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Cissé OH, Ma L, Kovacs JA. Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii. Microbiol Mol Biol Rev 2024:e0020222. [PMID: 38587383 DOI: 10.1128/mmbr.00202-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
SUMMARYEvery human being is presumed to be infected by the fungus Pneumocystis jirovecii at least once in his or her lifetime. This fungus belongs to a large group of species that appear to exclusively infect mammals, with P. jirovecii being the only one known to cause disease in humans. The mystery of P. jirovecii origin and speciation is just beginning to unravel. Here, we provide a review of the major steps of P. jirovecii evolution. The Pneumocystis genus likely originated from soil or plant-associated organisms during the period of Cretaceous ~165 million years ago and successfully shifted to mammals. The transition coincided with a substantial loss of genes, many of which are related to the synthesis of nutrients that can be scavenged from hosts or cell wall components that could be targeted by the mammalian immune system. Following the transition, the Pneumocystis genus cospeciated with mammals. Each species specialized at infecting its own host. Host specialization is presumably built at least partially upon surface glycoproteins, whose protogene was acquired prior to the genus formation. P. jirovecii appeared at ~65 million years ago, overlapping with the emergence of the first primates. P. jirovecii and its sister species P. macacae, which infects macaques nowadays, may have had overlapping host ranges in the distant past. Clues from molecular clocks suggest that P. jirovecii did not cospeciate with humans. Molecular evidence suggests that Pneumocystis speciation involved chromosomal rearrangements and the mounting of genetic barriers that inhibit gene flow among species.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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2
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Peng J, Wang X, Wang H, Li X, Zhang Q, Wang M, Yan J. Advances in understanding grapevine downy mildew: From pathogen infection to disease management. Mol Plant Pathol 2024; 25:e13401. [PMID: 37991155 PMCID: PMC10788597 DOI: 10.1111/mpp.13401] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/29/2023] [Indexed: 11/23/2023]
Abstract
Plasmopara viticola is geographically widespread in grapevine-growing regions. Grapevine downy mildew disease, caused by this biotrophic pathogen, leads to considerable yield losses in viticulture annually. Because of the great significance of grapevine production and wine quality, research on this disease has been widely performed since its emergence in the 19th century. Here, we review and discuss recent understanding of this pathogen from multiple aspects, including its infection cycle, disease symptoms, genome decoding, effector biology, and management and control strategies. We highlight the identification and characterization of effector proteins with their biological roles in host-pathogen interaction, with a focus on sustainable control methods against P. viticola, especially the use of biocontrol agents and environmentally friendly compounds.
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Affiliation(s)
- Junbo Peng
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Hui Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xinghong Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Qi Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Meng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North ChinaInstitute of Plant Protection, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
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Gómez-Pérez D, Schmid M, Chaudhry V, Hu Y, Velic A, Maček B, Ruhe J, Kemen A, Kemen E. Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria. New Phytol 2023; 239:2320-2334. [PMID: 37222268 DOI: 10.1111/nph.18995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/11/2023] [Indexed: 05/25/2023]
Abstract
Biotic and abiotic interactions shape natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein based, are not well understood. We hypothesize that released proteins with antimicrobial activity are a powerful and highly specific toolset to shape and defend plant niches. We have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to modulate the growth of bacteria through release of antimicrobial proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected wild Arabidopsis thaliana samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the apoplastic proteome of Albugo-colonized leaves combined with machine learning predictors enabled the selection of antimicrobial candidates for heterologous expression and study of their inhibitory function. We found for three candidate proteins selective antimicrobial activity against Gram-positive bacteria isolated from A. thaliana and demonstrate that these inhibited bacteria are precisely important for the stability of the community structure. We could ascribe the antibacterial activity of the candidates to intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins with antimicrobial activity under apoplastic conditions that therefore are potential biocontrol tools for targeted manipulation of the microbiome.
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Affiliation(s)
- Daniel Gómez-Pérez
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Monja Schmid
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Vasvi Chaudhry
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Yiheng Hu
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Ana Velic
- Department of Biology, Quantitative Proteomics Group, Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Boris Maček
- Department of Biology, Quantitative Proteomics Group, Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Jonas Ruhe
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ariane Kemen
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Eric Kemen
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
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Newman TE, Kim H, Khentry Y, Sohn KH, Derbyshire MC, Kamphuis LG. The broad host range pathogen Sclerotinia sclerotiorum produces multiple effector proteins that induce host cell death intracellularly. Mol Plant Pathol 2023; 24:866-881. [PMID: 37038612 PMCID: PMC10346375 DOI: 10.1111/mpp.13333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Sclerotinia sclerotiorum is a broad host range necrotrophic fungal pathogen, which causes disease on many economically important crop species. S. sclerotiorum has been shown to secrete small effector proteins to kill host cells and acquire nutrients. We set out to discover novel necrosis-inducing effectors and characterize their activity using transient expression in Nicotiana benthamiana leaves. Five intracellular necrosis-inducing effectors were identified with differing host subcellular localization patterns, which were named intracellular necrosis-inducing effector 1-5 (SsINE1-5). We show for the first time a broad host range pathogen effector, SsINE1, that uses an RxLR-like motif to enter host cells. Furthermore, we provide preliminary evidence that SsINE5 induces necrosis via an NLR protein. All five of the identified effectors are highly conserved in globally sourced S. sclerotiorum isolates. Taken together, these results advance our understanding of the virulence mechanisms employed by S. sclerotiorum and reveal potential avenues for enhancing genetic resistance to this damaging fungal pathogen.
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Affiliation(s)
- Toby E. Newman
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Haseong Kim
- Plant Immunity Research CenterSeoul National UniversitySeoul08826Republic of Korea
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Kee Hoon Sohn
- Plant Immunity Research CenterSeoul National UniversitySeoul08826Republic of Korea
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Republic of Korea
- Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoul08826Republic of Korea
| | - Mark C. Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
| | - Lars G. Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life SciencesCurtin UniversityBentleyWestern AustraliaAustralia
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5
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Rai P, Prasad L, Rai PK. Fungal effectors versus defense-related genes of B. juncea and the status of resistant transgenics against fungal pathogens. Front Plant Sci 2023; 14:1139009. [PMID: 37360735 PMCID: PMC10285668 DOI: 10.3389/fpls.2023.1139009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023]
Abstract
Oilseed brassica has become instrumental in securing global food and nutritional security. B. juncea, colloquially known as Indian mustard, is cultivated across tropics and subtropics including Indian subcontinent. The production of Indian mustard is severely hampered by fungal pathogens which necessitates human interventions. Chemicals are often resorted to as they are quick and effective, but due to their economic and ecological unsustainability, there is a need to explore their alternatives. The B. juncea-fungal pathosystem is quite diverse as it covers broad-host range necrotrophs (Sclerotinia sclerotiorum), narrow-host range necrotrophs (Alternaria brassicae and A. brassicicola) and biotrophic oomycetes (Albugo candida and Hyaloperonospora brassica). Plants ward off fungal pathogens through two-step resistance mechanism; PTI which involves recognition of elicitors and ETI where the resistance gene (R gene) interacts with the fungal effectors. The hormonal signalling is also found to play a vital role in defense as the JA/ET pathway is initiated at the time of necrotroph infection and SA pathway is induced when the biotrophs attack plants. The review discuss the prevalence of fungal pathogens of Indian mustard and the studies conducted on effectoromics. It covers both pathogenicity conferring genes and host-specific toxins (HSTs) that can be used for a variety of purposes such as identifying cognate R genes, understanding pathogenicity and virulence mechanisms, and establishing the phylogeny of fungal pathogens. It further encompasses the studies on identifying resistant sources and characterisation of R genes/quantitative trait loci and defense-related genes identified in Brassicaceae and unrelated species which, upon introgression or overexpression, confer resistance. Finally, the studies conducted on developing resistant transgenics in Brassicaceae have been covered in which chitinase and glucanase genes are mostly used. The knowledge gained from this review can further be used for imparting resistance against major fungal pathogens.
