1
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Paineau M, Minio A, Mestre P, Fabre F, Mazet ID, Couture C, Legeai F, Dumartinet T, Cantu D, Delmotte F. Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew. THE NEW PHYTOLOGIST 2024; 243:1490-1505. [PMID: 39021210 DOI: 10.1111/nph.19861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 03/21/2024] [Indexed: 07/20/2024]
Abstract
Grapevine downy mildew, caused by the oomycete Plasmopara viticola (P. viticola, Berk. & M. A. Curtis; Berl. & De Toni), is a global threat to Eurasian wine grapes Vitis vinifera. Although resistant grapevine varieties are becoming more accessible, P. viticola populations are rapidly evolving to overcome these resistances. We aimed to uncover avirulence genes related to Rpv3.1-mediated grapevine resistance. We sequenced the genomes and characterized the development of 136 P. viticola strains on resistant and sensitive grapevine cultivars. A genome-wide association study was conducted to identify genomic variations associated with resistant-breaking phenotypes. We identified a genomic region associated with the breakdown of Rpv3.1 grapevine resistance (avrRpv3.1 locus). A diploid-aware reassembly of the P. viticola INRA-Pv221 genome revealed structural variations in this locus, including a 30 kbp deletion. Virulent P. viticola strains displayed multiple deletions on both haplotypes at the avrRpv3.1 locus. These deletions involve two paralog genes coding for proteins with 800-900 amino acids and signal peptides. These proteins exhibited a structure featuring LWY-fold structural modules, common among oomycete effectors. When transiently expressed, these proteins induced cell death in grapevines carrying Rpv3.1 resistance, confirming their avirulence nature. This discovery sheds light on the genetic mechanisms enabling P. viticola to adapt to grapevine resistance, laying a foundation for developing strategies to manage this destructive crop pathogen.
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Affiliation(s)
- Manon Paineau
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
| | - Pere Mestre
- INRAE, Université de Strasbourg, SVQV, F-68125, Colmar, France
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Isabelle D Mazet
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Carole Couture
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
| | - Fabrice Legeai
- INRAE, IGEPP, F-35650, Le-Rheu, France
- INRIA, IRISA, GenOuest Core Facility, F-35000, Rennes, France
| | | | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, 95616, CA, USA
- Genome Center, University of California Davis, Davis, 95616, CA, USA
| | - François Delmotte
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, F-33340, Villenave d'Ornon, France
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2
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Shi X, Shen H, Wang Y, Yang X, Shi R, Tan W, Ran L. Potential Biocontrol Microorganisms Causing Attenuated Pathogenicity in Plasmopara viticola. PHYTOPATHOLOGY 2024; 114:1226-1236. [PMID: 38205803 DOI: 10.1094/phyto-10-23-0376-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
A phenomenon of pathogenicity attenuation of Plasmopara viticola was consistently observed during its subculture on grape. To clarify the causes of attenuated pathogenicity of P. viticola, culturable microbes were isolated from the P. viticola mass (mycelia, sporangiophores, and sporangia) in each generation and tested for their biocontrol efficacies on grape downy mildew (GDM). The results showed that the incidence of GDM decreased with the increase in the number of subculture times on both vineyard-collected leaves and grape leaves from in vitro-grown seedlings. The number of culturable microbial taxa on the surface of P. viticola decreased, whereas the population densities of four specific strains (i.e., K2, K7, P1, and P5) increased significantly with the increase in subculture times. Compared with the control, the biocontrol efficacies of the bacterial strain K2 reached 87.5%, and those of both fungal strains P1 and P5 reached 100.0%. Based on morphological characteristics and molecular sequences, strains K2, P1, and P5 were identified as Curtobacterium herbarum, Thecaphora amaranthi, and Acremonium sclerotigenum, respectively, and these three strains survived very well and multiplied on the surface of P. viticola. As the number of times P. viticola was subcultured increased, all three of these strains became the predominant strains, leading to greater P. viticola inhibition, attenuated P. viticola pathogenicity, and effective GDM biological control. To the best of our knowledge, this is the first report of C. herbarum and T. amaranthi having biological control activity against GDM.
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Affiliation(s)
- Xiaomeng Shi
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Forest Germplasm Resources and Forest Protection in Hebei Province, Baoding 071000, China
| | - Hongmiao Shen
- Center for Evaluation and Faculty Development, Hebei University of Economics and Business, Shijiazhuang 050061, China
| | - Yacong Wang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Xue Yang
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Ruolin Shi
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
| | - Wanzhong Tan
- College of Biotechnology and Engineering, West Yunnan University, Lincang 677000, China
| | - Longxian Ran
- College of Forestry, Hebei Agricultural University, Baoding 071000, China
- Key Laboratory of Forest Germplasm Resources and Forest Protection in Hebei Province, Baoding 071000, China
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3
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Gouveia C, Santos RB, Paiva-Silva C, Buchholz G, Malhó R, Figueiredo A. The pathogenicity of Plasmopara viticola: a review of evolutionary dynamics, infection strategies and effector molecules. BMC PLANT BIOLOGY 2024; 24:327. [PMID: 38658826 PMCID: PMC11040782 DOI: 10.1186/s12870-024-05037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
Oomycetes are filamentous organisms that resemble fungi in terms of morphology and life cycle, primarily due to convergent evolution. The success of pathogenic oomycetes lies in their ability to adapt and overcome host resistance, occasionally transitioning to new hosts. During plant infection, these organisms secrete effector proteins and other compounds during plant infection, as a molecular arsenal that contributes to their pathogenic success. Genomic sequencing, transcriptomic analysis, and proteomic studies have revealed highly diverse effector repertoires among different oomycete pathogens, highlighting their adaptability and evolution potential.The obligate biotrophic oomycete Plasmopara viticola affects grapevine plants (Vitis vinifera L.) causing the downy mildew disease, with significant economic impact. This disease is devastating in Europe, leading to substantial production losses. Even though Plasmopara viticola is a well-known pathogen, to date there are scarce reviews summarising pathogenicity, virulence, the genetics and molecular mechanisms of interaction with grapevine.This review aims to explore the current knowledge of the infection strategy, lifecycle, effector molecules, and pathogenicity of Plasmopara viticola. The recent sequencing of the Plasmopara viticola genome has provided new insights into understanding the infection strategies employed by this pathogen. Additionally, we will highlight the contributions of omics technologies in unravelling the ongoing evolution of this oomycete, including the first in-plant proteome analysis of the pathogen.
