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Midgley KA, van den Berg N, Backer R, Swart V. Identification of Phytophthora cinnamomi CRN effectors and their roles in manipulating cell death during Persea americana infection. BMC Genomics 2024; 25:435. [PMID: 38698341 PMCID: PMC11064341 DOI: 10.1186/s12864-024-10358-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
The oomycete Phytophthora cinnamomi is a devastating plant pathogen with a notably broad host range. It is the causal agent of Phytophthora root rot (PRR), arguably the most economically important yield-limiting disease in Persea americana (avocado). Despite this, our understanding of the mechanisms P. cinnamomi employs to infect and successfully colonize avocado remains limited, particularly regarding the pathogen's ability to maintain its biotrophic and necrotrophic lifestyles during infection. The pathogen utilises a large repertoire of effector proteins which function in facilitating and establishing disease in susceptible host plants. Crinkling and necrosis effectors (CRN/Crinklers) are suspected to manipulate cell death to aid in maintenance of the pathogens biotrophic and necrotrophic lifestyles during different stages of infection. The current study identified 25 P. cinnamomi CRN effectors from the GKB4 genome using an HMM profile and assigned putative function to them as either cell death inducers or suppressors. Function was assigned to 10 PcinCRNs by analysing their RNA-seq expression profiles, relatedness to other functionally characterised Phytophthora CRNs and tertiary protein predictions. The full-length coding sequences for these PcinCRNs were confirmed by Sanger sequencing, six of which were found to have two divergent alleles. The presence of alleles indicates that the proteins encoded may perform contradicting functions in cell death manipulation, or function in different host plant species. Overall, this study provides a foundation for future research on P. cinnamomi infection and cell death manipulation mechanisms.
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Affiliation(s)
- Kayla A Midgley
- Hans Merensky Chair in Avocado Research, Department of Biochemistry; Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa
| | - Noëlani van den Berg
- Hans Merensky Chair in Avocado Research, Department of Biochemistry; Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa
| | - Robert Backer
- Hans Merensky Chair in Avocado Research, Department of Biochemistry; Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa
| | - Velushka Swart
- Hans Merensky Chair in Avocado Research, Department of Biochemistry; Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002, South Africa.
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2
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Fu Q, Yang J, Zhang K, Yin K, Xiang G, Yin X, Liu G, Xu Y. Plasmopara viticola effector PvCRN11 induces disease resistance to downy mildew in grapevine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:873-891. [PMID: 37950600 DOI: 10.1111/tpj.16534] [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: 07/27/2023] [Revised: 10/09/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
The downy mildew of grapevine (Vitis vinifera L.) is caused by Plasmopara viticola and is a major production problem in most grape-growing regions. The vast majority of effectors act as virulence factors and sabotage plant immunity. Here, we describe in detail one of the putative P. viticola Crinkler (CRN) effector genes, PvCRN11, which is highly transcribed during the infection stages in the downy mildew-susceptible grapevine V. vinifera cv. 'Pinot Noir' and V. vinifera cv. 'Thompson Seedless'. Cell death-inducing activity analyses reveal that PvCRN11 was able to induce spot cell death in the leaves of Nicotiana benthamiana but did not induce cell death in the leaves of the downy mildew-resistant V. riparia accession 'Beaumont' or of the downy mildew-susceptible 'Thompson Seedless'. Unexpectedly, stable expression of PvCRN11 inhibited the colonization of P. viticola in grapevine and Phytophthora capsici in Arabidopsis. Both transgenic grapevine and Arabidopsis constitutively expressing PvCRN11 promoted plant immunity. PvCRN11 is localized in the nucleus and cytoplasm, whereas PvCRN11-induced plant immunity is nucleus-independent. The purified protein PvCRN11Opt initiated significant plant immunity extracellularly, leading to enhanced accumulations of reactive oxygen species, activation of MAPK and up-regulation of the defense-related genes PR1 and PR2. Furthermore, PvCRN11Opt induces BAK1-dependent immunity in the apoplast, whereas PvCRN11 overexpression in intracellular induces BAK1-independent immunity. In conclusion, the PvCRN11 protein triggers resistance against P. viticola in grapevine, suggesting a potential for the use of PvCRN11 in grape production as a protectant against downy mildew.
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Affiliation(s)
- Qingqing Fu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Jing Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Kangzhuang Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Kaixin Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Gaoqing Xiang
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Xiao Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Guotian Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
| | - Yan Xu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi, P.R. China
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P.R. China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, P.R. China
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3
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Yang Z, Ai G, Lu X, Li Y, Miao J, Song W, Xu H, Liu J, Shen D, Dou D. Phytophthora sojae Effector PsCRN108 Targets CAMTA2 to Suppress HSP40 Expression and ROS Burst. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:15-24. [PMID: 37856777 DOI: 10.1094/mpmi-05-23-0058-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Oomycete pathogens secrete numerous crinkling and necrosis proteins (CRNs) to manipulate plant immunity and promote infection. However, the functional mechanism of CRN effectors is still poorly understood. Previous research has shown that the Phytophthora sojae effector PsCRN108 binds to the promoter of HSP90s and inhibits their expression, resulting in impaired plant immunity. In this study, we found that in addition to HSP90, PsCRN108 also suppressed other Heat Shock Protein (HSP) family genes, including HSP40. Interestingly, PsCRN108 inhibited the expression of NbHSP40 through its promoter, but did not directly bind to its promoter. Instead, PsCRN108 interacted with NbCAMTA2, a negative regulator of plant immunity. NbCAMTA2 was a negative regulator of NbHSP40 expression, and PsCRN108 could promote such inhibition activity of NbCAMTA2. Our results elucidated the multiple roles of PsCRN108 in the suppression of plant immunity and revealed a new mechanism by which the CRN effector hijacked transcription factors to affect immunity. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zitong Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Gan Ai
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Lu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yuke Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinlu Miao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wen Song
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Heng Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinding Liu
- Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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Quesada-Ocampo LM, Parada-Rojas CH, Hansen Z, Vogel G, Smart C, Hausbeck MK, Carmo RM, Huitema E, Naegele RP, Kousik CS, Tandy P, Lamour K. Phytophthora capsici: Recent Progress on Fundamental Biology and Disease Management 100 Years After Its Description. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:185-208. [PMID: 37257056 DOI: 10.1146/annurev-phyto-021622-103801] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Phytophthora capsici is a destructive oomycete pathogen of vegetable, ornamental, and tropical crops. First described by L.H. Leonian in 1922 as a pathogen of pepper in New Mexico, USA, P. capsici is now widespread in temperate and tropical countries alike. Phytophthora capsici is notorious for its capability to evade disease management strategies. High genetic diversity allows P. capsici populations to overcome fungicides and host resistance, the formation of oospores results in long-term persistence in soils, zoospore differentiation in the presence of water increases epidemic potential, and a broad host range maximizes economic losses and limits the effectiveness of crop rotation. The severity of disease caused by P. capsici and management challenges have led to numerous research efforts in the past 100 years. Here, we discuss recent findings regarding the biology, genetic diversity, disease management, fungicide resistance, host resistance, genomics, and effector biology of P. capsici.
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Affiliation(s)
- L M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, USA;
| | - C H Parada-Rojas
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, North Carolina, USA;
| | - Z Hansen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - G Vogel
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - C Smart
- School of Integrative Plant Science, Cornell University, Geneva, New York, USA
| | - M K Hausbeck
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - R M Carmo
- Division of Plant Sciences, University of Dundee, Dundee, United Kingdom
| | - E Huitema
- Division of Plant Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - R P Naegele
- Sugarbeet and Bean Research Unit, USDA, ARS, East Lansing, Michigan, USA
| | - C S Kousik
- US Vegetable Laboratory, USDA, ARS, Charleston, South Carolina, USA
| | - P Tandy
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - K Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
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5
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Kronmiller BA, Feau N, Shen D, Tabima JF, Ali SS, Armitage AD, Arredondo F, Bailey BA, Bollmann SR, Dale A, Harrison RJ, Hrywkiw K, Kasuga T, McDougal R, Nellist CF, Panda P, Tripathy S, Williams NM, Ye W, Wang Y, Hamelin RC, Grünwald NJ. Comparative Genomic Analysis of 31 Phytophthora Genomes Reveals Genome Plasticity and Horizontal Gene Transfer. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:26-46. [PMID: 36306437 DOI: 10.1094/mpmi-06-22-0133-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthora spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus Phytophthora. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Brent A Kronmiller
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Javier F Tabima
- Department of Biology, Clark University, Worcester, MA, U.S.A
| | - Shahin S Ali
- Sustainable Perennial Crops Laboratory, Northeast Area, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD, U.S.A
| | - Andrew D Armitage
- Natural Resources Institute, University of Greenwich, Chatham Maritime, U.K
| | - Felipe Arredondo
- Center for Quantitative Life Sciences, Oregon State University, Corvallis, OR, U.S.A
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, U.S.A
| | - Bryan A Bailey
- Sustainable Perennial Crops Laboratory, Northeast Area, USDA/ARS, Beltsville Agricultural Research Center-West, Beltsville, MD, U.S.A
| | - Stephanie R Bollmann
- Department of Integrative Biology, Oregon State University, Corvallis, OR, U.S.A
| | - Angela Dale
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
- SC-New Construction Materials, FPInnovations, Vancouver, V6T 1Z4, Canada
| | | | - Kelly Hrywkiw
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Davis, CA, U.S.A
| | - Rebecca McDougal
- Scion (Zealand Forest Research Institute), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua, New Zealand
| | | | - Preeti Panda
- The New Zealand Institute for Plant and Food Research Ltd, 74 Gerald Street, Lincoln, 7608, New Zealand
| | | | - Nari M Williams
- Scion (Zealand Forest Research Institute), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua, New Zealand
- Department of Pathogen Ecology and Control, Plant and Food Research, Private Bag 1401, Havelock North, New Zealand
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Département des sciences du bois et de la forêt, Faculté de Foresterie et Géographie, Université Laval, Québec, Canada
| | - Niklaus J Grünwald
- Horticultural Crop Research Unit, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, U.S.A
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Combier M, Evangelisti E, Piron MC, Schornack S, Mestre P. Candidate effector proteins from the oomycetes Plasmopara viticola and Phytophthora parasitica share similar predicted structures and induce cell death in Nicotiana species. PLoS One 2022; 17:e0278778. [PMID: 36459530 PMCID: PMC9718384 DOI: 10.1371/journal.pone.0278778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
Abstract
Effector proteins secreted by plant pathogens are essential for infection. Cytoplasmic RXLR effectors from oomycetes are characterized by the presence of RXLR and EER motifs that are frequently linked to WY- and/or LWY-domains, folds that are exclusive to this effector family. A related family of secreted candidate effector proteins, carrying WY-domains and the EER motif but lacking the canonical RXLR motif, has recently been described in oomycetes and is mainly found in downy mildew pathogens. Plasmopara viticola is an obligate biotrophic oomycete causing grapevine downy mildew. Here we describe a conserved Pl. viticola secreted candidate non-RXLR effector protein with cell death-inducing activity in Nicotiana species. A similar RXLR effector candidate from the broad host range oomycete pathogen Phytophthora parasitica also induces cell death in Nicotiana. Through comparative tertiary structure modelling, we reveal that both proteins are predicted to carry WY- and LWY-domains. Our work supports the presence of LWY-domains in non-RXLR effectors and suggests that effector candidates with similar domain architecture may exert similar activities.