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Affiliation(s)
- Prajjwal Rai
- Division of Plant Pathology, Indian Agriculture Research Institute, New Delhi, India
| | - Laxman Prasad
- Division of Plant Pathology, Indian Agriculture Research Institute, New Delhi, India
| | - Pramod Kumar Rai
- Division of Plant Pathology, Directorate of Rapeseed-Mustard Research, Bharatpur, India
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6
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Nirwan S, Sharma AK, Tripathi RM, Pati AM, Shrivastava N. Resistance strategies for defense against Albugo candida causing white rust disease. Microbiol Res 2023; 270:127317. [PMID: 36805163 DOI: 10.1016/j.micres.2023.127317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/12/2022] [Accepted: 02/01/2023] [Indexed: 02/11/2023]
Abstract
Albugo candida, the causal organism of white rust, is an oomycete obligate pathogen infecting crops of Brassicaceae family occurred on aerial part, including vegetable and oilseed crops at all growth stages. The disease expression is characterized by local infection appearing on the abaxial region developing white or creamy yellow blister (sori) on leaves and systemic infections cause hypertrophy and hyperplasia leading to stag-head of reproductive organ. To overcome this problem, several disease management strategies like fungicide treatments were used in the field and disease-resistant varieties have also been developed using conventional and molecular breeding. Due to high variability among A. candida isolates, there is no single approach available to understand the diverse spectrum of disease symptoms. In absence of resistance sources against pathogen, repetitive cultivation of genetically-similar varieties locally tends to attract oomycete pathogen causing heavy yield losses. In the present review, a deep insight into the underlying role of the non-host resistance (NHR) defence mechanism available in plants, and the strategies to exploit available gene pools from plant species that are non-host to A. candida could serve as novel sources of resistance. This work summaries the current knowledge pertaining to the resistance sources available in non-host germ plasm, the understanding of defence mechanisms and the advance strategies covers molecular, biochemical and nature-based solutions in protecting Brassica crops from white rust disease.
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7
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Xing Q, Zhou X, Cao Y, Peng J, Zhang W, Wang X, Wu J, Li X, Yan J. The woody plant-degrading pathogen Lasiodiplodia theobromae effector LtCre1 targets the grapevine sugar-signaling protein VvRHIP1 to suppress host immunity. J Exp Bot 2023; 74:2768-2785. [PMID: 36788641 PMCID: PMC10112684 DOI: 10.1093/jxb/erad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/14/2023] [Indexed: 06/06/2023]
Abstract
Lasiodiplodia theobromae is a causal agent of Botryosphaeria dieback, which seriously threatens grapevine production worldwide. Plant pathogens secrete diverse effectors to suppress host immune responses and promote the progression of infection, but the mechanisms underlying the manipulation of host immunity by L. theobromae effectors are poorly understood. In this study, we characterized LtCre1, which encodes a L. theobromae effector that suppresses BAX-triggered cell death in Nicotiana benthamiana. RNAi-silencing and overexpression of LtCre1 in L. theobromae showed impaired and increased virulence, respectively, and ectopic expression in N. benthamiana increased susceptibility. These results suggest that LtCre1 is as an essential virulence factor for L. theobromae. Protein-protein interaction studies revealed that LtCre1 interacts with grapevine RGS1-HXK1-interacting protein 1 (VvRHIP1). Ectopic overexpression of VvRHIP1 in N. benthamiana reduced infection, suggesting that VvRHIP1 enhances plant immunity against L. theobromae. LtCre1 was found to disrupt the formation of the VvRHIP1-VvRGS1 complex and to participate in regulating the plant sugar-signaling pathway. Thus, our results suggest that L. theobromae LtCre1 targets the grapevine VvRHIP1 protein to manipulate the sugar-signaling pathway by disrupting the association of the VvRHIP1-VvRGS1 complex.
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Affiliation(s)
| | | | - Yang Cao
- Beijing Key Laboratory of Environment Friendly Management on Fruits Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Junbo Peng
- Beijing Key Laboratory of Environment Friendly Management on Fruits Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wei Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruits Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruits Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jiahong Wu
- Beijing Key Laboratory of Environment Friendly Management on Fruits Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xinghong Li
- Beijing Key Laboratory of Environment Friendly Management on Fruits Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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8
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Chatterjee A, Nirwan S, Mohapatra S, Sharma P, Agnihotri A, Shrivastava N. Biochemical aspects of pathogenic variability in white rust infected Indian mustard. Mycologia 2022; 114:757-768. [PMID: 35648633 DOI: 10.1080/00275514.2022.2060007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
White rust caused by Albugo candida, an oomycete pathogen, is a devastating disease of Brassica juncea (Indian mustard) worldwide. There is a need to screen virulent white rust isolates to challenge the developed white rust-resistant B. juncea cultivars to screen their resistance potential. The current study explores pathogenic and biochemical response of Indian mustard to white rust isolates collected from three different geographic locations of India. The observations refine our understanding of the disease severity in India. Disease progression and biochemical responses were studied in the cotyledonary as well as true leaf stage of the B. juncea cultivar Varuna at different time points. The biochemical findings highlight the fluctuation of significant biochemical parameters such as total proteins, sugars, and phenols, superoxide dismutase, and hydrogen peroxide during the A. candida infection in B. juncea.
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Affiliation(s)
- Anupriya Chatterjee
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Shradha Nirwan
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Swati Mohapatra
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Pankaj Sharma
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, 201303, India
| | - Abha Agnihotri
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
| | - Neeraj Shrivastava
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida 201303, India
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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. Mol Plant Microbe Interact 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Yuan XL, Zhang CS, Kong FY, Zhang ZF, Wang FL. Genome Analysis of Phytophthora nicotianae JM01 Provides Insights into Its Pathogenicity Mechanisms. Plants (Basel) 2021; 10:plants10081620. [PMID: 34451665 PMCID: PMC8400872 DOI: 10.3390/plants10081620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/01/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022]
Abstract
Phytophthora nicotianae is a widely distributed plant pathogen that can cause serious disease and cause significant economic losses to various crops, including tomatoes, tobacco, onions, and strawberries. To understand its pathogenic mechanisms and explore strategies for controlling diseases caused by this pathogen, we sequenced and analyzed the whole genome of Ph. nicotianae JM01. The Ph. nicotianae JM01 genome was assembled using a combination of approaches including shotgun sequencing, single-molecule sequencing, and the Hi-C technique. The assembled Ph. nicotianae JM01 genome is about 95.32 Mb, with contig and scaffold N50 54.23 kb and 113.15 kb, respectively. The average GC content of the whole-genome is about 49.02%, encoding 23,275 genes. In addition, we identified 19.15% of interspersed elements and 0.95% of tandem elements in the whole genome. A genome-wide phylogenetic tree indicated that Phytophthora diverged from Pythium approximately 156.32 Ma. Meanwhile, we found that 252 and 285 gene families showed expansion and contraction in Phytophthora when compared to gene families in Pythium. To determine the pathogenic mechanisms Ph. nicotianae JM01, we analyzed a suite of proteins involved in plant-pathogen interactions. The results revealed that gene duplication contributed to the expansion of Cell Wall Degrading Enzymes (CWDEs) such as glycoside hydrolases, and effectors such as Arg-Xaa-Leu-Arg (RXLR) effectors. In addition, transient expression was performed on Nicotiana benthamiana by infiltrating with Agrobacterium tumefaciens cells containing a cysteine-rich (SCR) protein. The results indicated that SCR can cause symptoms of hypersensitive response. Moreover, we also conducted comparative genome analysis among four Ph. nicotianae genomes. The completion of the Ph. nicotianae JM01 genome can not only help us understand its genomic characteristics, but also help us discover genes involved in infection and then help us understand its pathogenic mechanisms.
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Affiliation(s)
- Xiao-Long Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Cheng-Sheng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (C.-S.Z.); (F.-L.W.); Tel.: +86-532-88701035 (C.-S.Z. & F.-L.W.)
| | - Fan-Yu Kong
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zhong-Feng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Feng-Long Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (X.-L.Y.); (F.-Y.K.); (Z.-F.Z.)