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Affiliation(s)
- Catarina Gouveia
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Science, University of Lisbon, Lisboa, Portugal
| | - Rita B Santos
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Science, University of Lisbon, Lisboa, Portugal
| | - Catarina Paiva-Silva
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Science, University of Lisbon, Lisboa, Portugal
| | - Günther Buchholz
- RLP AgroScience/AlPlanta-Institute for Plant Research, Neustadt an Der Weinstrasse, Germany
| | - Rui Malhó
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Science, University of Lisbon, Lisboa, Portugal
| | - Andreia Figueiredo
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Science, University of Lisbon, Lisboa, Portugal.
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4
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Peng J, Wang X, Wang H, Li X, Zhang Q, Wang M, Yan J. Advances in understanding grapevine downy mildew: From pathogen infection to disease management. MOLECULAR PLANT PATHOLOGY 2024; 25:e13401. [PMID: 37991155 PMCID: PMC10788597 DOI: 10.1111/mpp.13401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/29/2023] [Indexed: 11/23/2023]
Abstract
Plasmopara viticola is geographically widespread in grapevine-growing regions. Grapevine downy mildew disease, caused by this biotrophic pathogen, leads to considerable yield losses in viticulture annually. Because of the great significance of grapevine production and wine quality, research on this disease has been widely performed since its emergence in the 19th century. Here, we review and discuss recent understanding of this pathogen from multiple aspects, including its infection cycle, disease symptoms, genome decoding, effector biology, and management and control strategies. We highlight the identification and characterization of effector proteins with their biological roles in host-pathogen interaction, with a focus on sustainable control methods against P. viticola, especially the use of biocontrol agents and environmentally friendly compounds.
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Affiliation(s)
- Junbo Peng
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Hui Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xinghong Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Qi Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Meng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
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5
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Yacoub A, Haidar R, Mesguida O, Gerbore J, Hachicha M, Attard E, Guyoneaud R, Rey P. Deciphering Plant-Induced Responses toward Botrytis cinerea and Plasmopara viticola Attacks in Two Grapevine Cultivars Colonized by the Root Biocontrol Oomycete, Pythium oligandrum. J Fungi (Basel) 2023; 9:jof9050511. [PMID: 37233222 DOI: 10.3390/jof9050511] [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: 01/16/2023] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023] Open
Abstract
Two major diseases that affect grapevine leaves and berries are controlled by the oomycete Pythium oligandrum. As the efficacy of biocontrol agents strongly depends on factors such as the trophic behaviors of pathogens and cultivar susceptibility, a two-disease approach was implemented to evaluate the activity of P. oligandrum against Botrytis cinerea (the necrotrophic fungus of gray mold) and Plasmopara viticola (the biotrophic oomycete of downy mildew) on two grapevine cultivars with different susceptibilities to these two pathogens. The results show that grapevine root inoculation with P. oligandrum significantly reduced P. viticola and B. cinerea infection on the leaves of the two cultivars, but with differences. This was observed when the relative expression of 10 genes was measured in response to each pathogen, and could be attributed to their lifestyles, i.e., biotrophic or necrotrophic, which are related to the activation of specific metabolic pathways of the plant. In response to P. viticola infection, genes from the jasmonate and ethylene pathways were mainly induced, whereas for B. cinerea, the genes induced were those of the ethylene-jasmonate pathway. The different levels of defense against B. cinerea and P. viticola could also explain the difference in cultivar susceptibility to these pathogens.