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Affiliation(s)
- Maud Combier
- SVQV, UMR-A 1131, Université de Strasbourg, INRAE, Colmar, France
| | - Edouard Evangelisti
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
| | | | - Sebastian Schornack
- Sainsbury Laboratory (SLCU), University of Cambridge, Cambridge, United Kingdom
| | - Pere Mestre
- SVQV, UMR-A 1131, Université de Strasbourg, INRAE, Colmar, France
- * E-mail:
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Maillot G, Szadkowski E, Massire A, Brunaud V, Rigaill G, Caromel B, Chadœuf J, Bachellez A, Touhami N, Hein I, Lamour K, Balzergue S, Lefebvre V. Strive or thrive: Trends in Phytophthora capsici gene expression in partially resistant pepper. FRONTIERS IN PLANT SCIENCE 2022; 13:980587. [PMID: 36479518 PMCID: PMC9721114 DOI: 10.3389/fpls.2022.980587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Partial resistance in plants generally exerts a low selective pressure on pathogens, and thus ensuring their durability in agrosystems. However, little is known about the effect of partial resistance on the molecular mechanisms of pathogenicity, a knowledge that could advance plant breeding for sustainable plant health. Here we investigate the gene expression of Phytophthora capsici during infection of pepper (Capsicum annuum L.), where only partial genetic resistance is reported, using Illumina RNA-seq. Comparison of transcriptomes of P. capsici infecting susceptible and partially resistant peppers identified a small number of genes that redirected its own resources into lipid biosynthesis to subsist on partially resistant plants. The adapted and non-adapted isolates of P. capsici differed in expression of genes involved in nucleic acid synthesis and transporters. Transient ectopic expression of the RxLR effector genes CUST_2407 and CUST_16519 in pepper lines differing in resistance levels revealed specific host-isolate interactions that either triggered local necrotic lesions (hypersensitive response or HR) or elicited leave abscission (extreme resistance or ER), preventing the spread of the pathogen to healthy tissue. Although these effectors did not unequivocally explain the quantitative host resistance, our findings highlight the importance of plant genes limiting nutrient resources to select pepper cultivars with sustainable resistance to P. capsici.
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Affiliation(s)
| | | | | | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- LaMME, Université d'Evry Val d'Essonne, INRAE, Evry, France
| | | | | | | | | | - Ingo Hein
- Division Plant Sciences at the JHI, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- James Hutton Institute (JHI), Dundee, United Kingdom
| | - Kurt Lamour
- INRAE, GAFL, Montfavet, France
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
- Université Paris Cité, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette, France
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8
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Cox MP, Guo Y, Winter DJ, Sen D, Cauldron NC, Shiller J, Bradley EL, Ganley AR, Gerth ML, Lacey RF, McDougal RL, Panda P, Williams NM, Grunwald NJ, Mesarich CH, Bradshaw RE. Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families. Front Microbiol 2022; 13:1038444. [PMID: 36406440 PMCID: PMC9667082 DOI: 10.3389/fmicb.2022.1038444] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/11/2022] [Indexed: 01/25/2023] Open
Abstract
Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.
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Affiliation(s)
- Murray P. Cox
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Yanan Guo
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - David J. Winter
- Institute of Environmental Science and Research (ESR), Porirua, New Zealand
| | | | - Nicholas C. Cauldron
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | | | - Ellie L. Bradley
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Austen R. Ganley
- School of Biological Sciences and Digital Life Institute, University of Auckland, Auckland, New Zealand
| | - Monica L. Gerth
- Bioprotection Aotearoa, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Randy F. Lacey
- Bioprotection Aotearoa, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | | | | | | | - Niklaus J. Grunwald
- Horticultural Crops Disease and Pest Management Research Unit, USDA Agricultural Research Service, Corvallis, OR, United States
| | - Carl H. Mesarich
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Rosie E. Bradshaw
- Laboratory of Molecular Plant Pathology/Bioprotection Aotearoa, School of Natural Sciences, Massey University, Palmerston North, New Zealand,*Correspondence: Rosie E. Bradshaw,
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Vogel G, Giles G, Robbins KR, Gore MA, Smart CD. Quantitative Genetic Analysis of Interactions in the Pepper- Phytophthora capsici Pathosystem. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1018-1033. [PMID: 35914305 DOI: 10.1094/mpmi-12-21-0307-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of pepper cultivars with durable resistance to the oomycete Phytophthora capsici has been challenging due to differential interactions between the species that allow certain pathogen isolates to cause disease on otherwise resistant host genotypes. Currently, little is known about the pathogen genes involved in these interactions. To investigate the genetic basis of P. capsici virulence on individual pepper genotypes, we inoculated sixteen pepper accessions, representing commercial varieties, sources of resistance, and host differentials, with 117 isolates of P. capsici, for a total of 1,864 host-pathogen combinations. Analysis of disease outcomes revealed a significant effect of inter-species genotype-by-genotype interactions, although these interactions were quantitative rather than qualitative in scale. Isolates were classified into five pathogen subpopulations, as determined by their genotypes at over 60,000 single-nucleotide polymorphisms (SNPs). While absolute virulence levels on certain pepper accessions significantly differed between subpopulations, a multivariate phenotype reflecting relative virulence levels on certain pepper genotypes compared with others showed the strongest association with pathogen subpopulation. A genome-wide association study (GWAS) identified four pathogen loci significantly associated with virulence, two of which colocalized with putative RXLR effector genes and another with a polygalacturonase gene cluster. All four loci appeared to represent broad-spectrum virulence genes, as significant SNPs demonstrated consistent effects regardless of the host genotype tested. Host genotype-specific virulence variants in P. capsici may be difficult to map via GWAS with all but excessively large sample sizes, perhaps controlled by genes of small effect or by multiple allelic variants that have arisen independently. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Gregory Vogel
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Garrett Giles
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
| | - Kelly R Robbins
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, U.S.A
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, U.S.A
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10
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Liu S, Lenoir CJG, Amaro TMMM, Rodriguez PA, Huitema E, Bos JIB. Virulence strategies of an insect herbivore and oomycete plant pathogen converge on host E3 SUMO ligase SIZ1. THE NEW PHYTOLOGIST 2022; 235:1599-1614. [PMID: 35491752 PMCID: PMC9545238 DOI: 10.1111/nph.18184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Pathogens and pests secrete proteins (effectors) to interfere with plant immunity through modification of host target functions and disruption of immune signalling networks. The extent of convergence between pathogen and herbivorous insect virulence strategies is largely unexplored. We found that effectors from the oomycete pathogen, Phytophthora capsici, and the major aphid pest, Myzus persicae target the host immune regulator SIZ1, an E3 SUMO ligase. We used transient expression assays in Nicotiana benthamiana as well as Arabidopsis mutants to further characterize biological role of effector-SIZ1 interactions in planta. We show that the oomycete and aphid effector, which both contribute to virulence, feature different activities towards SIZ1. While M. persicae effector Mp64 increases SIZ1 protein levels in transient assays, P. capsici effector CRN83_152 enhances SIZ1-E3 SUMO ligase activity in vivo. SIZ1 contributes to host susceptibility to aphids and an oomycete pathogen. Knockout of SIZ1 in Arabidopsis decreased susceptibility to aphids, independent of SNC1, PAD4 and EDS1. Similarly SIZ1 knockdown in N. benthamiana led to reduced P. capsici infection. Our results suggest convergence of distinct pathogen and pest virulence strategies on an E3 SUMO ligase to enhance host susceptibility.
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Affiliation(s)
- Shan Liu
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Camille J. G. Lenoir
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Tiago M. M. M. Amaro
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | | | - Edgar Huitema
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Jorunn I. B. Bos
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
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11
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Gaibor-Vaca DG, García-Bazurto GL, Garcés-Fiallos FR. Mecanismos de defensa en plantas de Capsicum contra Phytophthora capsici. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.02.25] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Phytophthora capsici es un oomiceto causante de la pudrición de raíz, tallo, frutos y tizón foliar en varias especies vegetales de importancia agrícola, principalmente en Solanáceas del género Capsicum como ají y pimiento. Este fitopatógeno cosmopolita posee mecanismos de ataque que favorecen la rápida infección, colonización y reproducción en huéspedes susceptibles. Contrariamente, estos procesos son retrasados o evitados fuertemente por genotipos resistentes, debido principalmente a sus mecanismos de defensa. En esas interacciones incompatibles, las plantas resistentes de Capsicum reconocen el oomiceto y rápidamente expresan múltiples genes que posteriormente señalizan moléculas, que permiten la acumulación de compuestos fenólicos, fitoalexinas y especies reactivas de oxígeno, la actividad de diferentes enzimas, que pueden permitir incluso la formación de barreras físicas. Esta revisión aborda, expone y discute los avances y el progreso de las investigaciones a lo largo de los ultimos veinte años, referente a los mecanismos de defensa estructurales, bioquimicos y moleculares que utilizan las plantas resistentes de Capsicum para defenderse de P. capsici.
Palabras claves. ají, pimiento, pudrición de raíz y corona, tizón foliar, resistencia vegetal
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Affiliation(s)
- Darlyn G. Gaibor-Vaca
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Campus Experimental La Teodomira, Km 13, Lodana, Santa Ana, Manabí
| | - Génesis L García-Bazurto
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Campus Experimental La Teodomira, Km 13, Lodana, Santa Ana, Manabí
| | - Felipe R. Garcés-Fiallos
- Facultad de Ingeniería Agronómica, Universidad Técnica de Manabí, Campus Experimental La Teodomira, Km 13, Lodana, Santa Ana, Manabí
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12
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Mandal K, Dutta S, Upadhyay A, Panda A, Tripathy S. Comparative Genome Analysis Across 128 Phytophthora Isolates Reveal Species-Specific Microsatellite Distribution and Localized Evolution of Compartmentalized Genomes. Front Microbiol 2022; 13:806398. [PMID: 35369471 PMCID: PMC8967354 DOI: 10.3389/fmicb.2022.806398] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
Phytophthora sp. are invasive groups of pathogens belonging to class Oomycetes. In order to contain and control them, a deep knowledge of their biology and infection strategy is imperative. With the availability of large-scale sequencing data, it has been possible to look directly into their genetic material and understand the strategies adopted by them for becoming successful pathogens. Here, we have studied the genomes of 128 Phytophthora species available publicly with reasonable quality. Our analysis reveals that the simple sequence repeats (SSRs) of all Phytophthora sp. follow distinct isolate specific patterns. We further show that TG/CA dinucleotide repeats are far more abundant in Phytophthora sp. than other classes of repeats. In case of tri- and tetranucleotide SSRs also, TG/CA-containing motifs always dominate over others. The GC content of the SSRs are stable without much variation across the isolates of Phytophthora. Telomeric repeats of Phytophthora follow a pattern of (TTTAGGG)n or (TTAGGGT)n rather than the canonical (TTAGGG)n. RxLR (arginine-any amino acid-leucine-arginine) motifs containing effectors diverge rapidly in Phytophthora and do not show any core common group. The RxLR effectors of some Phytophthora isolates have a tendency to form clusters with RxLRs from other species than within the same species. An analysis of the flanking intergenic distance clearly indicates a two-speed genome organization for all the Phytophthora isolates. Apart from effectors and the transposons, a large number of other virulence genes such as carbohydrate-active enzymes (CAZymes), transcriptional regulators, signal transduction genes, ATP-binding cassette transporters (ABC), and ubiquitins are also present in the repeat-rich compartments. This indicates a rapid co-evolution of this powerful arsenal for successful pathogenicity. Whole genome duplication studies indicate that the pattern followed is more specific to a geographic location. To conclude, the large-scale genomic studies of Phytophthora have thrown light on their adaptive evolution, which is largely guided by the localized host-mediated selection pressure.