- Special Crops Research Center of Chinese Academy of Agricultural Sciences, Qingdao 266101, China
- Correspondence: (C.-S.Z.); (F.-L.W.); Tel.: +86-532-88701035 (C.-S.Z. & F.-L.W.)
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11
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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. Mol Plant Microbe Interact 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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Anupriya C, Shradha N, Prasun B, Abha A, Pankaj S, Abdin MZ, Neeraj S. Genomic and Molecular Perspectives of Host-pathogen Interaction and Resistance Strategies against White Rust in Oilseed Mustard. Curr Genomics 2020; 21:179-193. [PMID: 33071612 PMCID: PMC7521032 DOI: 10.2174/1389202921999200508075410] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/25/2020] [Accepted: 03/14/2020] [Indexed: 11/29/2022] Open
Abstract
Oilseed brassicas stand as the second most valuable source of vegetable oil and the third most traded one across the globe. However, the yield can be severely affected by infections caused by phytopathogens. White rust is a major oomycete disease of oilseed brassicas resulting in up to 60% yield loss globally. So far, success in the development of oomycete resistant Brassicas through conventional breeding has been limited. Hence, there is an imperative need to blend conventional and frontier biotechnological means to breed for improved crop protection and yield. This review provides a deep insight into the white rust disease and explains the oomycete-plant molecular events with special reference to Albugo candida describing the role of effector molecules, A. candida secretome, and disease response mechanism along with nucleotide-binding leucine-rich repeat receptor (NLR) signaling. Based on these facts, we further discussed the recent progress and future scopes of genomic approaches to transfer white rust resistance in the susceptible varieties of oilseed brassicas, while elucidating the role of resistance and susceptibility genes. Novel genomic technologies have been widely used in crop sustainability by deploying resistance in the host. Enrichment of NLR repertoire, over-expression of R genes, silencing of avirulent and disease susceptibility genes through RNA interference and CRSPR-Cas are technologies which have been successfully applied against pathogen-resistance mechanism. The article provides new insight into Albugo and Brassica genomics which could be useful for producing high yielding and WR resistant oilseed cultivars across the globe.
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Affiliation(s)
- Chatterjee Anupriya
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Nirwan Shradha
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Bandyopadhyay Prasun
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Agnihotri Abha
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Sharma Pankaj
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Malik Zainul Abdin
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
| | - Shrivastava Neeraj
- 1Amity Institute of Microbial Technology, Amity University, Uttar Pradesh, Noida-201313, India; 2International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India; 3Centre for Agricultural Biotechnology, Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Noida-201313, India; 4Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida-201313, India; 5Department of Biotechnology, Jamia Hamdard University, New Delhi-110062, India
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13
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Neik TX, Amas J, Barbetti M, Edwards D, Batley J. Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era. Plants (Basel) 2020; 9:E1336. [PMID: 33050509 PMCID: PMC7599536 DOI: 10.3390/plants9101336] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.
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Affiliation(s)
- Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway 47500, Selangor, Malaysia;
| | - Junrey Amas
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Martin Barbetti
- School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
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14
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Ai G, Yang K, Ye W, Tian Y, Du Y, Zhu H, Li T, Xia Q, Shen D, Peng H, Jing M, Xia A, Dou D. Prediction and Characterization of RXLR Effectors in Pythium Species. Mol Plant Microbe Interact 2020; 33:1046-1058. [PMID: 32330072 DOI: 10.1094/mpmi-01-20-0010-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
RXLR effectors, a class of secreted proteins that are transferred into host cells to manipulate host immunity, have been reported to widely exist in oomycetes, including those from genera Phytophthora, Hyaloperonospora, Albugo, and Saprolegnia. However, in Pythium species, no RXLR effector has yet been characterized, and the origin and evolution of such virulent effectors are still unknown. Here, we developed a modified regular expression method for de novo identification of RXLRs and characterized 359 putative RXLR effectors in nine Pythium species. Phylogenetic analysis revealed that all oomycetous RXLRs formed a single superfamily, suggesting that they might have a common ancestor. RXLR effectors from Pythium and Phytophthora species exhibited similar sequence features, protein structures, and genome locations. In particular, there were significantly more RXLR proteins in the mosquito biological control agent P. guiyangense than in the other eight Pythium species, and P. guiyangense RXLRs might be the result of gene duplication and genome rearrangement events, as indicated by synteny analysis. Expression pattern analysis of RXLR-encoding genes in the plant pathogen P. ultimum detected transcripts of the majority of the predicted RXLR genes, with some RXLR effectors induced in infection stages and one RXLR showing necrosis-inducing activity. Furthermore, all predicted RXLR genes were cloned from two biocontrol agents, P. oligandrum and P. periplocum, and three of the RXLR genes were found to induce a defense response in Nicotiana benthamiana. Taken together, our findings represent the first evidence of RXLR effectors in Pythium species, providing valuable information on their evolutionary patterns and the mechanisms of their interactions with diverse hosts.
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Affiliation(s)
- Gan Ai
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Kun Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwu Ye
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuee Tian
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Protection, Henan University of Science and Technology, Luoyang 471000, China
| | - Yaxin Du
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai Zhu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianli Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingyue Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hao Peng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, U.S.A
| | - Maofeng Jing
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai Xia
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Daolong Dou
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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15
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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. Mol Plant Microbe Interact 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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Abstract
The oomycetes are a class of ubiquitous, filamentous microorganisms that include some of the biggest threats to global food security and natural ecosystems. Within the oomycete class are highly diverse species that infect a broad range of animals and plants. Some of the most destructive plant pathogens are oomycetes, such as Phytophthora infestans, the agent of potato late blight and the cause of the Irish famine. Recent years have seen a dramatic increase in the number of sequenced oomycete genomes. Here we review the latest developments in oomycete genomics and some of the important insights that have been gained. Coupled with proteomic and transcriptomic analyses, oomycete genome sequences have revealed tremendous insights into oomycete biology, evolution, genome organization, mechanisms of infection, and metabolism. We also present an updated phylogeny of the oomycete class using a phylogenomic approach based on the 65 oomycete genomes that are currently available.
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Affiliation(s)
- Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, County Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, County Kildare, Ireland.
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17
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Zhang Y, Fletcher K, Han R, Michelmore R, Yang R. Genome-Wide Analysis of Cyclophilin Proteins in 21 Oomycetes. Pathogens 2019; 9:E24. [PMID: 31888032 DOI: 10.3390/pathogens9010024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
Cyclophilins (CYPs), a highly-conserved family of proteins, belong to a subgroup of immunophilins. Ubiquitous in eukaryotes and prokaryotes, CYPs have peptidyl-prolyl cis–trans isomerase (PPIase) activity and have been implicated as virulence factors in plant pathogenesis by oomycetes. We identified 16 CYP orthogroups from 21 diverse oomycetes. Each species was found to encode 15 to 35 CYP genes. Three of these orthogroups contained proteins with signal peptides at the N-terminal end, suggesting a role in secretion. Multidomain analysis revealed five conserved motifs of the CYP domain of oomycetes shared with other eukaryotic PPIases. Expression analysis of CYP proteins in different asexual life stages of the hemibiotrophic Phytophthora infestans and the biotrophic Plasmopara halstedii demonstrated distinct expression profiles between life stages. In addition to providing detailed comparative information on the CYPs in multiple oomycetes, this study identified candidate CYP effectors that could be the foundation for future studies of virulence.
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18
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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 Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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Tabima JF, Grünwald NJ. effectR: An Expandable R Package to Predict Candidate RxLR and CRN Effectors in Oomycetes Using Motif Searches. Mol Plant Microbe Interact 2019; 32:1067-1076. [PMID: 30951442 DOI: 10.1094/mpmi-10-18-0279-ta] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Effectors are small, secreted proteins that facilitate infection of host plants by all major groups of plant pathogens. Effector protein identification in oomycetes relies on identification of open reading frames with certain amino acid motifs among additional minor criteria. To date, identification of effectors relies on custom scripts to identify motifs in candidate open reading frames. Here, we developed the R package effectR, which provides a convenient tool for rapid prediction of effectors in oomycete genomes, or with custom scripts for any genome, in a reproducible way. The effectR package relies on a combination of regular expressions statements and hidden Markov model approaches to predict candidate RxLR and crinkler effectors. Other custom motifs for novel effectors can easily be implemented and added to package updates. The effectR package has been validated with published oomycete genomes. This package provides a convenient tool for wet lab researchers interested in reproducible identification of candidate effectors in oomycete genomes.