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Affiliation(s)
- Amira Yacoub
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, 64000 Pau, France
- INRAE, UMR1065, Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883 Villenave d'Ornon, France
| | - Rana Haidar
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, 64000 Pau, France
- INRAE, UMR1065, Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883 Villenave d'Ornon, France
| | - Ouiza Mesguida
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, 64000 Pau, France
- GreenCell, Biopôle Clermont-Limagne, 63360 Saint Beauzire, France
| | - Jonathan Gerbore
- GreenCell, Biopôle Clermont-Limagne, 63360 Saint Beauzire, France
| | - Maya Hachicha
- INRAE, UMR1065, Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883 Villenave d'Ornon, France
| | - Eléonore Attard
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, 64000 Pau, France
| | - Rémy Guyoneaud
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, 64000 Pau, France
| | - Patrice Rey
- E2S UPPA, CNRS, IPREM, Université de Pau et des Pays de l'Adour, 64000 Pau, France
- INRAE, UMR1065, Santé et Agroécologie du Vignoble (SAVE), ISVV, 33883 Villenave d'Ornon, France
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6
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Figueiredo J, Santos RB, Guerra-Guimarães L, Leclercq CC, Renaut J, Malhó R, Figueiredo A. An in-planta comparative study of Plasmopara viticola proteome reveals different infection strategies towards susceptible and Rpv3-mediated resistance hosts. Sci Rep 2022; 12:20794. [PMID: 36456634 PMCID: PMC9715676 DOI: 10.1038/s41598-022-25164-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Plasmopara viticola, an obligate biotrophic oomycete, is the causal agent of one of the most harmful grapevine diseases, downy mildew. Within this pathosystem, much information is gathered on the host, as characterization of pathogenicity and infection strategy of a biotrophic pathogen is quite challenging. Molecular insights into P. viticola development and pathogenicity are just beginning to be uncovered, mainly by transcriptomic studies. Plasmopara viticola proteome and secretome were only predicted based on transcriptome data. In this study, we have identified the in-planta proteome of P. viticola during infection of a susceptible ('Trincadeira') and a Rpv3-mediated resistance ('Regent') grapevine cultivar. Four hundred and twenty P. viticola proteins were identified on a label-free mass spectrometry-based approach of the apoplastic fluid of grapevine leaves. Overall, our study suggests that, in the compatible interaction, P. viticola manipulates salicylic-acid pathway and isoprenoid biosynthesis to enhance plant colonization. Furthermore, during the incompatible interaction, development-associated proteins increased while oxidoreductases protect P. viticola from ROS-associated plant defence mechanism. Up to our knowledge this is the first in-planta proteome characterization of this biotrophic pathogen, thus this study will open new insights into our understanding of this pathogen colonization strategy of both susceptible and Rpv3-mediated resistance grapevine genotypes.
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Affiliation(s)
- Joana Figueiredo
- Grapevine Pathogen Systems Lab, Plant Biology Department, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisboa, Portugal.
- Plant Biology Department, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisboa, Portugal.
| | - Rita B Santos
- Grapevine Pathogen Systems Lab, Plant Biology Department, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisboa, Portugal
- Plant Biology Department, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisboa, Portugal
| | - Leonor Guerra-Guimarães
- CIFC - Centro de Investigação das Ferrugens Do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017, Lisboa, Portugal
- LEAF - Linking Landscape, Environment, Agriculture and Food & Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017, Lisboa, Portugal
| | - Céline C Leclercq
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 4362, Esch-Sur-Alzette, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 4362, Esch-Sur-Alzette, Luxembourg
| | - Rui Malhó
- Plant Biology Department, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisboa, Portugal
| | - Andreia Figueiredo
- Grapevine Pathogen Systems Lab, Plant Biology Department, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisboa, Portugal
- Plant Biology Department, BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016, Lisboa, Portugal
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7
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Koledenkova K, Esmaeel Q, Jacquard C, Nowak J, Clément C, Ait Barka E. Plasmopara viticola the Causal Agent of Downy Mildew of Grapevine: From Its Taxonomy to Disease Management. Front Microbiol 2022; 13:889472. [PMID: 35633680 PMCID: PMC9130769 DOI: 10.3389/fmicb.2022.889472] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/19/2022] [Indexed: 01/25/2023] Open
Abstract
Plasmopara viticola (P. viticola, Berk. & M. A. Curtis; Berl. & De Toni) causing grapevine downy mildew is one of the most damaging pathogens to viticulture worldwide. Since its recognition in the middle of nineteenth century, this disease has spread from America to Europe and then to all grapevine-growing countries, leading to significant economic losses due to the lack of efficient disease control. In 1885 copper was found to suppress many pathogens, and is still the most effective way to control downy mildews. During the twentieth century, contact and penetrating single-site fungicides have been developed for use against plant pathogens including downy mildews, but wide application has led to the appearance of pathogenic strains resistant to these treatments. Additionally, due to the negative environmental impact of chemical pesticides, the European Union restricted their use, triggering a rush to develop alternative tools such as resistant cultivars breeding, creation of new active ingredients, search for natural products and biocontrol agents that can be applied alone or in combination to kill the pathogen or mitigate its effect. This review summarizes data about the history, distribution, epidemiology, taxonomy, morphology, reproduction and infection mechanisms, symptoms, host-pathogen interactions, host resistance and control of the P. viticola, with a focus on sustainable methods, especially the use of biocontrol agents.
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Affiliation(s)
- Kseniia Koledenkova
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Cédric Jacquard
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Jerzy Nowak
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Saunders Hall, Blacksburg, VA, United States
| | - Christophe Clément
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - Essaid Ait Barka
- Université de Reims Champagne Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, Reims, France
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8
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Delmotte F, Paineau M, Mazet ID, Delière L, Fabre F, Dussert Y. Identifying the genetic architecture of Plamopara viticola traits of interest by genome-wide association studies: case study of mating-type locus and effectors genes involved in the breakdown of grapevine Rpv3 resistance. BIO WEB OF CONFERENCES 2022. [DOI: 10.1051/bioconf/20225002004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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9
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Santos RB, Figueiredo A. Two sides of the same story in grapevine-pathogen interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3367-3380. [PMID: 33631010 DOI: 10.1093/jxb/erab091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Proteases are an integral part of plant defence systems, and their role in plant-pathogen interactions is unequivocal. Emerging evidence suggests that different protease families contribute to the establishment not only of hypersensitive response, priming, and signalling, but also of recognition events through complex proteolytic cascades. Moreover, they play a crucial role in pathogen/microbe-associated molecular pattern (PAMP/MAMP)-triggered immunity as well as in effector-triggered immunity. However, despite important advances in our understanding of the role of proteases in plant defence, the contribution of proteases to pathogen defence in grapevine remains poorly understood. In this review, we summarize current knowledge of the main grapevine pathosystems and explore the role of serine, cysteine, and aspartic proteases from both the host and pathogen point of views.
