species for the family Solanaceae, is severely affected by Tomato spotted wilt virus (TSWV) worldwide. To elucidate the systemic transcriptional response of plants to TSWV infection, microarray experiments were performed on tomato. Parallel analysis of both shoots and roots revealed organ-specific responses, although the virus was present in similar concentration. In the shoots, genes related to defense and to signal transduction were induced, while there was general repression of genes related to primary and secondary metabolism as well as to amino acid metabolism. In roots, expression of genes involved in primary metabolism and signal transduction appear unaffected by TSWV infection, while those related to the response to biotic stimuli were induced and those associated to the response to abiotic stress were generally repressed or unaltered. Genes related to amino acid metabolism were unaffected, except for those involved in synthesis of secondary compounds, where induction was evident. Differential expression of genes involved in metabolism and response to ethylene and abscisic acid was observed in the two organs. Our results provide new insight into the biology of the economically important interaction between tomato and TSWV.
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Affiliation(s)
- Marco Catoni
- Institute of Plant Virology, Consiglio Nazionale delle Ricerche, Strada delle Cacce 73, Turin, Italy
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30
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Martín S, Sambade A, Rubio L, Vives MC, Moya P, Guerri J, Elena SF, Moreno P. Contribution of recombination and selection to molecular evolution of Citrus tristeza virus. J Gen Virol 2009; 90:1527-1538. [PMID: 19264625 DOI: 10.1099/vir.0.008193-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The genetic variation of Citrus tristeza virus (CTV) was analysed by comparing the predominant sequence variants in seven genomic regions (p33, p65, p61, p18, p13, p20 and p23) of 18 pathogenically distinct isolates from seven different countries. Analyses of the selective constraints acting on each codon suggest that most regions were under purifying selection. Phylogenetic analysis shows diverse patterns of molecular evolution for different genomic regions. A first clade composed of isolates that are genetically close to the reference mild isolates T385 or T30 was inferred from all genomic regions. A second clade, mostly comprising virulent isolates, was defined from regions p33, p65, p13 and p23. For regions p65, p61, p18, p13 and p23, a third clade that mostly included South American isolates could not be related to any reference genotype. Phylogenetic relationships among isolates did not reflect their geographical origin, suggesting significant gene flow between geographically distant areas. Incongruent phylogenetic trees for different genomic regions suggested recombination events, an extreme that was supported by several recombination-detecting methods. A phylogenetic network incorporating the effect of recombination showed an explosive radiation pattern for the evolution of some isolates and also grouped isolates by virulence. Taken together, the above results suggest that negative selection, gene flow, sequence recombination and virulence may be important factors driving CTV evolution.
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Affiliation(s)
- Susana Martín
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain.,Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 Valencia, Spain
| | - Adrián Sambade
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 Valencia, Spain
| | - Luis Rubio
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 Valencia, Spain
| | - María C Vives
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 Valencia, Spain
| | - Patricia Moya
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 Valencia, Spain
| | - José Guerri
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
| | - Pedro Moreno
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, 46113 Valencia, Spain
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31
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Alfenas-Zerbini P, Maia IG, Fávaro RD, Cascardo JCM, Brommonschenkel SH, Zerbini FM. Genome-wide analysis of differentially expressed genes during the early stages of tomato infection by a potyvirus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:352-61. [PMID: 19245329 DOI: 10.1094/mpmi-22-3-0352] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant responses against pathogens cause up- and downward shifts in gene expression. To identify differentially expressed genes in a plant-virus interaction, susceptible tomato plants were inoculated with the potyvirus Pepper yellow mosaic virus (PepYMV) and a subtractive library was constructed from inoculated leaves at 72 h after inoculation. Several genes were identified as upregulated, including genes involved in plant defense responses (e.g., pathogenesis-related protein 5), regulation of the cell cycle (e.g., cytokinin-repressed proteins), signal transduction (e.g., CAX-interacting protein 4, SNF1 kinase), transcriptional regulators (e.g., WRKY and SCARECROW transcription factors), stress response proteins (e.g., Hsp90, DNA-J, 20S proteasome alpha subunit B, translationally controlled tumor protein), ubiquitins (e.g., polyubiquitin, ubiquitin activating enzyme 2), among others. Downregulated genes were also identified, which likewise display identity with genes involved in several metabolic pathways. Differential expression of selected genes was validated by macroarray analysis and quantitative real-time polymerase chain reaction. The possible roles played by some of these genes in the viral infection cycle are discussed.