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Affiliation(s)
- Javier F Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR 97330, U.S.A
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20
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Tabima JF, Grünwald NJ. effectR: An Expandable R Package to Predict Candidate RxLR and CRN Effectors in Oomycetes Using Motif Searches. Mol Plant Microbe Interact 2019; 32:1067-1076. [PMID: 30951442 DOI: 10.1101/398404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Effectors are small, secreted proteins that facilitate infection of host plants by all major groups of plant pathogens. Effector protein identification in oomycetes relies on identification of open reading frames with certain amino acid motifs among additional minor criteria. To date, identification of effectors relies on custom scripts to identify motifs in candidate open reading frames. Here, we developed the R package effectR, which provides a convenient tool for rapid prediction of effectors in oomycete genomes, or with custom scripts for any genome, in a reproducible way. The effectR package relies on a combination of regular expressions statements and hidden Markov model approaches to predict candidate RxLR and crinkler effectors. Other custom motifs for novel effectors can easily be implemented and added to package updates. The effectR package has been validated with published oomycete genomes. This package provides a convenient tool for wet lab researchers interested in reproducible identification of candidate effectors in oomycete genomes.
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Affiliation(s)
- Javier F Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis, OR 97330, U.S.A
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21
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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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22
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Abstract
Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLP) have an extremely broad taxonomic distribution; they occur in bacteria, fungi, and oomycetes. NLPs come in two forms, those that are cytotoxic to eudicot plants and those that are noncytotoxic. Cytotoxic NLPs bind to glycosyl inositol phosphoryl ceramide (GIPC) sphingolipids that are abundant in the outer leaflet of plant plasma membranes. Binding allows the NLP to become cytolytic in eudicots but not monocots. The function of noncytotoxic NLPs remains enigmatic, but the expansion of NLP genes in oomycete genomes suggests they are important. Several plant species have evolved the capacity to recognize NLPs as molecular patterns and trigger plant immunity, e.g., Arabidopsis thaliana detects nlp peptides via the receptor-like protein RLP23. In this review, we provide a historical perspective from discovery to understanding of molecular mechanisms and describe the latest developments in the NLP field to shed light on these fascinating microbial proteins.
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Affiliation(s)
- Michael F Seidl
- Laboratory of Phytopathology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Guido Van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands;
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Magray AR, Lone SA, Ganai BA, Ahmad F, Dar GJ, Dar JS, Rehman S. Comprehensive, classical and molecular characterization methods of Saprolegnia (Oomycota; Stramnipila), an important fungal pathogen of fish. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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25
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Jouet A, Saunders DGO, McMullan M, Ward B, Furzer O, Jupe F, Cevik V, Hein I, Thilliez GJA, Holub E, van Oosterhout C, Jones JDG. Albugo candida race diversity, ploidy and host-associated microbes revealed using DNA sequence capture on diseased plants in the field. New Phytol 2019; 221:1529-1543. [PMID: 30288750 DOI: 10.1111/nph.15417] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/20/2018] [Indexed: 05/28/2023]
Abstract
Physiological races of the oomycete Albugo candida are biotrophic pathogens of diverse plant species, primarily the Brassicaceae, and cause infections that suppress host immunity to other pathogens. However, A. candida race diversity and the consequences of host immunosuppression are poorly understood in the field. We report a method that enables sequencing of DNA of plant pathogens and plant-associated microbes directly from field samples (Pathogen Enrichment Sequencing: PenSeq). We apply this method to explore race diversity in A. candida and to detect A. candida-associated microbes in the field (91 A. candida-infected plants). We show with unprecedented resolution that each host plant species supports colonization by one of 17 distinct phylogenetic lineages, each with an unique repertoire of effector candidate alleles. These data reveal the crucial role of sexual and asexual reproduction, polyploidy and host domestication in A. candida specialization on distinct plant species. Our bait design also enabled phylogenetic assignment of DNA sequences from bacteria and fungi from plants in the field. This paper shows that targeted sequencing has a great potential for the study of pathogen populations while they are colonizing their hosts. This method could be applied to other microbes, especially to those that cannot be cultured.
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Affiliation(s)
- Agathe Jouet
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Mark McMullan
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Ben Ward
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- The Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Oliver Furzer
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- University of North Carolina, Chapel Hill, NC, 27599-2200, USA
| | - Florian Jupe
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA, 92037, USA
| | - Volkan Cevik
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Ingo Hein
- The James Hutton Institute, CMS, Dundee, DD2 5DA, UK
- Division of Plant Sciences at the James Hutton Institute, the University of Dundee, Dundee, DD2 5DA, UK
| | - Gaetan J A Thilliez
- The James Hutton Institute, CMS, Dundee, DD2 5DA, UK
- Quadram Institute Bioscience, Norwich Research Park, Colney Lane, NR4 7UH, Norwich, UK
| | - Eric Holub
- School of Life Sciences, Warwick Crop Centre, University of Warwick, Warwick, CV35 9EF, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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26
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McGowan J, Byrne KP, Fitzpatrick DA. Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). Genome Biol Evol 2019; 11:189-206. [PMID: 30535146 PMCID: PMC6330052 DOI: 10.1093/gbe/evy267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 01/01/2023] Open
Abstract
The oomycetes are a class of microscopic, filamentous eukaryotes within the stramenopiles–alveolates–rhizaria eukaryotic supergroup. They include some of the most destructive pathogens of animals and plants, such as Phytophthora infestans, the causative agent of late potato blight. Despite the threat they pose to worldwide food security and natural ecosystems, there is a lack of tools and databases available to study oomycete genetics and evolution. To this end, we have developed the Oomycete Gene Order Browser (OGOB), a curated database that facilitates comparative genomic and syntenic analyses of oomycete species. OGOB incorporates genomic data for 20 oomycete species including functional annotations and a number of bioinformatics tools. OGOB hosts a robust set of orthologous oomycete genes for evolutionary analyses. Here, we present the structure and function of OGOB as well as a number of comparative genomic analyses we have performed to better understand oomycete genome evolution. We analyze the extent of oomycete gene duplication and identify tandem gene duplication as a driving force of the expansion of secreted oomycete genes. We identify core genes that are present and microsyntenically conserved (termed syntenologs) in oomycete lineages and identify the degree of microsynteny between each pair of the 20 species housed in OGOB. Consistent with previous comparative synteny analyses between a small number of oomycete species, our results reveal an extensive degree of microsyntenic conservation amongst genes with housekeeping functions within the oomycetes. OGOB is available at https://ogob.ie.
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Affiliation(s)
- Jamie McGowan
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Co. Kildare, Ireland.,Human Health Research Institute, Maynooth University, Co. Kildare, Ireland
| | - Kevin P Byrne
- School of Medicine, UCD Conway Institute, University College Dublin, Ireland
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, Co. Kildare, Ireland.,Human Health Research Institute, Maynooth University, Co. Kildare, Ireland
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27
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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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28
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Bollmann SR, Press CM, Tyler BM, Grünwald NJ. Expansion and Divergence of Argonaute Genes in the Oomycete Genus Phytophthora. Front Microbiol 2018; 9:2841. [PMID: 30555430 PMCID: PMC6284064 DOI: 10.3389/fmicb.2018.02841] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/05/2018] [Indexed: 01/17/2023] Open
Abstract
Modulation of gene expression through RNA interference is well conserved in eukaryotes and is involved in many cellular processes. In the oomycete Phytophthora, research on the small RNA machinery and function has started to reveal potential roles in the pathogen, but much is still unknown. We examined Argonaute (AGO) homologs within oomycete genome sequences, especially among Phytophthora species, to gain a clearer understanding of the evolution of this well-conserved protein family. We identified AGO homologs across many representative oomycete and stramenopile species, and annotated representative homologs in P. sojae. Furthermore, we demonstrate variable transcript levels of all identified AGO homologs in comparison to previously identified Dicer-like (DCL) and RNA-dependent RNA polymerase (RDR) homologs. Our phylogenetic analysis further refines the relationship of the AGO homologs in oomycetes and identifies a conserved tandem duplication of AGO homologs in a subset of Phytophthora species.