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Affiliation(s)
- Rita B Santos
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Andreia Figueiredo
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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10
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Xiang G, Yin X, Niu W, Chen T, Liu R, Shang B, Fu Q, Liu G, Ma H, Xu Y. Characterization of CRN-Like Genes From Plasmopara viticola: Searching for the Most Virulent Ones. Front Microbiol 2021; 12:632047. [PMID: 33868192 PMCID: PMC8044898 DOI: 10.3389/fmicb.2021.632047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/26/2021] [Indexed: 11/13/2022] Open
Abstract
Grapevine downy mildew is an insurmountable disease that endangers grapevine production and the wine industry worldwide. The causal agent of the disease is the obligate biotrophic oomycete Plasmopara viticola, for which the pathogenic mechanism remains largely unknown. Crinkling and necrosis proteins (CRN) are an ancient class of effectors utilized by pathogens, including oomycetes, that interfere with host plant defense reactions. In this study, 27 CRN-like genes were cloned from the P. viticola isolate YL genome, hereafter referred to as PvCRN genes, and characterized in silico and in planta. PvCRN genes in ‘YL’ share high sequence identities with their ortholog genes in the other three previously sequenced P. viticola isolates. Sequence divergence among the genes in the PvCRN family indicates that different PvCRN genes have different roles. Phylogenetic analysis of the PvCRN and the CRN proteins encoded by genes in the P. halstedii genome suggests that various functions might have been acquired by the CRN superfamily through independent evolution of Plasmopara species. When transiently expressed in plant cells, the PvCRN protein family shows multiple subcellular localizations. None of the cloned PvCRN proteins induced hypersensitive response (HR)-like cell death on the downy mildew-resistant grapevine Vitis riparia. This was in accordance with the result that most PvCRN proteins, except PvCRN11, failed to induce necrosis in Nicotiana benthamiana. Pattern-triggered immunity (PTI) induced by INF1 was hampered by several PvCRN proteins. In addition, 15 PvCRN proteins prevented Bax-induced plant programmed cell death. Among the cell death-suppressing members, PvCRN17, PvCRN20, and PvCRN23 were found to promote the susceptibility of N. benthamiana to Phytophthora capsici, which is a semi-biotrophic oomycete. Moreover, the nucleus-targeting member, PvCRN19, promoted the susceptibility of N. benthamiana to P. capsici. Therefore, these PvCRN proteins were estimated to be virulent effectors involved in the pathogenicity of P. viticola YL. Collectively, this study provides comprehensive insight into the CRN effector repertoire of P. viticola YL, which will help further elucidate the molecular mechanisms of the pathogenesis of grapevine downy mildew.
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Affiliation(s)
- Gaoqing Xiang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Xiao Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Weili Niu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Tingting Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Ruiqi Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Boxing Shang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Qingqing Fu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Guotian Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Hui Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
| | - Yan Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China
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11
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Chiapello M, Rodríguez-Romero J, Ayllón MA, Turina M. Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages. Virus Evol 2020; 6:veaa058. [PMID: 33324489 PMCID: PMC7724247 DOI: 10.1093/ve/veaa058] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The obligatory biotrophic oomycetes Plasmopara viticola is the causal agent of downy mildew, a destructive disease of grapevine worldwide. So far, chemical fungicides are widely employed to limit this pathogen, but their adverse effects are stimulating the quest for environmentally friendly alternative approaches. Here, we report on the search for mycoviruses that might be later developed as biocontrol agents for this pathogen. Symptomatic leaves were collected from various regions in Spain and Italy and mycelia associated to leaf lesions was harvested. Total RNA extractions were depleted of rRNA and metatranscriptomes were generated using a high-throughput sequencing approach. The virome associated to leaf lesions was then characterized through a bioinformatic pipeline relying on blast searches against current viral databases. Here, we present an inventory of 283 new RNA viruses: 222 positive strand RNA viruses, 29 negative strand RNA viruses, 27 double-stranded RNA viruses and 5 ORFan virus RdRP segments, which could not be reliably assigned to any existing group in the Riboviria. In addition to ORFan viruses, we found other surprising new evolutionary trajectories in this wide inventory of viruses. The most represented viruses in our collection are those in phylum Lenarviricota, and, among them, a group of mycovirus segments distantly related to narnaviruses, but characterized by a polymerase palm domain lacking subdomain C, with the putative GDD catalytic triad. We also provided evidence of a strict association between two RNA segments that form a new mycovirus clade of positive strand RNA in the phylum Kitrinoviricota, order Martellivirales. In the phylum Negarnaviricota, we report for the first time in the order Mononegavirales a clade of viruses that is ambisense, a feature that so far was present only in the order Bunyavirales. Furthermore, in the same phylum we detected the widespread occurrence and abundant accumulation in our libraries of a distinct mycovirus clade distantly related to the Muvirales and Goujanvirales orders, which so far include only viruses infecting invertebrates. Possible new oomycetes-specific virus clades are also described in the phylum Duplornaviricota. These data greatly expand the evolutionary history of mycoviruses adding new layers of diversity to the realm Riboviria.