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Affiliation(s)
- Kajal Mandal
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Subhajeet Dutta
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Upadhyay
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Arijit Panda
- Department of Quantitative Health Science, Mayo Clinic, Rochester, MN, United States
| | - Sucheta Tripathy
- Computational Genomics Laboratory, Department of Structural Biology and Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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13
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Camborde L, Kiselev A, Pel MJC, Le Ru A, Jauneau A, Pouzet C, Dumas B, Gaulin E. An oomycete effector targets a plant RNA helicase involved in root development and defense. THE NEW PHYTOLOGIST 2022; 233:2232-2248. [PMID: 34913494 DOI: 10.1111/nph.17918] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Oomycete plant pathogens secrete effector proteins to promote disease. The damaging soilborne legume pathogen Aphanomyces euteiches harbors a specific repertoire of Small Secreted Protein effectors (AeSSPs), but their biological functions remain unknown. Here we characterize AeSSP1256. The function of AeSSP1256 is investigated by physiological and molecular characterization of Medicago truncatula roots expressing the effector. A potential protein target of AeSSP1256 is identified by yeast-two hybrid, co-immunoprecipitation, and fluorescent resonance energy transfer-fluorescence lifetime imaging microscopy (FRET-FLIM) assays, as well as promoter studies and mutant characterization. AeSSP1256 impairs M. truncatula root development and promotes pathogen infection. The effector is localized to the nucleoli rim, triggers nucleoli enlargement and downregulates expression of M. truncatula ribosome-related genes. AeSSP1256 interacts with a functional nucleocytoplasmic plant RNA helicase (MtRH10). AeSSP1256 relocates MtRH10 to the perinucleolar space and hinders its binding to plant RNA. MtRH10 is associated with ribosome-related genes, root development and defense. This work reveals that an oomycete effector targets a plant RNA helicase, possibly to trigger nucleolar stress and thereby promote pathogen infection.
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Affiliation(s)
- Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Andrei Kiselev
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Michiel J C Pel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Aurélie Le Ru
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Alain Jauneau
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Cécile Pouzet
- Plateforme d'Imagerie FRAIB-TRI, Université de Toulouse, CNRS, Auzeville-Tolosane, 31320, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, 31320, France
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14
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Furzer OJ, Cevik V, Fairhead S, Bailey K, Redkar A, Schudoma C, MacLean D, Holub EB, Jones JDG. An Improved Assembly of the Albugo candida Ac2V Genome Reveals the Expansion of the "CCG" Class of Effectors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:39-48. [PMID: 34546764 DOI: 10.1094/mpmi-04-21-0075-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Oliver J Furzer
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Volkan Cevik
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Kate Bailey
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Amey Redkar
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
- Department of Genetics, University of Córdoba, Córdoba 14071, Spain
| | - Christian Schudoma
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Eric B Holub
- University of Warwick, School of Life Sciences, Warwick Crop Centre, Wellesbourne, CV35 9EF, United Kingdom
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
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15
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Amoozadeh S, Johnston J, Meisrimler CN. Exploiting Structural Modelling Tools to Explore Host-Translocated Effector Proteins. Int J Mol Sci 2021; 22:12962. [PMID: 34884778 PMCID: PMC8657640 DOI: 10.3390/ijms222312962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Oomycete and fungal interactions with plants can be neutral, symbiotic or pathogenic with different impact on plant health and fitness. Both fungi and oomycetes can generate so-called effector proteins in order to successfully colonize the host plant. These proteins modify stress pathways, developmental processes and the innate immune system to the microbes' benefit, with a very different outcome for the plant. Investigating the biological and functional roles of effectors during plant-microbe interactions are accessible through bioinformatics and experimental approaches. The next generation protein modeling software RoseTTafold and AlphaFold2 have made significant progress in defining the 3D-structure of proteins by utilizing novel machine-learning algorithms using amino acid sequences as their only input. As these two methods rely on super computers, Google Colabfold alternatives have received significant attention, making the approaches more accessible to users. Here, we focus on current structural biology, sequence motif and domain knowledge of effector proteins from filamentous microbes and discuss the broader use of novel modelling strategies, namely AlphaFold2 and RoseTTafold, in the field of effector biology. Finally, we compare the original programs and their Colab versions to assess current strengths, ease of access, limitations and future applications.
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Affiliation(s)
- Sahel Amoozadeh
- School of Biological Science, University of Canterbury, Christchurch 8041, New Zealand;
| | - Jodie Johnston
- School of Physical and Chemical Sciences, University of Canterbury, Christchurch 8041, New Zealand;
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16
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Sun F, Sun S, Ye W, Duan C, Li B, Shan W, Zhu Z. Genome Sequence Data of Three Formae Speciales of Phytophthora vignae Causing Phytophthora Stem Rot on Different Vigna Species. PLANT DISEASE 2021; 105:3732-3735. [PMID: 34003033 DOI: 10.1094/pdis-11-20-2546-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytophthora vignae is an important oomycete pathogen causing Phytophthora stem rot on some Vigna spp. Three P. vignae isolates obtained from mung bean, adzuki bean, and cowpea exhibited high similarities in morphology and physiology but are specialized to infect different hosts. Here, we report the first de novo assembly of the draft genomes of three P. vignae isolates, which were performed using the PacBio SMRT Sequel platform. This study will extend the genomic resource available for the Phytophthora genus and provide a good foundation for further research on comparative genomics of Phytophthora spp. and interaction mechanism between hosts and pathogens.
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Affiliation(s)
- Feifei Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- College of Agronomy of Northwest Agriculture & Forestry University, Yangling, 712100, P. R. China
| | - Suli Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, P. R. China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Benjin Li
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, P. R. China
| | - Weixing Shan
- College of Agronomy of Northwest Agriculture & Forestry University, Yangling, 712100, P. R. China
| | - Zhendong Zhu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
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17
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Lee JH, Siddique MI, Kwon JK, Kang BC. Comparative Genomic Analysis Reveals Genetic Variation and Adaptive Evolution in the Pathogenicity-Related Genes of Phytophthora capsici. Front Microbiol 2021; 12:694136. [PMID: 34484141 PMCID: PMC8415033 DOI: 10.3389/fmicb.2021.694136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/20/2021] [Indexed: 12/03/2022] Open
Abstract
Phytophthora capsici is an oomycete pathogen responsible for damping off, root rot, fruit rot, and foliar blight in popular vegetable and legume crops. The existence of distinct aggressiveness levels and physiological races among the P. capsici population is a major constraint to developing resistant varieties of host crops. In the present study, we compared the genomes of three P. capsici isolates with different aggressiveness levels to reveal their genomic differences. We obtained genome sequences using short-read and long-read technologies, which yielded an average genome size of 76 Mbp comprising 514 contigs and 15,076 predicted genes. A comparative genomic analysis uncovered the signatures of accelerated evolution, gene family expansions in the pathogenicity-related genes among the three isolates. Resequencing two additional P. capsici isolates enabled the identification of average 1,023,437 SNPs, revealing the frequent accumulation of non-synonymous substitutions in pathogenicity-related gene families. Furthermore, pathogenicity-related gene families, cytoplasmic effectors and ATP binding cassette (ABC) transporters, showed expansion signals in the more aggressive isolates, with a greater number of non-synonymous SNPs. This genomic information explains the plasticity, difference in aggressiveness levels, and genome structural variation among the P. capsici isolates, providing insight into the genomic features related to the evolution and pathogenicity of this oomycete pathogen.
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Affiliation(s)
- Joung-Ho Lee
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Muhammad Irfan Siddique
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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18
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Nellist CF, Armitage AD, Bates HJ, Sobczyk MK, Luberti M, Lewis LA, Harrison RJ. Comparative Analysis of Host-Associated Variation in Phytophthora cactorum. Front Microbiol 2021; 12:679936. [PMID: 34276614 PMCID: PMC8285097 DOI: 10.3389/fmicb.2021.679936] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/21/2021] [Indexed: 12/30/2022] Open
Abstract
Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well-supported non-recombining clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologues in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.
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Affiliation(s)
| | - Andrew D. Armitage
- NIAB EMR, East Malling, United Kingdom
- National Resources Institute, University of Greenwich, Chatham, United Kingdom
| | - Helen J. Bates
- NIAB EMR, East Malling, United Kingdom
- NIAB, Cambridge, United Kingdom
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19
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High-Quality Reference Genome Sequence for the Oomycete Vegetable Pathogen Phytophthora capsici Strain LT1534. Microbiol Resour Announc 2021; 10:e0029521. [PMID: 34042486 PMCID: PMC8201633 DOI: 10.1128/mra.00295-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The oomycete Phytophthora capsici is a destructive pathogen of a wide range of vegetable hosts, especially peppers and cucurbits. A 94.17-Mb genome assembly was constructed using PacBio and Illumina data and annotated with support from transcriptome sequencing (RNA-Seq) reads.