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Affiliation(s)
- Stephanie R Bollmann
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Caroline M Press
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
| | - Brett M Tyler
- Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Niklaus J Grünwald
- Horticultural Crop Research Unit, Agricultural Research Service, United States Department of Agriculture, Corvallis, OR, United States
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29
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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: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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30
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Kijpornyongpan T, Mondo SJ, Barry K, Sandor L, Lee J, Lipzen A, Pangilinan J, LaButti K, Hainaut M, Henrissat B, Grigoriev IV, Spatafora JW, Aime MC. Broad Genomic Sampling Reveals a Smut Pathogenic Ancestry of the Fungal Clade Ustilaginomycotina. Mol Biol Evol 2018; 35:1840-1854. [DOI: 10.1093/molbev/msy072] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Laura Sandor
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Juna Lee
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | | | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN
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31
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Deb D, Mackey D, Opiyo SO, McDowell JM. Application of alignment-free bioinformatics methods to identify an oomycete protein with structural and functional similarity to the bacterial AvrE effector protein. PLoS One 2018; 13:e0195559. [PMID: 29641586 PMCID: PMC5895030 DOI: 10.1371/journal.pone.0195559] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/23/2018] [Indexed: 11/23/2022] Open
Abstract
Diverse plant pathogens export effector proteins to reprogram host cells. One of the most challenging goals in the molecular plant-microbe field is to functionally characterize the complex repertoires of effectors secreted by these pathogens. For bacterial pathogens, the predominant class of effectors is delivered to host cells by Type III secretion. For oomycetes, the predominant class of effectors is defined by a signal peptide that mediates secretion from the oomycete and a conserved RxLR motif. Downy mildew pathogens and Phytophthora species maintain hundreds of candidate RxLR effector genes in their genomes. Although no primary sequence similarity is evident between bacterial Type III effectors (T3Es) and oomycete RXLR effectors, some bacterial and oomycete effectors have convergently evolved to target the same host proteins. Such effectors might have evolved domains that are functionally similar but sequence-unrelated. We reasoned that alignment-free bioinformatics approaches could be useful to identify structural similarities between bacterial and oomycete effectors. To test this approach, we used partial least squares regression, alignment-free bioinformatics methods to identify effector proteins from the genome of the oomycete Hyaloperonospora arabidopsidis that are similar to the well-studied AvrE1 effector from Pseudomonas syringae. This approach identified five RxLR proteins with putative structural similarity to AvrE1. We focused on one, HaRxL23, because it is an experimentally validated effector and it is conserved between distantly related oomycetes. Several experiments indicate that HaRxL23 is functionally similar to AvrE1, including the ability to partially rescue an AvrE1 loss-of-function mutant. This study provides an example of how an alignment-free bioinformatics approach can identify functionally similar effector proteins in the absence of primary sequence similarity. This approach could be useful to identify effectors that have convergently evolved regardless of whether the shared host target is known.
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Affiliation(s)
- Devdutta Deb
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
| | - David Mackey
- Departments of Horticulture and Crop Science and Molecular Genetics, Ohio State University, Columbus, Ohio, United States of America
| | - Stephen O. Opiyo
- Molecular and Cellular Imaging Center-Columbus, Ohio Agricultural Research and Development Center, Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (SOO); (JMM)
| | - John M. McDowell
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, Virginia, United States of America
- * E-mail: (SOO); (JMM)
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32
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Dalio RJD, Herlihy J, Oliveira TS, McDowell JM, Machado M. Effector Biology in Focus: A Primer for Computational Prediction and Functional Characterization. Mol Plant Microbe Interact 2018; 31:22-33. [PMID: 29023190 DOI: 10.1094/mpmi-07-17-0174-fi] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant-pathogen interactions are controlled by a multilayered immune system, which is activated by pathogen recognition in the host. Pathogens secrete effector molecules to interfere with the immune recognition or signaling network and reprogram cell structure or metabolism. Understanding the effector repertoires of diverse pathogens will contribute to unraveling the molecular mechanism of virulence and developing sustainable disease-control strategies for crops and natural ecosystems. Effector functionality has been investigated extensively in only a small number of pathogen species. However, many more pathogen genomes are becoming available, and much can be learned from a broader view of effector biology in diverse pathosystems. The purpose of this review is to summarize methodology for computational prediction of protein effectors, functional characterization of effector proteins and their targets, and the use of effectors as probes to screen for new sources of host resistance. Although these techniques were generally developed in model pathosystems, many of the approaches are directly applicable for exploration and exploitation of effector biology in pathosystems that are less well studied. We hope to facilitate such exploration, which will broaden understanding of the mechanisms that underpin the biological diversity of plant-pathogen interactions, and maximize the impact of new approaches that leverage effector biology for disease control.
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Affiliation(s)
- Ronaldo J D Dalio
- 1 Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IA, Cordeirópolis-SP, Brazil; and
| | - John Herlihy
- 2 Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, 24061-0329, U.S.A
| | - Tiago S Oliveira
- 1 Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IA, Cordeirópolis-SP, Brazil; and
| | - John M McDowell
- 2 Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, 24061-0329, U.S.A
| | - Marcos Machado
- 1 Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IA, Cordeirópolis-SP, Brazil; and
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33
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Kobayashi M, Hiraka Y, Abe A, Yaegashi H, Natsume S, Kikuchi H, Takagi H, Saitoh H, Win J, Kamoun S, Terauchi R. Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews. BMC Genomics 2017; 18:897. [PMID: 29166857 PMCID: PMC5700566 DOI: 10.1186/s12864-017-4296-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/13/2017] [Indexed: 11/30/2022] Open
Abstract
Background Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches’ broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S. graminicola. Results Sequence reads were generated from S. graminicola using an Illumina sequencing platform and assembled de novo into a draft genome sequence comprising approximately 360 Mbp. Of this sequence, 73% comprised repetitive elements, and a total of 16,736 genes were predicted from the RNA-seq data. The predicted genes included those encoding effector-like proteins with high sequence similarity to those previously identified in other oomycete pathogens. Genes encoding jacalin-like lectin-domain-containing secreted proteins were enriched in S. graminicola compared to other oomycetes. Of a total of 1220 genes encoding putative secreted proteins, 91 significantly changed their expression levels during the infection of plant tissues compared to the sporangia and zoospore stages of the S. graminicola lifecycle. Conclusions We established the draft genome sequence of a downy mildew pathogen that infects Gramineae plants. Based on this sequence and our transcriptome analysis, we generated a catalog of in planta-induced candidate effector genes, providing a solid foundation from which to identify the effectors causing phyllody. Electronic supplementary material The online version of this article (10.1186/s12864-017-4296-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Yukie Hiraka
- Iwate Biotechnology Research Center, Iwate, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Iwate, Japan
| | | | | | | | | | - Hiromasa Saitoh
- Iwate Biotechnology Research Center, Iwate, Japan.,Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Joe Win
- The Sainsbury Laboratory, Norwich, UK
| | | | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Iwate, Japan. .,Kyoto University, Kyoto, Japan.