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Affiliation(s)
- M Chiapello
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - J Rodríguez-Romero
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid 28040, Spain
| | - M A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain.,Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid 28040, Spain
| | - M Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
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12
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Dussert Y, Legrand L, Mazet ID, Couture C, Piron MC, Serre RF, Bouchez O, Mestre P, Toffolatti SL, Giraud T, Delmotte F. Identification of the First Oomycete Mating-type Locus Sequence in the Grapevine Downy Mildew Pathogen, Plasmopara viticola. Curr Biol 2020; 30:3897-3907.e4. [PMID: 32795448 DOI: 10.1016/j.cub.2020.07.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/02/2020] [Accepted: 07/16/2020] [Indexed: 02/02/2023]
Abstract
Mating types are self-incompatibility systems that promote outcrossing in plants, fungi, and oomycetes. Mating-type genes have been widely studied in plants and fungi but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type locus of Plasmopara viticola, the oomycete responsible for grapevine downy mildew, one of the most damaging grapevine diseases worldwide. Using a genome-wide association approach, we identified a 570-kb repeat-rich non-recombining region controlling mating types, with two highly divergent alleles. We showed that one mating type was homozygous, whereas the other was heterozygous at this locus. The mating-type locus encompassed 40 genes, including one encoding a putative hormone receptor. Functional studies will, however, be required to validate the function of these genes and find the actual determinants of mating type. Our findings have fundamental implications for our understanding of the evolution of mating types, as they reveal a unique determinism involving an asymmetry of heterozygosity, as in sex chromosomes and unlike other mating-type systems. This identification of the mating-type locus in such an economically important crop pathogen also has applied implications, as outcrossing facilitates rapid evolution and resistance to harsh environmental conditions.
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Affiliation(s)
- Yann Dussert
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, F-33140 Villenave d'Ornon, France.
| | - Ludovic Legrand
- LIPM, INRAE, Université de Toulouse, CNRS, Castanet-Tolosan, France
| | - Isabelle D Mazet
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, F-33140 Villenave d'Ornon, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, F-33140 Villenave d'Ornon, France
| | | | | | - Olivier Bouchez
- INRAE, US 1426 GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Pere Mestre
- SVQV, INRAE, Université de Strasbourg, F-68000 Colmar, France
| | - Silvia Laura Toffolatti
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Milano, Italy
| | - Tatiana Giraud
- Ecologie Systematique et Evolution, CNRS, AgroParisTech, Universite Paris-Saclay, 91400 Orsay, France
| | - François Delmotte
- SAVE, INRAE, Bordeaux Sciences Agro, Université de Bordeaux, F-33140 Villenave d'Ornon, France.
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13
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Purayannur S, Cano LM, Bowman MJ, Childs KL, Gent DH, Quesada-Ocampo LM. The Effector Repertoire of the Hop Downy Mildew Pathogen Pseudoperonospora humuli. Front Genet 2020; 11:910. [PMID: 32849854 PMCID: PMC7432248 DOI: 10.3389/fgene.2020.00910] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/22/2020] [Indexed: 01/18/2023] Open
Abstract
Pseudoperonospora humuli is an obligate biotrophic oomycete that causes downy mildew (DM), one of the most destructive diseases of cultivated hop that can lead to 100% crop loss in susceptible cultivars. We used the published genome of P. humuli to predict the secretome and effectorome and analyze the transcriptome variation among diverse isolates and during infection of hop leaves. Mining the predicted coding genes of the sequenced isolate OR502AA of P. humuli revealed a secretome of 1,250 genes. We identified 296 RXLR and RXLR-like effector-encoding genes in the secretome. Among the predicted RXLRs, there were several WY-motif-containing effectors that lacked canonical RXLR domains. Transcriptome analysis of sporangia from 12 different isolates collected from various hop cultivars revealed 754 secreted proteins and 201 RXLR effectors that showed transcript evidence across all isolates with reads per kilobase million (RPKM) values > 0. RNA-seq analysis of OR502AA-infected hop leaf samples at different time points after infection revealed highly expressed effectors that may play a relevant role in pathogenicity. Quantitative RT-PCR analysis confirmed the differential expression of selected effectors. We identified a set of P. humuli core effectors that showed transcript evidence in all tested isolates and elevated expression during infection. These effectors are ideal candidates for functional analysis and effector-assisted breeding to develop DM resistant hop cultivars.
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Affiliation(s)
- Savithri Purayannur
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Liliana M. Cano
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
- Indian River Research and Education Center, Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, United States
| | - Megan J. Bowman
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Ball Horticultural Company, West Chicago, IL, United States
| | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - David H. Gent
- United States Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Oregon State University, Corvallis, OR, United States
| | - Lina M. Quesada-Ocampo
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
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14
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Natesan K, Park JY, Kim CW, Park DS, Kwon YS, Back CG, Cho H. High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:718-720. [PMID: 32237963 DOI: 10.1094/mpmi-10-19-0280-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.
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Affiliation(s)
- Karthi Natesan
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Ji Yeon Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Cheol-Woo Kim
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Dong Suk Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Young-Seok Kwon
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Chang-Gi Back
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Heejung Cho
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
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15
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Chen T, Liu R, Dou M, Li M, Li M, Yin X, Liu GT, Wang Y, Xu Y. Insight Into Function and Subcellular Localization of Plasmopara viticola Putative RxLR Effectors. Front Microbiol 2020; 11:692. [PMID: 32373100 PMCID: PMC7186587 DOI: 10.3389/fmicb.2020.00692] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/15/2022] Open
Abstract
Grapevine downy mildew, caused by oomycete fungus Plasmopara viticola, is one of the most devastating diseases of grapes across the major production regions of the world. Although many putative effector molecules have been identified from this pathogen, the functions of the majority of these are still unknown. In this study, we analyzed the potential function of 26 P. viticola effectors from the highly virulent strain YL. Using transient expression in leaf cells of the tobacco Nicotiana benthamiana, we found that the majority of the effectors could suppress cell death triggered by BAX and INF1, while seven could induce cell death. The subcellular localization of effectors in N. benthamiana was consistent with their localization in cells of Vitis vinifera. Those effectors that localized to the nucleus (17/26) showed a variety of subnuclear localization. Ten of the effectors localized predominantly to the nucleolus, whereas the remaining seven localized to nucleoplasm. Interestingly, five of the effectors were strongly related in sequence and showed identical subcellular localization, but had different functions in N. benthamiana leaves and expression patterns in grapevine in response to P. viticola. This study highlights the potential functional diversity of P. viticola effectors.