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20
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Engelbrecht J, Duong TA, Prabhu SA, Seedat M, van den Berg N. Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential. BMC Genomics 2021; 22:302. [PMID: 33902447 PMCID: PMC8074420 DOI: 10.1186/s12864-021-07552-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/24/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops. There is currently a lack of a high-quality reference genome for this species despite several attempts that have been made towards sequencing its genome. The lack of a good quality genome sequence has been a setback for various genetic and genomic research to be done on this species. As a consequence, little is known regarding its genome characteristics and how these contribute to its pathogenicity and invasiveness. RESULTS In this work we generated a high-quality genome sequence and annotation for P. cinnamomi using a combination of Oxford Nanopore and Illumina sequencing technologies. The annotation was done using RNA-Seq data as supporting gene evidence. The final assembly consisted of 133 scaffolds, with an estimated genome size of 109.7 Mb, N50 of 1.18 Mb, and BUSCO completeness score of 97.5%. Genome partitioning analysis revealed that P. cinnamomi has a two-speed genome characteristic, similar to that of other oomycetes and fungal plant pathogens. In planta gene expression analysis revealed up-regulation of pathogenicity-related genes, suggesting their important roles during infection and host degradation. CONCLUSION This study has provided a high-quality reference genome and annotation for P. cinnamomi. This is among the best assembled genomes for any Phytophthora species assembled to date and thus resulted in improved identification and characterization of pathogenicity-related genes, some of which were undetected in previous versions of genome assemblies. Phytophthora cinnamomi harbours a large number of effector genes which are located in the gene-poor regions of the genome. This unique genomic partitioning provides P. cinnamomi with a high level of adaptability and could contribute to its success as a highly invasive species. Finally, the genome sequence, its annotation and the pathogenicity effectors identified in this study will serve as an important resource that will enable future studies to better understand and mitigate the impact of this important pathogen.
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Affiliation(s)
- Juanita Engelbrecht
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - S Ashok Prabhu
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Mohamed Seedat
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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21
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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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22
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Ai G, Xia Q, Song T, Li T, Zhu H, Peng H, Liu J, Fu X, Zhang M, Jing M, Xia A, Dou D. A Phytophthora sojae CRN effector mediates phosphorylation and degradation of plant aquaporin proteins to suppress host immune signaling. PLoS Pathog 2021; 17:e1009388. [PMID: 33711077 PMCID: PMC7990189 DOI: 10.1371/journal.ppat.1009388] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 03/24/2021] [Accepted: 02/15/2021] [Indexed: 12/31/2022] Open
Abstract
Phytophthora genomes encode a myriad of Crinkler (CRN) effectors, some of which contain putative kinase domains. Little is known about the host targets of these kinase-domain-containing CRNs and their infection-promoting mechanisms. Here, we report the host target and functional mechanism of a conserved kinase CRN effector named CRN78 in a notorious oomycete pathogen, Phytophthora sojae. CRN78 promotes Phytophthora capsici infection in Nicotiana benthamiana and enhances P. sojae virulence on the host plant Glycine max by inhibiting plant H2O2 accumulation and immunity-related gene expression. Further investigation reveals that CRN78 interacts with PIP2-family aquaporin proteins including NbPIP2;2 from N. benthamiana and GmPIP2-13 from soybean on the plant plasma membrane, and membrane localization is necessary for virulence of CRN78. Next, CRN78 promotes phosphorylation of NbPIP2;2 or GmPIP2-13 using its kinase domain in vivo, leading to their subsequent protein degradation in a 26S-dependent pathway. Our data also demonstrates that NbPIP2;2 acts as a H2O2 transporter to positively regulate plant immunity and reactive oxygen species (ROS) accumulation. Phylogenetic analysis suggests that the phosphorylation sites of PIP2 proteins and the kinase domains of CRN78 homologs are highly conserved among higher plants and oomycete pathogens, respectively. Therefore, this study elucidates a conserved and novel pathway used by effector proteins to inhibit host cellular defenses by targeting and hijacking phosphorylation of plant aquaporin proteins. CRN effectors are conserved in diverse pathogens of plants, animals, and insects, and highly expanded in Phytophthora species. Nevertheless, little is known about their functions, targets, and action mechanisms. Here, we characterized a kinase-domain-containing CRN effector (CRN78) in a notorious oomycete pathogen, P. sojae. CRN78 is a virulence-essential effector of P. sojae infection, and acts via suppression of plant H2O2 accumulation and defense gene expressions. We demonstrated that CRN78 might interact with plant PIP2-family aquaporin proteins, including N. benthamiana NbPIP2;2 and soybean GmPIP2-13, and regulate their phosphorylation, resulting in subsequent 26S-dependent protein degradation. Furthermore, we revealed that NbPIP2;2 was an apoplast-to-cytoplast H2O2 transporter and positively regulated plant immunity and ROS accumulation. Importantly, this phosphorylation may be highly conserved in many plant aquaporin proteins. Thus, this study identifies a virulence-related effector from P. sojae and a novel plant immunity-related gene, and reveals a detailed mechanism of effector-mediated phosphorylation and degradation of plant aquaporin proteins.
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Affiliation(s)
- Gan Ai
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Qingyue Xia
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Tianqiao Song
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- Institute of plant protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tianli Li
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hai Zhu
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, United States of America
| | - Jin Liu
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Xiaowei Fu
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ming Zhang
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Maofeng Jing
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ai Xia
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Key Laboratory of Plant Immunity, Academy for Advanced Interdisciplinary Studies, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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23
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Stam R, Motion GB, Martinez-Heredia V, Boevink PC, Huitema E. A Conserved Oomycete CRN Effector Targets Tomato TCP14-2 to Enhance Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:309-318. [PMID: 33258418 DOI: 10.1094/mpmi-06-20-0172-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytophthora spp. secrete vast arrays of effector molecules during infection to aid in host colonization. The crinkling and necrosis (CRN) protein family forms an extensive repertoire of candidate effectors that accumulate in the host nucleus to perturb processes required for immunity. Here, we show that CRN12_997 from Phytophthora capsici binds a TCP transcription factor, SlTCP14-2, to inhibit its immunity-associated activity against Phytophthora spp. Coimmunoprecipitation and bimolecular fluorescence complementation studies confirm a specific CRN12_997-SlTCP14-2 interaction in vivo. Coexpression of CRN12_997 specifically counteracts the TCP14-enhanced immunity phenotype, suggesting that CRN mediated perturbation of SlTCP14-2 function. We show that SlTCP14-2 associates with nuclear chromatin and that CRN12_997 diminishes SlTCP14-2 DNA binding. Collectively, our data support a model in which SlTCP14-2 associates with chromatin to enhance immunity. The interaction between CRN12_997 and SlTCP14-2 reduces DNA binding of the immune regulator. We propose that the modulation of SlTCP14-2 chromatin affinity, caused by CRN12-997, enhances susceptibility to P. capsici.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Remco Stam
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Graham B Motion
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Victor Martinez-Heredia
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Petra C Boevink
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Edgar Huitema
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
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24
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Phytopathogenic oomycetes: a review focusing on Phytophthora cinnamomi and biotechnological approaches. Mol Biol Rep 2020; 47:9179-9188. [PMID: 33068230 DOI: 10.1007/s11033-020-05911-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/10/2020] [Indexed: 10/23/2022]
Abstract
The Phytophthora genus is composed, mainly, of plant pathogens. This genus belongs to the Oomycete class, also known as "pseudo-fungi", within the Chromista Kingdom. Phytophthora spp. is highlighted due to the significant plant diseases that they cause, which represents some of the most economically and cultural losses, such as European chestnut ink disease, which is caused by P. cinnamomi. Currently, there have been four genome assemblies placed at the National Center for Biotechnology Information (NCBI), although the progress to understand and elucidate the pathogenic process of P. cinnamomi by its genome is progressing slowly. In this review paper, we aim to report and discuss the recent findings related to P. cinnamomi and its genomic information. Our research is based on paper databases that reported probable functions to P. cinnamomi proteins using sequence alignments, bioinformatics, and biotechnology approaches. Some of these proteins studied have functions that are proposed to be involved in the asexual sporulation and zoosporogenesis leading to the host colonization and consequently associated with pathogenicity. Some remarkable genes and proteins discussed here are related to oospore development, inhibition of sporangium formation and cleavage, inhibition of flagellar assembly, blockage of cyst germination and hyphal extension, and biofilm proteins. Lastly, we report some biotechnological approaches using biological control, studies with genome sequencing of P. cinnamomi resistant plants, and gene silencing through RNA interference (iRNA).
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25
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Dampened virulence and limited proliferation of Batrachochytrium salamandrivorans during subclinical infection of the troglobiont olm (Proteus anguinus). Sci Rep 2020; 10:16480. [PMID: 33020584 PMCID: PMC7536193 DOI: 10.1038/s41598-020-73800-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/15/2020] [Indexed: 11/25/2022] Open
Abstract
Emerging infections add to existing threats to the survival of amphibians worldwide. The olm (Proteus anguinus) is a vulnerable, troglobiont urodele species with a small European range and restricted to underground karstic systems. Population declines to emerging threats like the chytrid fungus Batrachochytrium salamandrivorans, are likely to go unnoticed due to inaccessibility of the species’ habitat. We here studied the interaction between olms and B. salamandrivorans. Experimental inoculation of olms resulted in low-level, asymptomatic but persistent infections, with limbs as predilection sites. The lack of exponential fungal growth in the olms’ epidermis correlated with limited fungal proliferation and dampened virulence gene expression after exposure to olm skin compounds. The olm is one of few western Palearctic urodeles that is tolerant to B. salamandrivorans infection and may act as a subterranean disease reservoir, yet costs of subclinical infection may compromise olm fitness on the long term.
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26
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Boevink PC, Birch PRJ, Turnbull D, Whisson SC. Devastating intimacy: the cell biology of plant-Phytophthora interactions. THE NEW PHYTOLOGIST 2020; 228:445-458. [PMID: 32394464 PMCID: PMC7540312 DOI: 10.1111/nph.16650] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/15/2020] [Indexed: 05/07/2023]
Abstract
An understanding of the cell biology underlying the burgeoning molecular genetic and genomic knowledge of oomycete pathogenicity is essential to gain the full context of how these pathogens cause disease on plants. An intense research focus on secreted Phytophthora effector proteins, especially those containing a conserved N-terminal RXLR motif, has meant that most cell biological studies into Phytophthora diseases have focussed on the effectors and their host target proteins. While these effector studies have provided novel insights into effector secretion and host defence mechanisms, there remain many unanswered questions about fundamental processes involved in spore biology, host penetration and haustorium formation and function.
