101
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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102
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Draft Genome Sequences of the Oomycete Pilasporangium apinafurcum Strains JCM 30513 and JCM 30514, Formerly Classified as Pythium apinafurcum. GENOME ANNOUNCEMENTS 2017; 5:5/35/e00899-17. [PMID: 28860253 PMCID: PMC5578851 DOI: 10.1128/genomea.00899-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pilasporangium apinafurcum, formerly classified as Pythium apinafurcum, is a unique oomycete that infects plants asymptomatically. Here, we present the draft genome sequences of two variants of P. apinafurcum, JCM 30513 and JCM 30514, isolated from uncultivated field soil in Wakayama Prefecture, Japan.
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103
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Tomada S, Sonego P, Moretto M, Engelen K, Pertot I, Perazzolli M, Puopolo G. Dual RNA-Seq of Lysobacter capsici
AZ78 - Phytophthora infestans
interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses. Environ Microbiol 2017; 19:4113-4125. [DOI: 10.1111/1462-2920.13861] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Selena Tomada
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
- Agricultural Science and Biotechnology, Department of Agricultural, Food, Environmental and Animal Sciences; University of Udine; Udine Italy
| | - Paolo Sonego
- Department of Computational Biology, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Marco Moretto
- Department of Computational Biology, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Kristof Engelen
- Department of Computational Biology, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Ilaria Pertot
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
- Center Agriculture Food Environment; University of Trento; San Michele all'Adige Italy
| | - Michele Perazzolli
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre; Fondazione Edmund Mach (FEM); San Michele all'Adige Italy
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104
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Yuan X, Feng C, Zhang Z, Zhang C. Complete Mitochondrial Genome of Phytophthora nicotianae and Identification of Molecular Markers for the Oomycetes. Front Microbiol 2017; 8:1484. [PMID: 28848506 PMCID: PMC5550686 DOI: 10.3389/fmicb.2017.01484] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/24/2017] [Indexed: 11/13/2022] Open
Abstract
Phytophthora nicotianae is one of the most destructive plant pathogens affecting a variety of plants, causing black shank of tobacco, among several other devastating diseases. Herein, we assembled the mitochondrial genome of P. nicotianae and analyzed its gene content and genome structure, performed comparative mitochondrial genomics analysis, and assessed phylogenetic relationships among oomycetes species. The circular mitogenome is 37,561 bp long, with 38 protein-coding genes, 25 transfer RNA (tRNA) genes, and 2 ribosomal RNA genes (rrnl and rrns). The mitochondrial genome showed a biased A/T usage versus G/C. The overall gene content and size of the P. nicotianae mitogenome are identical to those of other published Phytophthora mitogenomes. Interestingly, collinearity analysis using an existing ∼10 k inversion region (including 11 genes and 8 tRNAs) revealed that Phytophthora andina, Phytophthora infestans, Phytophthora mirabilis, Phytophthora ipomoeae, and Phytophthora phaseoli differed from Phytophthora nicotianae, Phytophthora sojae, Phytophthora ramorum, and Phytophthora polonica. Moreover, inverted repeat regions were found to be absent among species of the Peronosporales when compared with species from the Pythiales and Saprolegniales. A phylogenomic investigation based on 29 protein-coding genes demonstrated that Phytophthora is monophyletic, and placed P. nicotianae close to the clade including P. mirabilis, P. ipomoeae, P. andina, P. infestans, and P. phaseoli. Furthermore, we discovered six new candidate DNA molecular markers (rpl6, atp8, nad11, rps2, rps3, and rps4) based on these mitogenomes that would be suitable for species identification in the oomycetes, which have the same identification level as the whole mitogenome and ribosomal DNA sequences. These new molecular markers can not only provide a quick preview of the species without mitogenome information, but will also help to gain better understanding of the oomycetes pathogens and developing treatment or monitoring strategies.