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Affiliation(s)
- Tingting Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Ruiqi Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Mengru Dou
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Mengyuan Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Meijie Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Xiao Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Guo-Tian Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Yan Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, China.,College of Horticulture, Northwest A&F University, Yangling, China.,Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, China
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16
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Rahman A, Góngora-Castillo E, Bowman MJ, Childs KL, Gent DH, Martin FN, Quesada-Ocampo LM. Genome Sequencing and Transcriptome Analysis of the Hop Downy Mildew Pathogen Pseudoperonospora humuli Reveal Species-Specific Genes for Molecular Detection. PHYTOPATHOLOGY 2019; 109:1354-1366. [PMID: 30939079 DOI: 10.1094/phyto-11-18-0431-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pseudoperonospora humuli is an obligate oomycete pathogen of hop (Humulus lupulus) that causes downy mildew, an important disease in most production regions in the Northern Hemisphere. The pathogen can cause a systemic infection in hop, overwinter in the root system, and infect propagation material. Substantial yield loss may occur owing to P. humuli infection of strobiles (seed cones), shoots, and cone-bearing branches. Fungicide application and cultural practices are the primary methods to manage hop downy mildew. However, effective, sustainable, and cost-effective management of downy mildew can be improved by developing early detection systems to inform on disease risk and timely fungicide application. However, no species-specific diagnostic assays or genomic resources are available for P. humuli. The genome of the P. humuli OR502AA isolate was partially sequenced using Illumina technology and assembled with ABySS. The assembly had a minimum scaffold length of 500 bp and an N50 (median scaffold length of the assembled genome) of 19.2 kbp. A total number of 18,656 genes were identified using MAKER standard gene predictions. Additionally, transcriptome assemblies were generated using RNA-seq and Trinity for seven additional P. humuli isolates. Bioinformatics analyses of next generation sequencing reads of P. humuli and P. cubensis (a closely related sister species) identified 242 candidate species-specific P. humuli genes that could be used as diagnostic molecular markers. These candidate genes were validated using polymerase chain reaction against a diverse collection of isolates from P. humuli, P. cubensis, and other oomycetes. Overall, four diagnostic markers were found to be uniquely present in P. humuli. These candidate markers identified through comparative genomics can be used for pathogen diagnostics in propagation material, such as rhizomes and vegetative cuttings, or adapted for biosurveillance of airborne sporangia, an important source of inoculum in hop downy mildew epidemics.
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Affiliation(s)
- A Rahman
- 1Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
| | - E Góngora-Castillo
- 1Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
- 2Department of Biotechnology, Yucatan Center for Scientific Research, 97205 Mérida, Yucatán, México
| | - M J Bowman
- 3Department of Plant Biology, Michigan State University, East Lansing, MI 48823, U.S.A
| | - K L Childs
- 3Department of Plant Biology, Michigan State University, East Lansing, MI 48823, U.S.A
| | - D H Gent
- 4Forage Seed and Cereal Research Unit, U.S. Department of Agriculture-Agricultural Research Service and Oregon State University, Corvallis 97331, OR, U.S.A
| | - F N Martin
- 5Crop Improvement and Protection Research Station, U.S. Department of Agriculture-Agricultural Research Service, Salinas, CA 93905, U.S.A
| | - L M Quesada-Ocampo
- 1Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
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17
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Combier M, Evangelisti E, Piron MC, Rengel D, Legrand L, Shenhav L, Bouchez O, Schornack S, Mestre P. A secreted WY-domain-containing protein present in European isolates of the oomycete Plasmopara viticola induces cell death in grapevine and tobacco species. PLoS One 2019; 14:e0220184. [PMID: 31356604 PMCID: PMC6663016 DOI: 10.1371/journal.pone.0220184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/10/2019] [Indexed: 01/02/2023] Open
Abstract
Plasmopara viticola is a biotrophic oomycete pathogen causing grapevine downy mildew. We characterized the repertoire of P. viticola effector proteins which may be translocated into plants to support the disease. We found several secreted proteins that contain canonical dEER motifs and conserved WY-domains but lack the characteristic RXLR motif reported previously from oomycete effectors. We cloned four candidates and showed that one of them, Pv33, induces plant cell death in grapevine and Nicotiana species. This activity is dependent on the nuclear localization of the protein. Sequence similar effectors were present in seven European, but in none of the tested American isolates. Together our work contributes a new type of conserved P. viticola effector candidates.