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Affiliation(s)
- Petra C. Boevink
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Paul R. J. Birch
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
- Division of Plant SciencesUniversity of DundeeErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Dionne Turnbull
- Division of Plant SciencesUniversity of DundeeErrol RoadInvergowrieDundeeDD2 5DAUK
| | - Stephen C. Whisson
- Cell and Molecular SciencesJames Hutton InstituteErrol RoadInvergowrieDundeeDD2 5DAUK
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27
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Zhao S, Shang X, Bi W, Yu X, Liu D, Kang Z, Wang X, Wang X. Genome-Wide Identification of Effector Candidates With Conserved Motifs From the Wheat Leaf Rust Fungus Puccinia triticina. Front Microbiol 2020; 11:1188. [PMID: 32582112 PMCID: PMC7283542 DOI: 10.3389/fmicb.2020.01188] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
Rust fungi secrete various specialized effectors into host cells to manipulate the plant defense response. Conserved motifs, including RXLR, LFLAK-HVLVxxP (CRN), Y/F/WxC, CFEM, LysM, EAR, [SG]-P-C-[KR]-P, DPBB_1 (PNPi), and ToxA, have been identified in various oomycete and fungal effectors and are reported to be crucial for effector translocation or function. However, little is known about potential effectors containing any of these conserved motifs in the wheat leaf rust fungus (Puccinia triticina, Pt). In this study, sequencing was performed on RNA samples collected from the germ tubes (GT) of uredospores of an epidemic Pt pathotype PHTT(P) and Pt-infected leaves of a susceptible wheat cultivar "Chinese Spring" at 4, 6, and 8 days post-inoculation (dpi). The assembled transcriptome data were compared to the reference genome of "Pt 1-1 BBBD Race 1." A total of 17,976 genes, including 2,284 "novel" transcripts, were annotated. Among all these genes, we identified 3,149 upregulated genes upon Pt infection at all time points compared to GT, whereas 1,613 genes were more highly expressed in GT. A total of 464 secreted proteins were encoded by those upregulated genes, with 79 of them also predicted as possible effectors by EffectorP. Using hmmsearch and Regex, we identified 719 RXLR-like, 19 PNPi-like, 19 CRN-like, 138 Y/F/WxC, and 9 CFEM effector candidates from the deduced protein database including data based on the "Pt 1-1 BBBD Race 1" genome and the transcriptome data collected here. Four of the PNPi-like effector candidates with DPBB_1 conserved domain showed physical interactions with wheat NPR1 protein in yeast two-hybrid assay. Nine Y/F/WxC and seven CFEM effector candidates were transiently expressed in Nicotiana benthamiana. None of these effector candidates showed induction or suppression of cell death triggered by BAX protein, but the expression of one CFEM effector candidate, PTTG_08198, accelerated the progress of cell death and promoted the accumulation of reactive oxygen species (ROS). In conclusion, we profiled genes associated with the infection process of the Pt pathotype PHTT(P). The identified effector candidates with conserved motifs will help guide the investigation of virulent mechanisms of leaf rust fungus.
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Affiliation(s)
- Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Xiaofeng Shang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Weishuai Bi
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Xiumei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Daqun Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
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28
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Organize, Don't Agonize: Strategic Success of Phytophthora Species. Microorganisms 2020; 8:microorganisms8060917. [PMID: 32560346 PMCID: PMC7355776 DOI: 10.3390/microorganisms8060917] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
Plants are constantly challenged by various environmental stressors ranging from abiotic-sunlight, elevated temperatures, drought, and nutrient deficits, to biotic factors-microbial pathogens and insect pests. These not only affect the quality of harvest but also the yield, leading to substantial annual crop losses, worldwide. Although plants have a multi-layered immune system, phytopathogens such as species of the oomycete genus Phytophthora, can employ elaborate mechanisms to breach this defense. For the last two decades, researchers have focused on the co-evolution between Phytophthora and interacting hosts to decouple the mechanisms governing their molecular associations. This has provided a comprehensive understanding of the pathobiology of plants affected by oomycetes. Ultimately, this is important for the development of strategies to sustainably improve agricultural production. Therefore, this paper discusses the present-day state of knowledge of the strategic mode of operation employed by species of Phytophthora for successful infection. Specifically, we consider motility, attachment, and host cell wall degradation used by these pathogenic species to obtain nutrients from their host. Also discussed is an array of effector types from apoplastic (hydrolytic proteins, protease inhibitors, elicitins) to cytoplastic (RxLRs, named after Arginine-any amino acid-Leucine-Arginine consensus sequence and CRNs, for CRinkling and Necrosis), which upon liberation can subvert the immune response and promote diseases in plants.
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29
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Rojas-Estevez P, Urbina-Gómez DA, Ayala-Usma DA, Guayazan-Palacios N, Mideros MF, Bernal AJ, Cardenas M, Restrepo S. Effector Repertoire of Phytophthora betacei: In Search of Possible Virulence Factors Responsible for Its Host Specificity. Front Genet 2020; 11:579. [PMID: 32582295 PMCID: PMC7295944 DOI: 10.3389/fgene.2020.00579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/11/2020] [Indexed: 11/17/2022] Open
Abstract
Phytophthora betacei is an oomycete plant pathogen closely related to Phytophthora infestans. It infects tree tomato (Solanum betaceum) in northern South America, but is, under natural conditions, unable to infect potatoes or tomatoes, the main hosts of its sister species P. infestans. We characterized, and compared the effector repertoires of P. betacei and other Phytophthora species. To this end, we used in silico approaches to predict and describe the repertoire of secreted proteins in Phytophthora species and determine unique and core effectors. P. betacei has the largest proteome and secretome of all Phytophthora species evaluated. We identified between 450 and 1933 candidate effector genes in Phytophthora ramorum, Phytophthora sojae, Phytophthora cactorum, Phytophthora parasitica, Phytophthora palmivora, P. infestans, and P. betacei genomes. The P. betacei predicted secretome contains 5653 proteins, 1126 of which are apoplastic effectors and 807cytoplasmic effectors. Genes encoding cytoplasmic effectors include 791 genes with an RxLR domain (the largest number known so far in a Phytophthora species) and 16 with a Crinkler (CRN) domain. We detected homologs of previously described avirulence gene (Avr) present in Phytophthora spp., such as Avr1, Avr3b, Avr4, and Avrblb1, suggesting a high level of effector gene conservation among Phytophthora species. Nonetheless, fewer CRN effectors were obtained in P. betacei compared to all other Phytophthora species analyzed. The comparison between P. infestans and P. betacei effector profiles shows unique features in P. betacei that might be involved in pathogenesis and host preference. Indeed, 402 unique predicted effector genes were detected in P. betacei, corresponding to 197 apoplastic effector genes, 203 RxLR cytoplasmic effector genes, and 2 effector genes with CRN domain. This is the first characterization of the effector profile of P. betacei and the broadest comparison of predicted effector repertoires in the genus Phytophthora following a standardized prediction pipeline. The resultant P. betacei putative effector repertoire provides a reasonable set of proteins whose experimental validation could lead to understand the specific virulence factors responsible for the host specificity of this species.
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Affiliation(s)
- Paola Rojas-Estevez
- Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota
| | - David A Urbina-Gómez
- Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota
| | - David A Ayala-Usma
- Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota.,Laboratorio de Biología Computacional y Ecología Microbiana, Universidad de los Andes, Colombia, Bogota
| | - Natalia Guayazan-Palacios
- Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota
| | - Maria Fernanda Mideros
- Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota
| | - Adriana J Bernal
- Laboratorio de Interacciones Moleculares de Microorganismos en Agricultura, Universidad de los Andes, Colombia, Bogota
| | - Martha Cardenas
- Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología, Facultad de Ingeniería, Universidad de los Andes, Colombia, Bogota
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Cheng W, Jiang Y, Peng J, Guo J, Lin M, Jin C, Huang J, Tang W, Guan D, He S. The transcriptional reprograming and functional identification of WRKY family members in pepper's response to Phytophthora capsici infection. BMC PLANT BIOLOGY 2020; 20:256. [PMID: 32493221 PMCID: PMC7271409 DOI: 10.1186/s12870-020-02464-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/24/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Plant transcription factors (TFs) are key transcriptional regulators to manipulate the regulatory network of host immunity. However, the globally transcriptional reprogramming of plant TF families in response to pathogens, especially between the resistant and susceptible host plants, remains largely unknown. RESULTS Here, we performed time-series RNA-seq from a resistant pepper line CM334 and a susceptible pepper line EC01 upon challenged with Phytophthora capsici, and enrichment analysis indicated that WRKY family most significantly enriched in both CM334 and EC01. Interestingly, we found that nearly half of the WRKY family members were significantly up-regulated, whereas none of them were down-regulated in the two lines. These induced WRKY genes were greatly overlapped between CM334 and EC01. More strikingly, most of these induced WRKY genes were expressed in time-order patterns, and could be mainly divided into three subgroups: early response (3 h-up), mid response (24 h-up) and mid-late response (ML-up) genes. Moreover, it was found that the responses of these ML-up genes were several hours delayed in EC01. Furthermore, a total of 19 induced WRKY genes were selected for functional identification by virus-induced gene silencing. The result revealed that silencing of CaWRKY03-6, CaWRKY03-7, CaWRKY06-5 or CaWRKY10-4 significantly increase the susceptibility to P. capsici both in CM334 and EC01, indicating that they might contribute to pepper's basal defense against P. capsici; while silencing of CaWRKY08-4 and CaWRKY01-10 significantly impaired the disease resistance in CM334 but not in EC01, suggesting that these two WRKY genes are prominent modulators specifically in the resistant pepper plants. CONCLUSIONS These results considerably extend our understanding of WRKY gene family in pepper's resistance against P. capsici and provide potential applications for genetic improvement against phytophthora blight.
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Affiliation(s)
- Wei Cheng
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yan Jiang
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiangtao Peng
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jianwen Guo
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Menglan Lin
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chengting Jin
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jinfeng Huang
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Weiqi Tang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Deyi Guan
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Shuilin He
- National Education Minister Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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Thines M, Sharma R, Rodenburg SYA, Gogleva A, Judelson HS, Xia X, van den Hoogen J, Kitner M, Klein J, Neilen M, de Ridder D, Seidl MF, van den Ackerveken G, Govers F, Schornack S, Studholme DJ. The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:742-753. [PMID: 32237964 DOI: 10.1094/mpmi-07-19-0211-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here, we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was around 35.4 Mbp in length, with an N50 scaffold length of around 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of around 40.1 kbp. From the repeat-masked genome, 9,049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16% of the genome consists of repetitive sequences, and, based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of P. belbahrii. P. belbahrii has undergone a high degree of convergent evolution with other obligate parasitic pathogen groups, reflecting its obligate biotrophic lifestyle. Features of its secretome, signaling networks, and promoters are presented, and some patterns are hypothesized to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
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Affiliation(s)
- Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
- Integrative Fungal Research (IPF) and Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt (Main), Germany
| | - Rahul Sharma
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
- Integrative Fungal Research (IPF) and Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt (Main), Germany
| | - Sander Y A Rodenburg
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Anna Gogleva
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge, CB2 1LR, U.K
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521 U.S.A
| | - Xiaojuan Xia
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Johan van den Hoogen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Miloslav Kitner
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Joël Klein
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Manon Neilen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guido van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sebastian Schornack
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge, CB2 1LR, U.K
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
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McGowan J, O’Hanlon R, Owens RA, Fitzpatrick DA. Comparative Genomic and Proteomic Analyses of Three Widespread Phytophthora Species: Phytophthora chlamydospora, Phytophthora gonapodyides and Phytophthora pseudosyringae. Microorganisms 2020; 8:microorganisms8050653. [PMID: 32365808 PMCID: PMC7285336 DOI: 10.3390/microorganisms8050653] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
The Phytophthora genus includes some of the most devastating plant pathogens. Here we report draft genome sequences for three ubiquitous Phytophthora species—Phytophthora chlamydospora, Phytophthora gonapodyides, and Phytophthora pseudosyringae. Phytophthora pseudosyringae is an important forest pathogen that is abundant in Europe and North America. Phytophthora chlamydospora and Ph. gonapodyides are globally widespread species often associated with aquatic habitats. They are both regarded as opportunistic plant pathogens. The three sequenced genomes range in size from 45 Mb to 61 Mb. Similar to other oomycete species, tandem gene duplication appears to have played an important role in the expansion of effector arsenals. Comparative analysis of carbohydrate-active enzymes (CAZymes) across 44 oomycete genomes indicates that oomycete lifestyles may be linked to CAZyme repertoires. The mitochondrial genome sequence of each species was also determined, and their gene content and genome structure were compared. Using mass spectrometry, we characterised the extracellular proteome of each species and identified large numbers of proteins putatively involved in pathogenicity and osmotrophy. The mycelial proteome of each species was also characterised using mass spectrometry. In total, the expression of approximately 3000 genes per species was validated at the protein level. These genome resources will be valuable for future studies to understand the behaviour of these three widespread Phytophthora species.