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Affiliation(s)
- Poliane Alfenas-Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
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32
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Brumós J, Colmenero-Flores JM, Conesa A, Izquierdo P, Sánchez G, Iglesias DJ, López-Climent MF, Gómez-Cadenas A, Talón M. Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks. Funct Integr Genomics 2009; 9:293-309. [PMID: 19190944 DOI: 10.1007/s10142-008-0107-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 12/20/2008] [Indexed: 11/29/2022]
Abstract
Salinity tolerance in Citrus is strongly related to leaf chloride accumulation. Both chloride homeostasis and specific genetic responses to Cl(-) toxicity are issues scarcely investigated in plants. To discriminate the transcriptomic network related to Cl(-) toxicity and salinity tolerance, we have used two Cl(-) salt treatments (NaCl and KCl) to perform a comparative microarray approach on two Citrus genotypes, the salt-sensitive Carrizo citrange, a poor Cl(-) excluder, and the tolerant Cleopatra mandarin, an efficient Cl(-) excluder. The data indicated that Cl(-) toxicity, rather than Na(+) toxicity and/or the concomitant osmotic perturbation, is the primary factor involved in the molecular responses of citrus plant leaves to salinity. A number of uncharacterized membrane transporter genes, like NRT1-2, were differentially regulated in the tolerant and the sensitive genotypes, suggesting its potential implication in Cl(-) homeostasis. Analyses of enriched functional categories showed that the tolerant rootstock induced wider stress responses in gene expression while repressing central metabolic processes such as photosynthesis and carbon utilization. These features were in agreement with phenotypic changes in the patterns of photosynthesis, transpiration, and stomatal conductance and support the concept that regulation of transpiration and its associated metabolic adjustments configure an adaptive response to salinity that reduces Cl(-) accumulation in the tolerant genotype.
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Affiliation(s)
- Javier Brumós
- Instituto Valenciano de Investigaciones Agrarias, Centro de Genómica, Ctra Moncada-Náquera Km 4.6, Moncada, Valencia, Spain
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33
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Kim JS, Sagaram US, Burns JK, Li JL, Wang N. Response of sweet orange (Citrus sinensis) to 'Candidatus Liberibacter asiaticus' infection: microscopy and microarray analyses. PHYTOPATHOLOGY 2009; 99:50-7. [PMID: 19055434 DOI: 10.1094/phyto-99-1-0050] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Citrus greening or huanglongbing (HLB) is a devastating disease of citrus. HLB is associated with the phloem-limited fastidious prokaryotic alpha-proteobacterium 'Candidatus Liberibacter spp.' In this report, we used sweet orange (Citrus sinensis) leaf tissue infected with 'Ca. Liberibacter asiaticus' and compared this with healthy controls. Investigation of the host response was examined with citrus microarray hybridization based on 33,879 expressed sequence tag sequences from several citrus species and hybrids. The microarray analysis indicated that HLB infection significantly affected expression of 624 genes whose encoded proteins were categorized according to function. The categories included genes associated with sugar metabolism, plant defense, phytohormone, and cell wall metabolism, as well as 14 other gene categories. The anatomical analyses indicated that HLB bacterium infection caused phloem disruption, sucrose accumulation, and plugged sieve pores. The up-regulation of three key starch biosynthetic genes including ADP-glucose pyrophosphorylase, starch synthase, granule-bound starch synthase and starch debranching enzyme likely contributed to accumulation of starch in HLB-affected leaves. The HLB-associated phloem blockage resulted from the plugged sieve pores rather than the HLB bacterial aggregates since 'Ca. Liberibacter asiaticus' does not form aggregate in citrus. The up-regulation of pp2 gene is related to callose deposition to plug the sieve pores in HLB-affected plants.
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Affiliation(s)
- Jeong-Soon Kim
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA
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34
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Martinez-Godoy MA, Mauri N, Juarez J, Marques MC, Santiago J, Forment J, Gadea J. A genome-wide 20 K citrus microarray for gene expression analysis. BMC Genomics 2008; 9:318. [PMID: 18598343 PMCID: PMC2483987 DOI: 10.1186/1471-2164-9-318] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Accepted: 07/03/2008] [Indexed: 11/24/2022] Open
Abstract
Background Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant. Results We have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database [1] was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability. Conclusion This new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global studies in citrus by using it to catalogue genes expressed in citrus globular embryos.
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Affiliation(s)
- M Angeles Martinez-Godoy
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Laboratorio de Genomica (Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas), Avenida de los Naranjos s/n, E46022 Valencia, Spain.