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Affiliation(s)
- Maud Combier
- SVQV, Université de Strasbourg, INRA, Colmar, France
| | - Edouard Evangelisti
- University of Cambridge, Sainsbury Laboratory (SLCU), Cambridge, United Kingdom
| | | | - David Rengel
- LIPM Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Ludovic Legrand
- LIPM Laboratoire des Interactions Plantes-Microorganismes, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Liron Shenhav
- University of Cambridge, Sainsbury Laboratory (SLCU), Cambridge, United Kingdom
| | | | - Sebastian Schornack
- University of Cambridge, Sainsbury Laboratory (SLCU), Cambridge, United Kingdom
| | - Pere Mestre
- SVQV, Université de Strasbourg, INRA, Colmar, France
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18
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Dussert Y, Mazet ID, Couture C, Gouzy J, Piron MC, Kuchly C, Bouchez O, Rispe C, Mestre P, Delmotte F. A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes. Genome Biol Evol 2019; 11:954-969. [PMID: 30847481 PMCID: PMC6660063 DOI: 10.1093/gbe/evz048] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant–pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
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Affiliation(s)
- Yann Dussert
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | | | - Carole Couture
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Jérôme Gouzy
- LIPM, INRA, Université de Toulouse, CNRS, Castanet-Tolosan, France
| | | | - Claire Kuchly
- US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France
| | | | | | - Pere Mestre
- SVQV, INRA, Université de Strasbourg, Colmar, France
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19
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Kandel SL, Mou B, Shishkoff N, Shi A, Subbarao KV, Klosterman SJ. Spinach Downy Mildew: Advances in Our Understanding of the Disease Cycle and Prospects for Disease Management. PLANT DISEASE 2019; 103:791-803. [PMID: 30939071 DOI: 10.1094/pdis-10-18-1720-fe] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildew on spinach is caused by Peronospora effusa, an oomycete pathogen that poses a challenge to spinach production worldwide, especially in organic production. Following infection, P. effusa produces abundant amounts of asexual sporangia. Sporangia become windborne and initiate new infections locally or distantly, leading to widespread epidemics. Oospores produced from the union of opposite mating types have been observed within infected leaves and seeds and may remain viable for many years. Sexual reproduction increases the genetic diversity of P. effusa through sexual recombination, and thus, the movement of oospores on seed has likely fueled the rapid explosion of new pathotypes in different regions of the world over the past 20 years. This review summarizes recent advances in spinach downy mildew research, especially in light of the findings of oospores in contemporary commercial spinach seed lots as well as their germination. Knowledge of the role of the oospores and other aspects of the disease cycle can directly translate into new and effective disease management strategies.
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Affiliation(s)
- Shyam L Kandel
- 1 USDA-ARS Crop Improvement and Protection Research Unit, Salinas, CA 93905
| | - Beiquan Mou
- 1 USDA-ARS Crop Improvement and Protection Research Unit, Salinas, CA 93905
| | - Nina Shishkoff
- 2 USDA-ARS Foreign Disease Weed Science Research Unit, Frederick, MD 21702
| | - Ainong Shi
- 3 Department of Horticulture, University of Arkansas, Fayetteville, AR; and
| | - Krishna V Subbarao
- 4 Department of Plant Pathology, University of California-Davis, Salinas, CA
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20
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Dussert Y, Mazet ID, Couture C, Gouzy J, Piron MC, Kuchly C, Bouchez O, Rispe C, Mestre P, Delmotte F. A High-Quality Grapevine Downy Mildew Genome Assembly Reveals Rapidly Evolving and Lineage-Specific Putative Host Adaptation Genes. Genome Biol Evol 2019. [PMID: 30847481 DOI: 10.1101/350041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high contiguity (359 scaffolds for a N50 of 706.5 kb) due to a better resolution of repeat regions. This assembly presented a high level of gene completeness, recovering 1,592 genes encoding secreted proteins involved in plant-pathogen interactions. Plasmopara viticola had a two-speed genome architecture, with secreted protein-encoding genes preferentially located in gene-sparse, repeat-rich regions and evolving rapidly, as indicated by pairwise dN/dS values. We also used short reads to assemble the genome of Plasmopara muralis, a closely related species infecting grape ivy (Parthenocissus tricuspidata). The lineage-specific proteins identified by comparative genomics analysis included a large proportion of RxLR cytoplasmic effectors and, more generally, genes with high dN/dS values. We identified 270 candidate genes under positive selection, including several genes encoding transporters and components of the RNA machinery potentially involved in host specialization. Finally, the Pl. viticola genome assembly generated here will allow the development of robust population genomics approaches for investigating the mechanisms involved in adaptation to biotic and abiotic selective pressures in this species.
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Affiliation(s)
- Yann Dussert
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | | | - Carole Couture
- SAVE, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Jérôme Gouzy
- LIPM, INRA, Université de Toulouse, CNRS, Castanet-Tolosan, France
| | | | - Claire Kuchly
- US 1426 GeT-PlaGe, Genotoul, INRA, Castanet-Tolosan, France
| | | | | | - Pere Mestre
- SVQV, INRA, Université de Strasbourg, Colmar, France
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21
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Pecrix Y, Buendia L, Penouilh‐Suzette C, Maréchaux M, Legrand L, Bouchez O, Rengel D, Gouzy J, Cottret L, Vear F, Godiard L. Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:730-748. [PMID: 30422341 PMCID: PMC6849628 DOI: 10.1111/tpj.14157] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 10/31/2018] [Accepted: 11/06/2018] [Indexed: 05/20/2023]
Abstract
Over the last 40 years, new sunflower downy mildew isolates (Plasmopara halstedii) have overcome major gene resistances in sunflower, requiring the identification of additional and possibly more durable broad-spectrum resistances. Here, 354 RXLR effectors defined in silico from our new genomic data were classified in a network of 40 connected components sharing conserved protein domains. Among 205 RXLR effector genes encoding conserved proteins in 17 P. halstedii pathotypes of varying virulence, we selected 30 effectors that were expressed during plant infection as potentially essential genes to target broad-spectrum resistance in sunflower. The transient expression of the 30 core effectors in sunflower and in Nicotiana benthamiana leaves revealed a wide diversity of targeted subcellular compartments, including organelles not so far shown to be targeted by oomycete effectors such as chloroplasts and processing bodies. More than half of the 30 core effectors were able to suppress pattern-triggered immunity in N. benthamiana, and five of these induced hypersensitive responses (HR) in sunflower broad-spectrum resistant lines. HR triggered by PhRXLRC01 co-segregated with Pl22 resistance in F3 populations and both traits localized in 1.7 Mb on chromosome 13 of the sunflower genome. Pl22 resistance was physically mapped on the sunflower genome recently sequenced, unlike all the other downy mildew resistances published so far. PhRXLRC01 and Pl22 are proposed as an avirulence/resistance gene couple not previously described in sunflower. Core effector recognition is a successful strategy to accelerate broad-spectrum resistance gene identification in complex crop genomes such as sunflower.