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34
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McGowan J, Fitzpatrick DA. Genomic, Network, and Phylogenetic Analysis of the Oomycete Effector Arsenal. mSphere 2017; 2:e00408-17. [PMID: 29202039 DOI: 10.1128/mSphere.00408-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023] Open
Abstract
The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available. The oomycetes are a class of microscopic, filamentous eukaryotes within the stramenopiles-alveolate-Rhizaria (SAR) supergroup and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. This study investigated the expansion and evolution of effectors in 37 oomycete species in 4 oomycete orders, including Albuginales, Peronosporales, Pythiales, and Saprolegniales species. Our results highlight the large expansions of effector protein families, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, in Phytophthora species. Species-specific expansions, including expansions of chitinases in Aphanomyces astaci and Pythium oligandrum, were detected. Novel effectors which may be involved in suppressing animal immune responses in Ap. astaci and Py. insidiosum were also identified. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located in a number of oomycete species. We also investigated the "RxLR" effector complement of all 37 species and, as expected, observed large expansions in Phytophthora species numbers. Our results provide in-depth sequence information on all putative RxLR effectors from all 37 species. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available. IMPORTANCE The oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely sequenced. Large expansions of effector protein families in Phytophthora species, including glycoside hydrolases, pectinases, and necrosis-inducing proteins, were observed. Species-specific expansions were detected, including chitinases in Aphanomyces astaci and Pythium oligandrum. Novel effectors which may be involved in suppressing animal immune responses were identified in Ap. astaci and Py. oligandrum. Type 2 necrosis-inducing proteins with an unusual phylogenetic history were also located. This work represents an up-to-date in silico catalogue of the effector arsenal of the oomycetes based on the 37 genomes currently available.
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Ascunce MS, Huguet-Tapia JC, Ortiz-Urquiza A, Keyhani NO, Braun EL, Goss EM. Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage. Mol Phylogenet Evol 2017. [DOI: 10.1016/j.ympev.2017.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Abstract
Fungi are among the dominant causal agents of plant diseases. To colonize plants and cause disease, pathogenic fungi use diverse strategies. Some fungi kill their hosts and feed on dead material (necrotrophs), while others colonize the living tissue (biotrophs). For successful invasion of plant organs, pathogenic development is tightly regulated and specialized infection structures are formed. To further colonize hosts and establish disease, fungal pathogens deploy a plethora of virulence factors. Depending on the infection strategy, virulence factors perform different functions. While basically all pathogens interfere with primary plant defense, necrotrophs secrete toxins to kill plant tissue. In contrast, biotrophs utilize effector molecules to suppress plant cell death and manipulate plant metabolism in favor of the pathogen. This article provides an overview of plant pathogenic fungal species and the strategies they use to cause disease.
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Abstract
The eukaryotic microbes called oomycetes include many important saprophytes and pathogens, with the latter exhibiting necrotrophy, biotrophy, or obligate biotrophy. Understanding oomycete metabolism is fundamental to understanding these lifestyles. Genome mining and biochemical studies have shown that oomycetes, which belong to the kingdom Stramenopila, secrete suites of carbohydrate- and protein-degrading enzymes adapted to their environmental niches and produce unusual lipids and energy storage compounds. Despite having limited secondary metabolism, many oomycetes make chemicals for communicating within their species or with their hosts. Horizontal and endosymbiotic gene transfer events have diversified oomycete metabolism, resulting in biochemical pathways that often depart from standard textbook descriptions by amalgamating enzymes from multiple sources. Gene fusions and duplications have further shaped the composition and expression of the enzymes. Current research is helping us learn how oomycetes interact with host and environment, understand eukaryotic diversity and evolution, and identify targets for drugs and crop protection chemicals.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
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Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture &Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017; 7:46553. [PMID: 28417959 PMCID: PMC5394536 DOI: 10.1038/srep46553] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/22/2017] [Indexed: 12/17/2022] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture & Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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McCarthy CGP, Fitzpatrick DA. Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes. mSphere 2017; 2:e00095-17. [PMID: 28435885 DOI: 10.1128/mSphere.00095-17] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 03/24/2017] [Indexed: 12/17/2022] Open
Abstract
The oomycetes are a class of eukaryotes and include ecologically significant animal and plant pathogens. Single-gene and multigene phylogenetic studies of individual oomycete genera and of members of the larger classes have resulted in conflicting conclusions concerning interspecies relationships among these species, particularly for the Phytophthora genus. The onset of next-generation sequencing techniques now means that a wealth of oomycete genomic data is available. For the first time, we have used genome-scale phylogenetic methods to resolve oomycete phylogenetic relationships. We used supertree methods to generate single-gene and multigene species phylogenies. Overall, our supertree analyses utilized phylogenetic data from 8,355 oomycete gene families. We have also complemented our analyses with superalignment phylogenies derived from 131 single-copy ubiquitous gene families. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and clades. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes. The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus. Genome-scale phylogenetic studies have successfully resolved many eukaryotic relationships by using supertree methods, which combine large numbers of potentially disparate trees to determine evolutionary relationships that cannot be inferred from individual phylogenies alone. With a sufficient amount of genomic data now available, we have undertaken the first whole-genome phylogenetic analysis of the oomycetes using data from 37 oomycete species and 6 SAR species. In our analysis, we used established supertree methods to generate phylogenies from 8,355 homologous oomycete and SAR gene families and have complemented those analyses with both phylogenomic network and concatenated supermatrix analyses. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and individual clades within the problematic Phytophthora genus. Support for the resolution of the inferred relationships between individual Phytophthora clades varies depending on the methodology used. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes. IMPORTANCE The oomycetes are a class of eukaryotes and include ecologically significant animal and plant pathogens. Single-gene and multigene phylogenetic studies of individual oomycete genera and of members of the larger classes have resulted in conflicting conclusions concerning interspecies relationships among these species, particularly for the Phytophthora genus. The onset of next-generation sequencing techniques now means that a wealth of oomycete genomic data is available. For the first time, we have used genome-scale phylogenetic methods to resolve oomycete phylogenetic relationships. We used supertree methods to generate single-gene and multigene species phylogenies. Overall, our supertree analyses utilized phylogenetic data from 8,355 oomycete gene families. We have also complemented our analyses with superalignment phylogenies derived from 131 single-copy ubiquitous gene families. Our results show that a genome-scale approach to oomycete phylogeny resolves oomycete classes and clades. Our analysis represents an important first step in large-scale phylogenomic analysis of the oomycetes.
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Lerksuthirat T, Sangcakul A, Lohnoo T, Yingyong W, Rujirawat T, Krajaejun T. Evolution of the Sterol Biosynthetic Pathway of Pythium insidiosum and Related Oomycetes Contributes to Antifungal Drug Resistance. Antimicrob Agents Chemother 2017; 61:e02352-16. [PMID: 28115356 DOI: 10.1128/AAC.02352-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/19/2017] [Indexed: 11/20/2022] Open
Abstract
Pythiosis is a life-threatening infectious disease caused by the oomycete Pythium insidiosum Direct exposure to Py. insidiosum zoospores can initiate infections of the eye, limb, gastrointestinal tract, or skin/subcutaneous tissue. Treatments for pythiosis have mostly relied on surgery. Antifungal drugs are generally ineffective against Py. insidiosum However, one patient with an invasive Py. insidiosum infection recovered completely following treatment with terbinafine and itraconazole. Additionally, the drug target sterol biosynthetic enzymes have been identified in the oomycete Aphanomyces euteiches It remains an open question whether Py. insidiosum is susceptible to the antifungal drugs and harbors any of the known drug target enzymes. Here, we determined the in vitro susceptibilities of terbinafine and itraconazole against 30 isolates of Py. insidiosum We also analyzed endogenous sterols and searched for genes encoding the sterol biosynthetic enzymes in the genomes of Py. insidiosum and related oomycetes. The susceptibility assay showed that the growth of each of the Py. insidiosum isolates was inhibited by the antifungal agents, but only at difficult-to-achieve concentrations, which explains the clinical resistance of the drugs in the treatment of pythiosis patients. Genome searches of Py. insidiosum and related oomycetes demonstrated that these organisms contained an incomplete set of sterol biosynthetic enzymes. Gas chromatographic mass spectrometry did not detect any sterol end products in Py. insidiosum In conclusion, Py. insidiosum possesses an incomplete sterol biosynthetic pathway. Resistance to antifungal drugs targeting enzymes in the ergosterol biosynthetic pathway in Py. insidiosum was due to modifications or losses of some of the genes encoding the drug target enzymes.