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Affiliation(s)
- Xiaolong Yuan
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao, China
| | - Chao Feng
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao, China
- Tobacco Pest Integrated Management Key Laboratory of China TobaccoQingdao, China
| | - Zhongfeng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao, China
| | - Chengsheng Zhang
- Tobacco Research Institute of Chinese Academy of Agricultural SciencesQingdao, China
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105
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Shen D, Li Q, Sun P, Zhang M, Dou D. Intrinsic disorder is a common structural characteristic of RxLR effectors in oomycete pathogens. Fungal Biol 2017; 121:911-919. [PMID: 29029698 DOI: 10.1016/j.funbio.2017.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 07/05/2017] [Accepted: 07/21/2017] [Indexed: 01/31/2023]
Abstract
Intrinsic disorder is common in nature and has been studied to play important biological roles in bacterial effectors. However, disorder in oomycete RxLR effectors has not been investigated previously and the roles are unknown. Our results of PONDR VL-XT disorder analysis showed that predicted oomycete RxLR effectors were significantly more disordered than other effectors and secretome. The distribution of disorder content presented preference that RxLR-dEER regions were enriched in disordered residues, suggesting potential role of disorder in effector translocation. In contrast, the disorder content was depleted in the C-terminal regions, especially for W/Y/L motifs. We also found that around 42 % of putative RxLR proteins were predicted to contain at least one α-helix-forming molecular recognition feature (α-MoRF), and most α-MoRFs were located in the C-terminal regions. Furthermore, both of the disorder mutants of PsAvh18 and PcAvh207 lost the cell death-inducing activity, indicating the potential important role of disordered structure in RxLR effector function. Overall, these results demonstrate that intrinsic disorder is a common characteristic of oomycete RxLR proteins, and we postulate that such structure feature may be important for effector translocation or function. This study extends our understanding of RxLR effectors in protein structures, and opens up new directions to explore novel mechanisms of oomycete RxLR effectors.
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Affiliation(s)
- Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qingling Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Sun
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China.
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106
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Basu S, Patil S, Mapleson D, Russo MT, Vitale L, Fevola C, Maumus F, Casotti R, Mock T, Caccamo M, Montresor M, Sanges R, Ferrante MI. Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. THE NEW PHYTOLOGIST 2017; 215:140-156. [PMID: 28429538 PMCID: PMC5485032 DOI: 10.1111/nph.14557] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 02/25/2017] [Indexed: 05/03/2023]
Abstract
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes. We also identified a small number of conserved noncoding elements. Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein-coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis-related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient-replete conditions. The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.
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Affiliation(s)
- Swaraj Basu
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Shrikant Patil
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | | | - Monia Teresa Russo
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Laura Vitale
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Cristina Fevola
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | | | - Raffaella Casotti
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Thomas Mock
- School of Environmental SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Mario Caccamo
- Earlham InstituteNorwich Research ParkNorwichNR4 7UGUK
| | - Marina Montresor
- Integrative Marine EcologyStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
| | - Remo Sanges
- Biology and Evolution of Marine OrganismsStazione Zoologica Anton DohrnVilla Comunale 1Naples80121Italy
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107
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Pan Y, Ye T, Gao Z. Cloning and functional analysis of succinate dehydrogenase gene PsSDHA in Phytophthora sojae. Microb Pathog 2017; 108:40-48. [PMID: 28438637 DOI: 10.1016/j.micpath.2017.03.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 11/25/2022]
Abstract
Succinate dehydrogenase (SDH) is one of the key enzymes of the tricarboxylic acid cycle (TCA cycle) and a proven target of fungicides for true fungi. To explore the roles of the SDHA gene in Phytophthora sojae, we first cloned PsSDHA to construct the PsSDHA silenced expression vector pHAM34-PsSDHA, and then utilized PEG to mediate the P. sojae protoplast transformation experiment. Through transformation screening, we obtained the silenced mutants A1 and A3, which have significant suppressive effect. Further study showed that the hyphae of the silenced mutant strains were shorter and more bifurcated; the growth of the silenced mutants was clearly inhibited in 10% V8 agar medium containing sodium chloride (NaCl), hydrogen peroxide (H2O2) or Congo Red, respectively. The pathogenicity of the silenced mutants was significantly reduced compared with the wild-type strain and the mock. The results could help us better to understand the position and function of SDH in P. sojae and provide a proven target of fungicides for the oomycete.