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Affiliation(s)
- Jamie McGowan
- Department of Biology, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland; (R.A.O.); (D.A.F.)
- Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland
- Correspondence:
| | | | - Rebecca A. Owens
- Department of Biology, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland; (R.A.O.); (D.A.F.)
- Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland
| | - David A. Fitzpatrick
- Department of Biology, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland; (R.A.O.); (D.A.F.)
- Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, W23 F2H6 Co. Kildare, Ireland
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Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection. Genes (Basel) 2020; 11:genes11030261. [PMID: 32121150 PMCID: PMC7140796 DOI: 10.3390/genes11030261] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA (2017-2019). EFSA J 2020; 18:e05966. [PMID: 32874212 PMCID: PMC7448045 DOI: 10.2903/j.efsa.2020.5966] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The qualified presumption of safety (QPS) was developed to provide a safety pre-assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as 'qualifications'. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS-recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.
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La Spada F, Stracquadanio C, Riolo M, Pane A, Cacciola SO. Trichoderma Counteracts the Challenge of Phytophthora nicotianae Infections on Tomato by Modulating Plant Defense Mechanisms and the Expression of Crinkler, Necrosis-Inducing Phytophthora Protein 1, and Cellulose-Binding Elicitor Lectin Pathogenic Effectors. FRONTIERS IN PLANT SCIENCE 2020; 11:583539. [PMID: 33250912 PMCID: PMC7672019 DOI: 10.3389/fpls.2020.583539] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/06/2020] [Indexed: 05/04/2023]
Abstract
Decoding the mechanisms of plant defense against plant pathogens in a scenario where antagonistic activity and the plant growth-promoting effects of useful organisms intervene simultaneously is a new frontier of plant pathology. Here, we demonstrated that (i) two selected strains of Trichoderma asperellum and Trichoderma atroviride promoted tomato (Solanum lycopersicum) growth and reduced the severity of disease caused by the oomycete Phytophthora nicotianae and (ii) the genetic patterns of the components of the experimental model system tomato-Trichoderma spp.-P. nicotianae were differentially expressed. The beneficial effects in both the promotion of the growth of host plant and the biological control of the pathogen by two selected strains of different Trichoderma species were tested both in planta and in vitro. In both respects, T. atroviride demonstrated to be more effective than T. asperellum. Additionally, the simultaneous transcriptional reprogramming of several plant defense-related genes, pathogen effectors, and mycoparasitism-related genes in tomato, P. nicotianae, and Trichoderma spp., respectively, was evaluated during the three-component interaction. Results support the hypothesis that Trichoderma spp. elicit the expression of plant defense-related genes. As expected, a mycoparasitism-related gene was significantly up-regulated in Trichoderma-colonizing tomato plants infected by P. nicotianae. Finally, a marked up-regulation of the genes encoding two necrosis-inducing effectors was observed in P. nicotianae infecting tomato plants colonized by Trichoderma. In conclusion, this study is a contribution toward understanding the genetic pathways related with the ability of Trichoderma spp. to counteract the challenge of P. nicotianae infections on tomato. Additionally, the experiments revealed the beneficial effects in the tomato growth promotion of a new T. atroviride strain and its good antagonistic effectiveness in the biological control of root and crown rot incited by P. nicotianae, confirming that Trichoderma spp. can be a powerful tool in integrated pest management strategies of Phytophthora diseases of horticultural crops.
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Affiliation(s)
- Federico La Spada
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Claudia Stracquadanio
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
- Department of Agriculture, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
| | - Mario Riolo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
- Department of Agriculture, University Mediterranea of Reggio Calabria, Reggio Calabria, Italy
- Council for Agricultural Research and Agricultural Economy Analysis, Research Centre for Olive, Citrus and Tree Fruit-Rende CS (CREA-OFA), Rende, Italy
| | - Antonella Pane
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
- *Correspondence: Antonella Pane,
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
- Santa Olga Cacciola,
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Wu W, Nemri A, Blackman LM, Catanzariti AM, Sperschneider J, Lawrence GJ, Dodds PN, Jones DA, Hardham AR. Flax rust infection transcriptomics reveals a transcriptional profile that may be indicative for rust Avr genes. PLoS One 2019; 14:e0226106. [PMID: 31830116 PMCID: PMC6907798 DOI: 10.1371/journal.pone.0226106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 11/19/2019] [Indexed: 01/04/2023] Open
Abstract
Secreted effectors of fungal pathogens are essential elements for disease development. However, lack of sequence conservation among identified effectors has long been a problem for predicting effector complements in fungi. Here we have explored the expression characteristics of avirulence (Avr) genes and candidate effectors of the flax rust fungus, Melampsora lini. We performed transcriptome sequencing and real-time quantitative PCR (qPCR) on RNA extracted from ungerminated spores, germinated spores, isolated haustoria and flax seedlings inoculated with M. lini isolate CH5 during plant infection. Genes encoding two categories of M. lini proteins, namely Avr proteins and plant cell wall degrading enzymes (CWDEs), were investigated in detail. Analysis of the expression profiles of 623 genes encoding predicted secreted proteins in the M. lini transcriptome shows that the six known Avr genes (i.e. AvrM (avrM), AvrM14, AvrL2, AvrL567, AvrP123 (AvrP) and AvrP4) fall within a group of 64 similarly expressed genes that are induced in planta and show a peak of expression early in infection with a subsequent decline towards sporulation. Other genes within this group include two paralogues of AvrL2, an AvrL567 virulence allele, and a number of genes encoding putative effector proteins. By contrast, M. lini genes encoding CWDEs fall into different expression clusters with their distribution often unrelated to their catalytic activity or substrate targets. These results suggest that synthesis of M. lini Avr proteins may be regulated in a coordinated fashion and that the expression profiling-based analysis has significant predictive power for the identification of candidate Avr genes.
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Affiliation(s)
- Wenjie Wu
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
- * E-mail:
| | | | - Leila M. Blackman
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Ann-Maree Catanzariti
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, the Australian National University, Canberra, Australia
| | | | | | - David A. Jones
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
| | - Adrienne R. Hardham
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, Australia
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Maximo HJ, Dalio RJD, Dias RO, Litholdo CG, Felizatti HL, Machado MA. PpCRN7 and PpCRN20 of Phythophthora parasitica regulate plant cell death leading to enhancement of host susceptibility. BMC PLANT BIOLOGY 2019; 19:544. [PMID: 31810451 PMCID: PMC6896422 DOI: 10.1186/s12870-019-2129-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/08/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Phytophthora species secrete cytoplasmic effectors from a family named Crinkler (CRN), which are characterised by the presence of conserved specific domains in the N- and C-terminal regions. P. parasitica causes disease in a wide range of host plants, however the role of CRN effectors in these interactions remains unclear. Here, we aimed to: (i) identify candidate CRN encoding genes in P. parasitica genomes; (ii) evaluate the transcriptional expression of PpCRN (Phytophthora parasitica Crinkler candidate) during the P. parasitica interaction with Citrus sunki (high susceptible) and Poncirus trifoliata (resistant); and (iii) functionally characterize two PpCRNs in the model plant Nicotiana benthamiana. RESULTS Our in silico analyses identified 80 putative PpCRN effectors in the genome of P. parasitica isolate 'IAC 01/95.1'. Transcriptional analysis revealed differential gene expression of 20 PpCRN candidates during the interaction with the susceptible Citrus sunki and the resistant Poncirus trifoliata. We have also found that P. parasitica is able to recognize different citrus hosts and accordingly modulates PpCRNs expression. Additionally, two PpCRN effectors, namely PpCRN7 and PpCRN20, were further characterized via transient gene expression in N. benthamiana leaves. The elicitin INF-1-induced Hypersensitivity Response (HR) was increased by an additive effect driven by PpCRN7 expression, whereas PpCRN20 expression suppressed HR response in N. benthamiana leaves. Despite contrasting functions related to HR, both effectors increased the susceptibility of plants to P. parasitica. CONCLUSIONS PpCRN7 and PpCRN20 have the ability to increase P. parasitica pathogenicity and may play important roles at different stages of infection. These PpCRN-associated mechanisms are now targets of biotechnological studies aiming to break pathogen's virulence and to promote plant resistance.
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Affiliation(s)
- Heros J. Maximo
- Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico (IAC), Cordeirópolis, SP Brazil
| | - Ronaldo J. D. Dalio
- Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico (IAC), Cordeirópolis, SP Brazil
| | - Renata O. Dias
- Instituto de Química, Universidade de São Paulo (USP), São Paulo, SP Brazil
| | - Celso G. Litholdo
- Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico (IAC), Cordeirópolis, SP Brazil
| | - Henrique L. Felizatti
- Instituto de Matemática, Física e Computação Científica, Universidade Estadual de Campinas (UNICAMP), Campinas, SP Brazil
| | - Marcos A. Machado
- Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira/Instituto Agronômico (IAC), Cordeirópolis, SP Brazil
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Cui C, Herlihy JH, Bombarely A, McDowell JM, Haak DC. Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1559-1563. [PMID: 31479390 DOI: 10.1094/mpmi-04-19-0103-ta] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Resolving complex plant pathogen genomes is important for identifying the genomic shifts associated with rapid adaptation to selective agents such as hosts and fungicides, yet assembling these genomes remains challenging and expensive. Phytophthora capsici is an important, globally distributed plant pathogen that exhibits widespread fungicide resistance and a broad host range. As with other pathogenic oomycetes, P. capsici has a complex life history and a complex genome. Here, we leverage Oxford Nanopore Technologies and existing short-read resources to rapidly generate a low-cost, improved assembly. We generated 10 Gbp from a single MinION flow cell resulting in >1.25 million reads with an N50 of 13 kb. The resulting assembly is 95.2 Mbp in 424 scaffolds with an N50 length of 313 kb. This assembly is approximately 30 Mbp bigger than the current reference genome of 64 Mbp. We confirmed this larger genome size using flow cytometry, with an estimated size of 110 Mbp. BUSCO analysis identified 97.4% complete orthologs (19.2% duplicated). Evolutionary analysis supports a recent whole-genome duplication in this group. Our work provides a blueprint for rapidly integrating benchtop long-read sequencing with existing short-read data, to dramatically improve assembly quality and integrity of complex genomes and offer novel insights into pathogen genome function and evolution.