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Abstract
Background Retrotransposons comprise a ubiquitous and abundant class of eukaryotic transposable elements. All members of this class rely on reverse transcriptase activity to produce a DNA copy of the element from the RNA template. However, other activities of the retrotransposon-encoded polyprotein may differ between diverse retrotransposons. The polyprotein domains corresponding to each of these activities may have their own evolutionary history independent from that of the reverse transcriptase, thus underlying the modular view on the evolution of retrotransposons. Furthermore, some transposable elements can independently evolve similar domain architectures by acquiring functionally similar but phylogenetically distinct modules. This convergent evolution of retrotransposons may ultimately suggest similar regulatory pathways underlying the lifecycle of the elements. Results Here, we provide new examples of the convergent evolution of retrotransposons of species from two unrelated taxa: green plants and parasitic protozoan oomycetes. In the present study we first analyzed the available genomic sequences of oomycete species and characterized two groups of Ty3/Gypsy long terminal repeat retrotransposons, namely Chronos and Archon, and a subgroup of L1 non-long terminal repeat retrotransposons. The results demonstrated that the retroelements from these three groups each have independently acquired plant-related ribonuclease H domains. This process closely resembles the evolution of retrotransposons in the genomes of green plants. In addition, we showed that Chronos elements captured a chromodomain, mimicking the process of chromodomain acquisition by Chromoviruses, another group of Ty3/Gypsy retrotransposons of plants, fungi, and vertebrates. Conclusions Repeated and strikingly similar acquisitions of ribonuclease H domains and chromodomains by different retrotransposon groups from unrelated taxa indicate similar selection pressure acting on these elements. Thus, there are some major trends in the evolution of the structural composition of retrotransposons, and characterizing these trends may enhance the current understanding of the retrotransposon life cycle. Electronic supplementary material The online version of this article (doi:10.1186/s13100-017-0087-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kirill Ustyantsev
- Institute of Cytology and Genetics, Laboratory of Molecular Genetic Systems, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Alexandr Blinov
- Institute of Cytology and Genetics, Laboratory of Molecular Genetic Systems, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Georgy Smyshlyaev
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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Amaro TMMM, Thilliez GJA, Motion GB, Huitema E. A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited. Front Plant Sci 2017; 8:99. [PMID: 28217133 PMCID: PMC5289972 DOI: 10.3389/fpls.2017.00099] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/17/2017] [Indexed: 05/20/2023]
Abstract
Plant associated microbes rely on secreted virulence factors (effectors) to modulate host immunity and ensure progressive infection. Amongst the secreted protein repertoires defined and studied in pathogens to date, the CRNs (for CRinkling and Necrosis) have emerged as one of only a few highly conserved protein families, spread across several kingdoms. CRN proteins were first identified in plant pathogenic oomycetes where they were found to be modular factors that are secreted and translocated inside host cells by means of a conserved N-terminal domain. Subsequent localization and functional studies have led to the view that CRN C-termini execute their presumed effector function in the host nucleus, targeting processes required for immunity. These findings have led to great interest in this large protein family and driven the identification of additional CRN-like proteins in other organisms. The identification of CRN proteins and subsequent functional studies have markedly increased the number of candidate CRN protein sequences, expanded the range of phenotypes tentatively associated with function and revealed some of their molecular functions toward virulence. The increased number of characterized CRNs also has presented a set of challenges that may impede significant progress in the future. Here, we summarize our current understanding of the CRNs and re-assess some basic assumptions regarding this protein family. We will discuss the latest findings on CRN biology and highlight exciting new hypotheses that have emanated from the field. Finally, we will discuss new approaches to study CRN functions that would lead to a better understanding of CRN effector biology as well as the processes that lead to host susceptibility and immunity.
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Affiliation(s)
- Tiago M. M. M. Amaro
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
| | - Gaëtan J. A. Thilliez
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
- Cell and Molecular Sciences, The James Hutton InstituteInvergowrie, UK
| | - Graham B. Motion
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
| | - Edgar Huitema
- Division of Plant Sciences, University of DundeeDundee, UK
- Dundee Effector ConsortiumDundee, UK
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Belhaj K, Cano LM, Prince DC, Kemen A, Yoshida K, Dagdas YF, Etherington GJ, Schoonbeek H, van Esse HP, Jones JD, Kamoun S, Schornack S. Arabidopsis late blight: infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans. Cell Microbiol 2017; 19:e12628. [PMID: 27302335 PMCID: PMC5215655 DOI: 10.1111/cmi.12628] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 04/15/2016] [Accepted: 05/30/2016] [Indexed: 01/20/2023]
Abstract
The oomycete pathogen Phytophthora infestans causes potato late blight, and as a potato and tomato specialist pathogen, is seemingly poorly adapted to infect plants outside the Solanaceae. Here, we report the unexpected finding that P. infestans can infect Arabidopsis thaliana when another oomycete pathogen, Albugo laibachii, has colonized the host plant. The behaviour and speed of P. infestans infection in Arabidopsis pre-infected with A. laibachii resemble P. infestans infection of susceptible potato plants. Transcriptional profiling of P. infestans genes during infection revealed a significant overlap in the sets of secreted-protein genes that are induced in P. infestans upon colonization of potato and susceptible Arabidopsis, suggesting major similarities in P. infestans gene expression dynamics on the two plant species. Furthermore, we found haustoria of A. laibachii and P. infestans within the same Arabidopsis cells. This Arabidopsis-A. laibachii-P. infestans tripartite interaction opens up various possibilities to dissect the molecular mechanisms of P. infestans infection and the processes occurring in co-infected Arabidopsis cells.
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Affiliation(s)
- Khaoula Belhaj
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
| | - Liliana M. Cano
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- University of FloridaDepartment of Plant Pathology, Indian River Research and Education CenterFort PierceUSA
| | - David C. Prince
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- School of Biological SciencesUniversity of East AngliaNorwichUnited Kingdom
| | - Ariane Kemen
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Kentaro Yoshida
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- Organization of Advanced Science and TechnologyKobe UniversityKobeHyogoJapan
| | - Yasin F. Dagdas
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
| | - Graham J. Etherington
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- The Genome Analysis CentreNorwich Research ParkNorwichUnited Kingdom
| | - Henk‐jan Schoonbeek
- John Innes CentreDepartment of Crop Genetics, Norwich Research ParkNorwichUnited Kingdom
| | | | | | - Sophien Kamoun
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
| | - Sebastian Schornack
- The Sainsbury LaboratoryNorwich Research ParkNorwichUnited Kingdom
- Sainsbury LaboratoryUniversity of CambridgeCambridgeUnited Kingdom
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Withers S, Gongora-Castillo E, Gent D, Thomas A, Ojiambo PS, Quesada-Ocampo LM. Using Next-Generation Sequencing to Develop Molecular Diagnostics for Pseudoperonospora cubensis, the Cucurbit Downy Mildew Pathogen. Phytopathology 2016; 106:1105-1116. [PMID: 27314624 DOI: 10.1094/phyto-10-15-0260-fi] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Advances in next-generation sequencing (NGS) allow for rapid development of genomics resources needed to generate molecular diagnostics assays for infectious agents. NGS approaches are particularly helpful for organisms that cannot be cultured, such as the downy mildew pathogens, a group of biotrophic obligate oomycetes that infect crops of economic importance. Unlike most downy mildew pathogens that are highly host-specific, Pseudoperonospora cubensis causes disease on a broad range of crops belonging to the family Cucurbitaceae. In this study, we identified candidate diagnostic markers for P. cubensis by comparing NGS data from a diverse panel of P. cubensis and P. humuli isolates, two very closely related oomycete species. P. cubensis isolates from diverse hosts and geographical regions in the United States were selected for sequencing to ensure that candidates were conserved in P. cubensis isolates infecting different cucurbit hosts. Genomic regions unique to and conserved in P. cubensis isolates were identified through bioinformatics. These candidate regions were then validated using PCR against a larger collection of isolates from P. cubensis, P. humuli, and other oomycetes. Overall seven diagnostic markers were found to be specific to P. cubensis. These markers could be used for pathogen diagnostics on infected tissue, or adapted for monitoring airborne inoculum with real-time PCR and spore traps.