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Affiliation(s)
- Yuemin Pan
- Department of Plant Pathology, College of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Tao Ye
- Department of Plant Pathology, College of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Zhimou Gao
- Department of Plant Pathology, College of Plant Protection, Anhui Agricultural University, Hefei 230036, China.
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108
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Franceschetti M, Maqbool A, Jiménez-Dalmaroni MJ, Pennington HG, Kamoun S, Banfield MJ. Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity. Microbiol Mol Biol Rev 2017; 81:e00066-16. [PMID: 28356329 PMCID: PMC5485802 DOI: 10.1128/mmbr.00066-16] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization.
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Affiliation(s)
- Marina Franceschetti
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Abbas Maqbool
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Helen G Pennington
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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109
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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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110
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Chen L, Zhang X, Wang W, Geng X, Shi Y, Na R, Dou D, Li H. Network and role analysis of autophagy in Phytophthora sojae. Sci Rep 2017; 7:1879. [PMID: 28500315 PMCID: PMC5431975 DOI: 10.1038/s41598-017-01988-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/05/2017] [Indexed: 12/17/2022] Open
Abstract
Autophagy is an evolutionarily conserved mechanism in eukaryotes with roles in development and the virulence of plant fungal pathogens. However, few reports on autophagy in oomycete species have been published. Here, we identified 26 autophagy-related genes (ATGs) belonging to 20 different groups in Phytophthora sojae using a genome-wide survey, and core ATGs in oomycetes were used to construct a preliminary autophagy pathway model. Expression profile analysis revealed that these ATGs are broadly expressed and that the majority of them significantly increase during infection stages, suggesting a central role for autophagy in virulence. Autophagy in P. sojae was detected using a GFP-PsAtg8 fusion protein and the fluorescent dye MDC during rapamycin and starvation treatment. In addition, autophagy was significantly induced during sporangium formation and cyst germination. Silencing PsAtg6a in P. sojae significantly reduced sporulation and pathogenicity. Furthermore, a PsAtg6a-silenced strain showed haustorial formation defects. These results suggested that autophagy might play essential roles in both the development and infection mechanism of P. sojae.
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Affiliation(s)
- Linlin Chen
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wen Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuejing Geng
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yan Shi
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Risong Na
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Honglian Li
- Department of Plant Pathology, Henan Agricultural University, Zhengzhou, 450002, China.