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Affiliation(s)
- Chenming Cui
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - John H Herlihy
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Aureliano Bombarely
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - John M McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - David C Haak
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
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39
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Reyes-Tena A, Huguet-Tapia JC, Lamour KH, Goss EM, Rodríguez-Alvarado G, Vázquez-Marrufo G, Santillán-Mendoza R, Fernández-Pavía SP. Genome Sequence Data of Six Isolates of Phytophthora capsici from Mexico. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1267-1269. [PMID: 31425006 DOI: 10.1094/mpmi-01-19-0014-a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytophthora capsici is an oomycete plant pathogen with a wide host range. Worldwide, P. capsici is known for causing the principal disease of chili pepper crops. Our goal was to expand the available genome resources for this diverse pathogen by generating whole-genome sequences for six isolates of P. capsici from Mexico.
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Affiliation(s)
- Alfredo Reyes-Tena
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán, 58880, México
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - José C Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Kurt H Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, U.S.A
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, 32610, U.S.A
| | - Gerardo Rodríguez-Alvarado
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán, 58880, México
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, 58880, México
| | - Ricardo Santillán-Mendoza
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán, 58880, México
| | - Sylvia P Fernández-Pavía
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán, 58880, México
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40
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Herlihy J, Ludwig NR, van den Ackerveken G, McDowell JM. Oomycetes Used in Arabidopsis Research. THE ARABIDOPSIS BOOK 2019; 17:e0188. [PMID: 33149730 PMCID: PMC7592078 DOI: 10.1199/tab.0188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Arabidopsis plants in their natural environment are susceptible to infection by oomycete pathogens, in particular to downy mildew and white rust diseases. These naturally occurring infectious agents have imposed evolutionary pressures on Arabidopsis populations and are therefore highly relevant for the study of host-pathogen co-evolution. In addition, the study of oomycete diseases, including infections caused by several Phytophthora species, has led to many scientific discoveries on Arabidopsis immunity and disease. Herein, we describe the major oomycete species used for experiments on Arabidopsis, and how these pathosystems have been used to provide significant insights into mechanistic and evolutionary aspects of plant-oomycete interactions. We also highlight understudied aspects of plant-oomycete interactions, as well as translational approaches, that can be productively addressed using the reference pathosystems described in this article.
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Affiliation(s)
- John Herlihy
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Nora R. Ludwig
- Plant–Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Guido van den Ackerveken
- Plant–Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - John M. McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Chen XR, Zhang Y, Li HY, Zhang ZH, Sheng GL, Li YP, Xing YP, Huang SX, Tao H, Kuan T, Zhai Y, Ma W. The RXLR Effector PcAvh1 Is Required for Full Virulence of Phytophthora capsici. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:986-1000. [PMID: 30811314 DOI: 10.1094/mpmi-09-18-0251-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plant pathogens employ diverse secreted effector proteins to manipulate host physiology and defense in order to foster diseases. The destructive Phytophthora pathogens encode hundreds of cytoplasmic effectors, which are believed to function inside the plant cells. Many of these cytoplasmic effectors contain the conserved N-terminal RXLR motif. Understanding the virulence function of RXLR effectors will provide important knowledge of Phytophthora pathogenesis. Here, we report the characterization of RXLR effector PcAvh1 from the broad-host range pathogen Phytophthora capsici. Only expressed during infection, PcAvh1 is quickly induced at the early infection stages. CRISPR/Cas9-knockout of PcAvh1 in P. capsici severely impairs virulence while overexpression enhances disease development in Nicotiana benthamiana and bell pepper, demonstrating that PcAvh1 is an essential virulence factor. Ectopic expression of PcAvh1 induces cell death in N. benthamiana, tomato, and bell pepper. Using yeast two-hybrid screening, we found that PcAvh1 interacts with the scaffolding subunit of the protein phosphatase 2A (PP2Aa) in plant cells. Virus-induced gene silencing of PP2Aa in N. benthamiana attenuates resistance to P. capsici and results in dwarfism, suggesting that PP2Aa regulates plant immunity and growth. Collectively, these results suggest that PcAvh1 contributes to P. capsici infection, probably through its interaction with host PP2Aa.
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Affiliation(s)
- Xiao-Ren Chen
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
- 2Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Ye Zhang
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Hai-Yang Li
- 3College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, China
| | - Zi-Hui Zhang
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Gui-Lin Sheng
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Yan-Peng Li
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Yu-Ping Xing
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Shen-Xin Huang
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Hang Tao
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu Province 225009, China
| | - Tung Kuan
- 2Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Yi Zhai
- 2Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Wenbo Ma
- 2Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
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Malar C M, Yuzon JD, Das S, Das A, Panda A, Ghosh S, Tyler BM, Kasuga T, Tripathy S. Haplotype-Phased Genome Assembly of Virulent Phytophthora ramorum Isolate ND886 Facilitated by Long-Read Sequencing Reveals Effector Polymorphisms and Copy Number Variation. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1047-1060. [PMID: 30794480 DOI: 10.1094/mpmi-08-18-0222-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora ramorum is a destructive pathogen that causes sudden oak death disease. The genome sequence of P. ramorum isolate Pr102 was previously produced, using Sanger reads, and contained 12 Mb of gaps. However, isolate Pr102 had shown reduced aggressiveness and genome abnormalities. In order to produce an improved genome assembly for P. ramorum, we performed long-read sequencing of highly aggressive P. ramorum isolate CDFA1418886 (abbreviated as ND886). We generated a 60.5-Mb assembly of the ND886 genome using the Pacific Biosciences (PacBio) sequencing platform. The assembly includes 302 primary contigs (60.2 Mb) and nine unplaced contigs (265 kb). Additionally, we found a 'highly repetitive' component from the PacBio unassembled unmapped reads containing tandem repeats that are not part of the 60.5-Mb genome. The overall repeat content in the primary assembly was much higher than the Pr102 Sanger version (48 versus 29%), indicating that the long reads have captured repetitive regions effectively. The 302 primary contigs were phased into 345 haplotype blocks and 222,892 phased variants, of which the longest phased block was 1,513,201 bp with 7,265 phased variants. The improved phased assembly facilitated identification of 21 and 25 Crinkler effectors and 393 and 394 RXLR effector genes from two haplotypes. Of these, 24 and 25 RXLR effectors were newly predicted from haplotypes A and B, respectively. In addition, seven new paralogs of effector Avh207 were found in contig 54, not reported earlier. Comparison of the ND886 assembly with Pr102 V1 assembly suggests that several repeat-rich smaller scaffolds within the Pr102 V1 assembly were possibly misassembled; these regions are fully encompassed now in ND886 contigs. Our analysis further reveals that Pr102 is a heterokaryon with multiple nuclear types in the sequences corresponding to contig 10 of ND886 assembly.
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Affiliation(s)
- Mathu Malar C
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jennifer D Yuzon
- 3Department of Plant Pathology, University of California, Davis, CA, U.S.A
- 4USDA-ARS, Davis, CA, U.S.A
| | - Subhadeep Das
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhishek Das
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Arijit Panda
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Samrat Ghosh
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Brett M Tyler
- 5Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331-7303, U.S.A
| | - Takao Kasuga
- 3Department of Plant Pathology, University of California, Davis, CA, U.S.A
- 4USDA-ARS, Davis, CA, U.S.A
| | - Sucheta Tripathy
- 1Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
- 2Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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43
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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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44
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Fletcher K, Gil J, Bertier LD, Kenefick A, Wood KJ, Zhang L, Reyes-Chin-Wo S, Cavanaugh K, Tsuchida C, Wong J, Michelmore R. Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae. Nat Commun 2019; 10:2645. [PMID: 31201315 PMCID: PMC6570648 DOI: 10.1038/s41467-019-10550-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.
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Affiliation(s)
- Kyle Fletcher
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Juliana Gil
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, 95616, USA
| | - Lien D Bertier
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Aubrey Kenefick
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Kelsey J Wood
- Genome Center, University of California, Davis, CA, 95616, USA
- Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
| | - Lin Zhang
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Sebastian Reyes-Chin-Wo
- Genome Center, University of California, Davis, CA, 95616, USA
- Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
- Bayer Crop Science, 37437 CA-16, Woodland, CA, 95695, USA
| | - Keri Cavanaugh
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Cayla Tsuchida
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, 95616, USA
- Arcadia Biosciences, Davis, CA, 95616, USA
| | - Joan Wong
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
- Pacific Biosciences of California, Inc., Menlo Park, CA, 94025, USA
| | - Richard Michelmore
- Genome Center, University of California, Davis, CA, 95616, USA.
- Departments of Plant Sciences, Molecular and Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, CA, 95616, USA.
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45
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Thilliez GJA, Armstrong MR, Lim T, Baker K, Jouet A, Ward B, van Oosterhout C, Jones JDG, Huitema E, Birch PRJ, Hein I. Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes. THE NEW PHYTOLOGIST 2019; 221:1634-1648. [PMID: 30288743 PMCID: PMC6492278 DOI: 10.1111/nph.15441] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/13/2018] [Indexed: 05/11/2023]
Abstract
The oomycete pathogens Phytophthora infestans and P. capsici cause significant crop losses world-wide, threatening food security. In each case, pathogenicity factors, called RXLR effectors, contribute to virulence. Some RXLRs are perceived by resistance proteins to trigger host immunity, but our understanding of the demographic processes and adaptive evolution of pathogen virulence remains poor. Here, we describe PenSeq, a highly efficient enrichment sequencing approach for genes encoding pathogenicity determinants which, as shown for the infamous potato blight pathogen Phytophthora infestans, make up < 1% of the entire genome. PenSeq facilitates the characterization of allelic diversity in pathogen effectors, enabling evolutionary and population genomic analyses of Phytophthora species. Furthermore, PenSeq enables the massively parallel identification of presence/absence variations and sequence polymorphisms in key pathogen genes, which is a prerequisite for the efficient deployment of host resistance genes. PenSeq represents a cost-effective alternative to whole-genome sequencing and addresses crucial limitations of current plant pathogen population studies, which are often based on selectively neutral markers and consequently have limited utility in the analysis of adaptive evolution. The approach can be adapted to diverse microbes and pathogens.