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Affiliation(s)
- S Withers
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - E Gongora-Castillo
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - D Gent
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - A Thomas
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - P S Ojiambo
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
| | - L M Quesada-Ocampo
- First, second, fourth, fifth, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695-7616; third author: U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, and Oregon State University, Corvallis 97331; and fourth and fifth authors: Center for Integrated Fungal Research, North Carolina State University, Raleigh 27695-7567
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Ye W, Wang Y, Tyler BM, Wang Y. Comparative Genomic Analysis among Four Representative Isolates of Phytophthora sojae Reveals Genes under Evolutionary Selection. Front Microbiol 2016; 7:1547. [PMID: 27746768 PMCID: PMC5042962 DOI: 10.3389/fmicb.2016.01547] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/15/2016] [Indexed: 12/13/2022] Open
Abstract
Comparative genomic analysis is useful for identifying genes affected by evolutionary selection and for studying adaptive variation in gene functions. In Phytophthora sojae, a model oomycete plant pathogen, the related study is lacking. We compared sequence data among four isolates of P. sojae, which represent its four major genotypes. These isolates exhibited >99.688%, >99.864%, and >98.981% sequence identities at genome, gene, and non-gene regions, respectively. One hundred and fifty-three positive selection and 139 negative selection candidate genes were identified. Between the two categories of genes, the positive selection genes were flanked by larger intergenic regions, poorly annotated in function, and less conserved; they had relatively lower transcription levels but many genes had increased transcripts during infection. Genes coding for predicted secreted proteins, particularly effectors, were overrepresented in positive selection. Several RxLR effector genes were identified as positive selection genes, exhibiting much stronger positive selection levels. In addition, candidate genes with presence/absence polymorphism were analyzed. This study provides a landscape of genomic variation among four representative P. sojae isolates and characterized several evolutionary selection-affected gene candidates. The results suggest a relatively covert two-speed genome evolution pattern in P. sojae and will provide clues for identification of new virulence factors in the oomycete plant pathogens.
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Affiliation(s)
- Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University Nanjing, China
| | - Yang Wang
- Department of Plant Pathology, Nanjing Agricultural University Nanjing, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis OR, USA
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University Nanjing, China
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Abstract
Deciphering plant-microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various 'omics' tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant-microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses.
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Affiliation(s)
| | | | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India
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Buckley J, Kilbride E, Cevik V, Vicente JG, Holub EB, Mable BK. R-gene variation across Arabidopsis lyrata subspecies: effects of population structure, selection and mating system. BMC Evol Biol 2016; 16:93. [PMID: 27150007 PMCID: PMC4858910 DOI: 10.1186/s12862-016-0665-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/23/2016] [Indexed: 11/10/2022] Open
Abstract
Background Examining allelic variation of R-genes in closely related perennial species of Arabidopsis thaliana is critical to understanding how population structure and ecology interact with selection to shape the evolution of innate immunity in plants. We finely sampled natural populations of Arabidopsis lyrata from the Great Lakes region of North America (A. l. lyrata) and broadly sampled six European countries (A. l. petraea) to investigate allelic variation of two R-genes (RPM1 and WRR4) and neutral genetic markers (Restriction Associated DNA sequences and microsatellites) in relation to mating system, phylogeographic structure and subspecies divergence. Results Fine-scale sampling of populations revealed strong effects of mating system and population structure on patterns of polymorphism for both neutral loci and R-genes, with no strong evidence for selection. Broad geographic sampling revealed evidence of balancing selection maintaining polymorphism in R-genes, with elevated heterozygosity and diversity compared to neutral expectations and sharing of alleles among diverged subspecies. Codon-based tests detected both positive and purifying selection for both R-genes, as commonly found for animal immune genes. Conclusions Our results highlight that combining fine and broad-scale sampling strategies can reveal the multiple factors influencing polymorphism and divergence at potentially adaptive genes such as R-genes. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0665-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Buckley
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK. .,Current address: Center for Adaptation to a Changing Environment, ETH Zurich, Zurich, 8092, Switzerland.
| | - Elizabeth Kilbride
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Volkan Cevik
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK.,Current address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR47UH, UK
| | - Joana G Vicente
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK
| | - Eric B Holub
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Wellesbourne, CV359EF, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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Fawke S, Doumane M, Schornack S. Oomycete interactions with plants: infection strategies and resistance principles. Microbiol Mol Biol Rev 2015; 79:263-80. [PMID: 26041933 DOI: 10.1128/MMBR.00010-15] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Oomycota include many economically significant microbial pathogens of crop species. Understanding the mechanisms by which oomycetes infect plants and identifying methods to provide durable resistance are major research goals. Over the last few years, many elicitors that trigger plant immunity have been identified, as well as host genes that mediate susceptibility to oomycete pathogens. The mechanisms behind these processes have subsequently been investigated and many new discoveries made, marking a period of exciting research in the oomycete pathology field. This review provides an introduction to our current knowledge of the pathogenic mechanisms used by oomycetes, including elicitors and effectors, plus an overview of the major principles of host resistance: the established R gene hypothesis and the more recently defined susceptibility (S) gene model. Future directions for development of oomycete-resistant plants are discussed, along with ways that recent discoveries in the field of oomycete-plant interactions are generating novel means of studying how pathogen and symbiont colonizations overlap.
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Gascuel Q, Bordat A, Sallet E, Pouilly N, Carrere S, Roux F, Vincourt P, Godiard L. Effector Polymorphisms of the Sunflower Downy Mildew Pathogen Plasmopara halstedii and Their Use to Identify Pathotypes from Field Isolates. PLoS One 2016; 11:e0148513. [PMID: 26845339 PMCID: PMC4742249 DOI: 10.1371/journal.pone.0148513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/19/2016] [Indexed: 01/23/2023] Open
Abstract
The obligate biotroph oomycete Plasmopara halstedii causes downy mildew on sunflower crop, Helianthus annuus. The breakdown of several Pl resistance genes used in sunflower hybrids over the last 25 years came along with the appearance of new Pl. halstedii isolates showing modified virulence profiles. In oomycetes, two classes of effector proteins, key players of pathogen virulence, are translocated into the host: RXLR and CRN effectors. We identified 54 putative CRN or RXLR effector genes from transcriptomic data and analyzed their genetic diversity in seven Pl. halstedii pathotypes representative of the species variability. Pl. halstedii effector genes were on average more polymorphic at both the nucleic and protein levels than random non-effector genes, suggesting a potential adaptive dynamics of pathogen virulence over the last 25 years. Twenty-two KASP (Competitive Allele Specific PCR) markers designed on polymorphic effector genes were genotyped on 35 isolates belonging to 14 Pl. halstedii pathotypes. Polymorphism analysis based on eight KASP markers aims at proposing a determination key suitable to classify the eight multi-isolate pathotypes into six groups. This is the first report of a molecular marker set able to discriminate Pl. halstedii pathotypes based on the polymorphism of pathogenicity effectors. Compared to phenotypic tests handling living spores used until now to discriminate Pl. halstedii pathotypes, this set of molecular markers constitutes a first step in faster pathotype diagnosis of Pl. halstedii isolates. Hence, emerging sunflower downy mildew isolates could be more rapidly characterized and thus, assessment of plant resistance breakdown under field conditions should be improved.
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Affiliation(s)
- Quentin Gascuel
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Amandine Bordat
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Erika Sallet
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Nicolas Pouilly
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Sébastien Carrere
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Fabrice Roux
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Patrick Vincourt
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
| | - Laurence Godiard
- Institut National de la Recherche Agronomique, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR441, F-31326 Castanet-Tolosan, France
- Centre National de la Recherche Scientifique, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), Unité Mixte de Recherches UMR2594, F-31326 Castanet-Tolosan, France
- * E-mail:
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