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Affiliation(s)
- Yann Pecrix
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Luis Buendia
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Charlotte Penouilh‐Suzette
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Maude Maréchaux
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Ludovic Legrand
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Olivier Bouchez
- GeT‐PlaGeUS INRA 1426INRA AuzevilleF‐31326Castanet‐Tolosan CedexFrance
| | - David Rengel
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Jérôme Gouzy
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | - Ludovic Cottret
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
| | | | - Laurence Godiard
- LIPM Laboratoire des Interactions Plantes‐MicroorganismesUniversité de ToulouseINRACNRSF‐31326Castanet‐TolosanFrance
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22
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Fletcher K, Klosterman SJ, Derevnina L, Martin F, Bertier LD, Koike S, Reyes-Chin-Wo S, Mou B, Michelmore R. Comparative genomics of downy mildews reveals potential adaptations to biotrophy. BMC Genomics 2018; 19:851. [PMID: 30486780 PMCID: PMC6264045 DOI: 10.1186/s12864-018-5214-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/31/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. RESULTS We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. CONCLUSIONS We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven J. Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lida Derevnina
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Frank Martin
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lien D. Bertier
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven Koike
- UC Davis Cooperative Extension Monterey County, Salinas, CA 93901 USA
- Present Address: TriCal Diagnostics, Hollister, CA 95023 USA
| | - Sebastian Reyes-Chin-Wo
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Beiquan Mou
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, 95616 USA
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Bourret TB, Choudhury RA, Mehl HK, Blomquist CL, McRoberts N, Rizzo DM. Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora. PLoS One 2018. [PMID: 29529094 PMCID: PMC5846723 DOI: 10.1371/journal.pone.0192502] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the "subgeneric" clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.
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Affiliation(s)
- Tyler B. Bourret
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
- * E-mail:
| | - Robin A. Choudhury
- Plant Pathology Department, University of Florida, Gainesville, Florida, United States of America
| | - Heather K. Mehl
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
| | - Cheryl L. Blomquist
- California Department of Food and Agriculture, Sacramento, California, United States of America
| | - Neil McRoberts
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
| | - David M. Rizzo
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
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Crandall SG, Rahman A, Quesada-Ocampo LM, Martin FN, Bilodeau GJ, Miles TD. Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges. PLANT DISEASE 2018; 102:265-275. [PMID: 30673522 DOI: 10.1094/pdis-09-17-1455-fe] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States' economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection.
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Affiliation(s)
- Sharifa G Crandall
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
| | - Alamgir Rahman
- North Carolina State University, Department of Plant Pathology, Raleigh, NC, 27695
| | | | - Frank N Martin
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA, 93905
| | | | - Timothy D Miles
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
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25
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A multi-omics study of the grapevine-downy mildew (Plasmopara viticola) pathosystem unveils a complex protein coding- and noncoding-based arms race during infection. Sci Rep 2018; 8:757. [PMID: 29335535 PMCID: PMC5768699 DOI: 10.1038/s41598-018-19158-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/15/2017] [Indexed: 12/16/2022] Open
Abstract
Fungicides are applied intensively to prevent downy mildew infections of grapevines (Vitis vinifera) with high impact on the environment. In order to develop alternative strategies we sequenced the genome of the oomycete pathogen Plasmopara viticola causing this disease. We show that it derives from a Phytophthora-like ancestor that switched to obligate biotrophy by losing genes involved in nitrogen metabolism and γ-Aminobutyric acid catabolism. By combining multiple omics approaches we characterized the pathosystem and identified a RxLR effector that trigger an immune response in the wild species V. riparia. This effector is an ideal marker to screen novel grape resistant varieties. Our study reveals an unprecedented bidirectional noncoding RNA-based mechanism that, in one direction might be fundamental for P. viticola to proficiently infect its host, and in the other might reduce the effects of the infection on the plant.
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26
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017. [PMID: 28417959 DOI: 10.1038/srep4655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture &Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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27
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017; 7:46553. [PMID: 28417959 PMCID: PMC5394536 DOI: 10.1038/srep46553] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/22/2017] [Indexed: 12/17/2022] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture & Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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28
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Delmas CEL, Dussert Y, Delière L, Couture C, Mazet ID, Richart Cervera S, Delmotte F. Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew. Mol Ecol 2017; 26:1936-1951. [DOI: 10.1111/mec.14006] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 01/30/2023]
Affiliation(s)
| | - Yann Dussert
- SAVE; Bordeaux Sciences Agro; INRA; 33140 Villenave d'Ornon France
| | - Laurent Delière
- SAVE; Bordeaux Sciences Agro; INRA; 33140 Villenave d'Ornon France
| | - Carole Couture
- SAVE; Bordeaux Sciences Agro; INRA; 33140 Villenave d'Ornon France
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