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Affiliation(s)
- Gaetan J. A. Thilliez
- Cell and Molecular SciencesThe James Hutton InstituteErrol Road, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences at the James Hutton InstituteSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Miles R. Armstrong
- Cell and Molecular SciencesThe James Hutton InstituteErrol Road, InvergowrieDundeeDD2 5DAUK
| | - Tze‐Yin Lim
- Information and Computational SciencesThe James Hutton InstituteDundeeDD2 5DAUK
| | - Katie Baker
- Information and Computational SciencesThe James Hutton InstituteDundeeDD2 5DAUK
| | - Agathe Jouet
- The Sainsbury LaboratoryNorwich Research ParkNorwichNR4 7GJUK
| | - Ben Ward
- The Earlham InstituteNorwich Research ParkNorwichNR4 7UHUK
| | | | | | - Edgar Huitema
- Division of Plant Sciences at the James Hutton InstituteSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Paul R. J. Birch
- Cell and Molecular SciencesThe James Hutton InstituteErrol Road, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences at the James Hutton InstituteSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
| | - Ingo Hein
- Cell and Molecular SciencesThe James Hutton InstituteErrol Road, InvergowrieDundeeDD2 5DAUK
- Division of Plant Sciences at the James Hutton InstituteSchool of Life SciencesUniversity of DundeeDundeeDD2 5DAUK
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46
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Liu L, Xu L, Jia Q, Pan R, Oelmüller R, Zhang W, Wu C. Arms race: diverse effector proteins with conserved motifs. PLANT SIGNALING & BEHAVIOR 2019; 14:1557008. [PMID: 30621489 PMCID: PMC6351098 DOI: 10.1080/15592324.2018.1557008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Effector proteins play important roles in the infection by pathogenic oomycetes and fungi or the colonization by endophytic and mycorrhizal fungi. They are either translocated into the host plant cells via specific translocation mechanisms and function in the host's cytoplasm or nucleus, or they reside in the apoplast of the plant cells and act at the extracellular host-microbe interface. Many effector proteins possess conserved motifs (such as the RXLR, CRN, LysM, RGD, DELD, EAR, RYWT, Y/F/WXC or CFEM motifs) localized in their N- or C-terminal regions. Analysis of the functions of effector proteins, especially so-called "core effectors", is crucial for the understanding of pathogenicity/symbiosis mechanisms and plant defense strategies, and helps to develop breeding strategies for pathogen-resistant cultivars, and to increase crop yield and quality as well as abiotic stress resistance. This review summarizes current knowledge about these effector proteins with the conversed motifs and their involvement in pathogenic or mutualistic plant/fungal interactions.
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Affiliation(s)
- Liping Liu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Le Xu
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Qie Jia
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
| | - Rui Pan
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
| | - Ralf Oelmüller
- Plant Physiology, Matthias-Schleiden-Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou, China
- CONTACT Wenying Zhang Hubei Collaborative Innovation Center for Grain Industry/Research Center of Crop Stresses Resistance Technologies, Yangtze University, Jingzhou 434025, China; Chu Wu College of Horticulture & Gardening, Yangtze University, Jingzhou 434025, China
| | - Chu Wu
- College of Horticulture & Gardening, Yangtze University, Jingzhou, China
- Institute of Plant Ecology and Environmental Restoration, Yangtze University, Jingzhou, China
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47
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Stam R, Münsterkötter M, Pophaly SD, Fokkens L, Sghyer H, Güldener U, Hückelhoven R, Hess M. A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni. Genome Biol Evol 2018; 10:3243-3249. [PMID: 30371775 PMCID: PMC6301796 DOI: 10.1093/gbe/evy240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2018] [Indexed: 01/17/2023] Open
Abstract
Ramularia leaf spot has recently emerged as a major threat to barley production world-wide, causing 25% yield loss in many barley growing regions. Here, we provide a new reference genome of the causal agent, the Dothideomycete Ramularia collo-cygni. The assembly of 32 Mb consists of 78 scaffolds. We used RNA-seq to identify 11,622 genes of which 1,303 and 282 are coding for predicted secreted proteins and putative effectors respectively. The pathogen separated from its nearest sequenced relative, Zymoseptoria tritici ∼27 Ma. We calculated the divergence of the two species on protein level and see remarkably high synonymous and nonsynonymous divergence. Unlike in many other plant pathogens, the comparisons of transposable elements and gene distributions, show a very homogeneous genome for R. collo-cygni. We see no evidence for higher selective pressure on putative effectors or other secreted proteins and repetitive sequences are spread evenly across the scaffolds. These findings could be associated to the predominantly endophytic life-style of the pathogen. We hypothesize that R. collo-cygni only recently became pathogenic and that therefore its genome does not yet show the typical pathogen characteristics. Because of its high scaffold length and improved CDS annotations, our new reference sequence provides a valuable resource for the community for future comparative genomics and population genetics studies.
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Affiliation(s)
- Remco Stam
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Martin Münsterkötter
- Functional Genomics and Bioinformatics, Research Centre for Forestry and Wood Industry, University of Sopron, Hungary.,Institute of Bioinformatics and Systems Biology, Helmholtz Centre Munich, Germany
| | - Saurabh Dilip Pophaly
- Section of Population Genetics, School of Life Sciences Weihenstephan, Technische Universität München, Germany.,Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden and Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Germany
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Hind Sghyer
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Ulrich Güldener
- Department of Bioinformatics, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Michael Hess
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
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48
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Ahmed MB, Santos KCGD, Sanchez IB, Petre B, Lorrain C, Plourde MB, Duplessis S, Desgagné-Penix I, Germain H. A rust fungal effector binds plant DNA and modulates transcription. Sci Rep 2018; 8:14718. [PMID: 30283062 PMCID: PMC6170375 DOI: 10.1038/s41598-018-32825-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/21/2018] [Indexed: 02/08/2023] Open
Abstract
The basidiomycete Melampsora larici-populina causes poplar rust disease by invading leaf tissues and secreting effector proteins through specialized infection structures known as haustoria. The mechanisms by which rust effectors promote pathogen virulence are poorly understood. The present study characterized Mlp124478, a candidate effector of M. larici-populina. We used the models Arabidopsis thaliana and Nicotiana benthamiana to investigate the function of Mlp124478 in plant cells. We established that Mlp124478 accumulates in the nucleus and nucleolus, however its nucleolar accumulation is not required to promote growth of the oomycete pathogen Hyaloperonospora arabidopsidis. Stable constitutive expression of Mlp124478 in A. thaliana repressed the expression of genes involved in immune responses, and also altered leaf morphology by increasing the waviness of rosette leaves. Chip-PCR experiments showed that Mlp124478 associats'e with the TGA1a-binding DNA sequence. Our results suggest that Mlp124478 exerts a virulence activity and binds the TGA1a promoter to suppress genes induced in response to pathogen infection.
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Affiliation(s)
- Md Bulbul Ahmed
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Karen Cristine Gonçalves Dos Santos
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Ingrid Benerice Sanchez
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
- Department of Biotechnology and Engineering in Chemistry, Instituto Tecnológico y de Estudios Superiores de Monterrey, Campus Estado de México (ITESM CEM), Margarita Maza de Juárez, 52926, Cd, López Mateos, Mexico
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
- Université de Lorraine, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Faculté des Sciences et Technologies - Campus Aiguillettes, BP, 70239-54506, Vandoeuvre-lès-Nancy, France
| | - Cécile Lorrain
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
| | - Mélodie B Plourde
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada.
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada.
| | - Sébastien Duplessis
- INRA, UMR 1136 Interactions Arbres/Microorganismes, INRA/Université de Lorraine, Centre INRA Grand Est - Nancy, 54280, Champenoux, France
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada
| | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières (UQTR), Trois-Rivières, QC, G9A 5H7, Canada.
- Groupe de recherche en biologie végétale, UQTR, Trois-Rivières, QC, G9A 5H7, Canada.
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49
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Armitage AD, Lysøe E, Nellist CF, Lewis LA, Cano LM, Harrison RJ, Brurberg MB. Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum. PLoS One 2018; 13:e0202305. [PMID: 30278048 PMCID: PMC6168125 DOI: 10.1371/journal.pone.0202305] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 06/23/2018] [Indexed: 12/21/2022] Open
Abstract
The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.
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Affiliation(s)
| | - Erik Lysøe
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, Ås, Norway
| | | | | | - Liliana M. Cano
- University of Florida, UF/IFAS Indian River Research and Education Center, Fort Pierce, Florida, United States of America
- The Sainsbury Laboratory, Norwich, United Kingdom
| | | | - May B. Brurberg
- Norwegian Institute of Bioeconomy Research (NIBIO), Division of Biotechnology and Plant Health, Ås, Norway
- Norwegian University of Life Sciences (NMBU), Department of Plant Sciences, Ås, Norway
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50
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Voß S, Betz R, Heidt S, Corradi N, Requena N. RiCRN1, a Crinkler Effector From the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis, Functions in Arbuscule Development. Front Microbiol 2018; 9:2068. [PMID: 30233541 PMCID: PMC6131194 DOI: 10.3389/fmicb.2018.02068] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/13/2018] [Indexed: 01/10/2023] Open
Abstract
Arbuscular mycorrhizal (AM) symbiosis is one of the most prominent and beneficial plant–microbe interactions that facilitates mineral nutrition and confers tolerance to biotic and abiotic stresses. AM fungi colonize the root cortex and develop specialized structures called arbuscules where the nutrient exchange takes place. Arbuscule development is a highly controlled and coordinated process requiring the involvement of many plant proteins recruited at that interface. In contrast, much less is known about the fungal proteins involved in this process. Here, we have identified an AM fungal effector that participates in this developmental step of the symbiosis. RiCRN1 is a crinkler (CRN) effector that belongs to a subfamily of secreted CRN proteins from R. irregularis. CRNs have been so far only functionally characterized in pathogenic microbes and shown to participate in processes controlling plant cell death and immunity. RiCRN1 accumulates during symbiosis establishment parallel to MtPT4, the gene coding for an arbuscule-specific phosphate transporter. Expression in Nicotiana benthamiana leaves and in Medicago truncatula roots suggest that RiCRN1 is not involved in cell death processes. RiCRN1 dimerizes and localizes to nuclear bodies, suggesting that, similar to other CRNs, it functions in the plant nucleus. Downregulation of RiCRN1 using host-induced gene silencing led to an impairment of the symbiosis in M. truncatula and to a reduction of MtPT4, while ectopic expression of RiCRN1, surprisingly, led to a drastic reduction in arbuscule size that correlated with a decrease not only in MtPT4 but also in MtBCP1, a marker for initial stages of arbuscule development. Altogether, our results suggest that a tightly regulated expression in time and space of RiCRN1 is critical for symbiosis progression and for the proper initiation of arbuscule development.
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Affiliation(s)
- Stefanie Voß
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Ruben Betz
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Sven Heidt
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Nicolas Corradi
- Department of Biology, Canadian Institute for Advanced Research, University of Ottawa, Ottawa, ON, Canada
| | - Natalia Requena
- Molecular Phytopathology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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