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35
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Götz S, García-Gómez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talón M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008; 36:3420-35. [PMID: 18445632 PMCID: PMC2425479 DOI: 10.1093/nar/gkn176] [Citation(s) in RCA: 2896] [Impact Index Per Article: 181.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.
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Affiliation(s)
- Stefan Götz
- Bioinformatics Department, Centro de Investigación Principe Felipe, Valencia, Spain
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Moreno P, Ambrós S, Albiach-Martí MR, Guerri J, Peña L. Citrus tristeza virus: a pathogen that changed the course of the citrus industry. MOLECULAR PLANT PATHOLOGY 2008; 9:251-68. [PMID: 18705856 PMCID: PMC6640355 DOI: 10.1111/j.1364-3703.2007.00455.x] [Citation(s) in RCA: 202] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Citrus tristeza virus (CTV) (genus Closterovirus, family Closteroviridae) is the causal agent of devastating epidemics that changed the course of the citrus industry. Adapted to replicate in phloem cells of a few species within the family Rutaceae and to transmission by a few aphid species, CTV and citrus probably coevolved for centuries at the site of origin of citrus plants. CTV dispersal to other regions and its interaction with new scion varieties and rootstock combinations resulted in three distinct syndromes named tristeza, stem pitting and seedling yellows. The first, inciting decline of varieties propagated on sour orange, has forced the rebuilding of many citrus industries using tristeza-tolerant rootstocks. The second, inducing stunting, stem pitting and low bearing of some varieties, causes economic losses in an increasing number of countries. The third is usually observed by biological indexing, but rarely in the field. CTV polar virions are composed of two capsid proteins and a single-stranded, positive-sense genomic RNA (gRNA) of approximately 20 kb, containing 12 open reading frames (ORFs) and two untranslated regions (UTRs). ORFs 1a and 1b, encoding proteins of the replicase complex, are directly translated from the gRNA, and together with the 5' and 3'UTRs are the only regions required for RNA replication. The remaining ORFs, expressed via 3'-coterminal subgenomic RNAs, encode proteins required for virion assembly and movement (p6, p65, p61, p27 and p25), asymmetrical accumulation of positive and negative strands during RNA replication (p23), or suppression of post-transcriptional gene silencing (p25, p20 and p23), with the role of proteins p33, p18 and p13 as yet unknown. Analysis of genetic variation in CTV isolates revealed (1) conservation of genomes in distant geographical regions, with a limited repertoire of genotypes, (2) uneven distribution of variation along the gRNA, (3) frequent recombination events and (4) different selection pressures shaping CTV populations. Measures to control CTV damage include quarantine and budwood certification programmes, elimination of infected trees, use of tristeza-tolerant rootstocks, or cross protection with mild isolates, depending on CTV incidence and on the virus strains and host varieties predominant in each region. Incorporating resistance genes into commercial varieties by conventional breeding is presently unfeasible, whereas incorporation of pathogen-derived resistance by plant transformation has yielded variable results, indicating that the CTV-citrus interaction may be more specific and complex than initially thought. A deep understanding of the interactions between viral proteins and host and vector factors will be necessary to develop reliable and sound control measures.
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Affiliation(s)
- Pedro Moreno
- Instituto Valenciano de Investigaciones Agrarias, Cra. Moncada-Náquera Km. 4.5, Moncada, 46113- Valencia, Spain.
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Talon M, Gmitter Jr. FG. Citrus genomics. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:528361. [PMID: 18509486 PMCID: PMC2396216 DOI: 10.1155/2008/528361] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 03/15/2008] [Indexed: 05/18/2023]
Abstract
Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop.
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Affiliation(s)
- Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia, Spain
| | - Fred G. Gmitter Jr.
- Citrus Research and Education Center (CREC), University of Florida, IFAS, Lake Alfred, FL 33850, USA
- *Fred G. Gmitter Jr.:
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Conesa A, Götz S. Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:619832. [PMID: 18483572 PMCID: PMC2375974 DOI: 10.1155/2008/619832] [Citation(s) in RCA: 1344] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 11/26/2007] [Indexed: 05/09/2023]
Abstract
Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. Blast2GO is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use.
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Affiliation(s)
- Ana Conesa
- Bioinformatics Department,
Centro de Investigación Príncipe Felipe,
4012 Valencia,
Spain
- *Ana Conesa:
| | - Stefan Götz
- Bioinformatics Department,
Centro de Investigación Príncipe Felipe,
4012 Valencia,
Spain
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