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111
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Marano AV, Gleason FH, Rocha SCO, Pires-Zottarelli CLA, Souza JID. Chapter 17 Crown Oomycetes Have Evolved as Effective Plant and Animal Parasites. Mycology 2017. [DOI: 10.1201/9781315119496-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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112
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017. [PMID: 28417959 DOI: 10.1038/srep4655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture &Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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113
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017; 7:46553. [PMID: 28417959 PMCID: PMC5394536 DOI: 10.1038/srep46553] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/22/2017] [Indexed: 12/17/2022] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture & Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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114
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Phylogenomic Reconstruction of the Oomycete Phylogeny Derived from 37 Genomes. mSphere 2017; 2:mSphere00095-17. [PMID: 28435885 PMCID: PMC5390094 DOI: 10.1128/msphere.00095-17] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [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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115
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Evolution of the Sterol Biosynthetic Pathway of Pythium insidiosum and Related Oomycetes Contributes to Antifungal Drug Resistance. Antimicrob Agents Chemother 2017; 61:AAC.02352-16. [PMID: 28115356 DOI: 10.1128/aac.02352-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [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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Gul IS, Hulpiau P, Saeys Y, van Roy F. Evolution and diversity of cadherins and catenins. Exp Cell Res 2017; 358:3-9. [PMID: 28268172 DOI: 10.1016/j.yexcr.2017.03.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 01/07/2023]
Abstract
Cadherin genes encode a superfamily of conserved transmembrane proteins that share an adhesive ectodomain composed of tandem cadherin repeats. More than 100 human cadherin superfamily members have been identified, which can be classified into three families: major cadherins, protocadherins and cadherin-related proteins. These superfamily members are involved in diverse fundamental cellular processes including cell-cell adhesion, morphogenesis, cell recognition and signaling. Epithelial cadherin (E-cadherin) is the founding cadherin family member. Its cytoplasmic tail interacts with the armadillo catenins, p120 and β-catenin. Further, α-catenin links the cadherin/armadillo catenin complex to the actin filament network. Even genomes of ancestral metazoan species such as cnidarians and placozoans encode a limited number of distinct cadherins and catenins, emphasizing the conservation and functional importance of these gene families. Moreover, a large expansion of the cadherin and catenin families coincides with the emergence of vertebrates and reflects a major functional diversification in higher metazoans. Here, we revisit and review the functions, phylogenetic classifications and co-evolution of the cadherin and catenin protein families.
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Affiliation(s)
- Ismail Sahin Gul
- Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Paco Hulpiau
- Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Yvan Saeys
- Center for Inflammation Research, VIB, Ghent, Belgium; Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Frans van Roy
- Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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Dalio RJD, Magalhães DM, Rodrigues CM, Arena GD, Oliveira TS, Souza-Neto RR, Picchi SC, Martins PMM, Santos PJC, Maximo HJ, Pacheco IS, De Souza AA, Machado MA. PAMPs, PRRs, effectors and R-genes associated with citrus-pathogen interactions. ANNALS OF BOTANY 2017; 119:749-774. [PMID: 28065920 PMCID: PMC5571375 DOI: 10.1093/aob/mcw238] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 07/08/2016] [Accepted: 10/22/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Recent application of molecular-based technologies has considerably advanced our understanding of complex processes in plant-pathogen interactions and their key components such as PAMPs, PRRs, effectors and R-genes. To develop novel control strategies for disease prevention in citrus, it is essential to expand and consolidate our knowledge of the molecular interaction of citrus plants with their pathogens. SCOPE This review provides an overview of our understanding of citrus plant immunity, focusing on the molecular mechanisms involved in the interactions with viruses, bacteria, fungi, oomycetes and vectors related to the following diseases: tristeza, psorosis, citrus variegated chlorosis, citrus canker, huanglongbing, brown spot, post-bloom, anthracnose, gummosis and citrus root rot.
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Affiliation(s)
- Ronaldo J. D. Dalio
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Diogo M. Magalhães
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Carolina M. Rodrigues
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Gabriella D. Arena
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Tiago S. Oliveira
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Reinaldo R. Souza-Neto
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Simone C. Picchi
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Paula M. M. Martins
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Paulo J. C. Santos
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Heros J. Maximo
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Inaiara S. Pacheco
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Alessandra A. De Souza
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
| | - Marcos A. Machado
- Citrus Biotechnology Lab, Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis-SP, Brazil
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Guzmán-Guzmán P, Alemán-Duarte MI, Delaye L, Herrera-Estrella A, Olmedo-Monfil V. Identification of effector-like proteins in Trichoderma spp. and role of a hydrophobin in the plant-fungus interaction and mycoparasitism. BMC Genet 2017; 18:16. [PMID: 28201981 PMCID: PMC5310080 DOI: 10.1186/s12863-017-0481-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 02/07/2017] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Trichoderma spp. can establish beneficial interactions with plants by promoting plant growth and defense systems, as well as, antagonizing fungal phytopathogens in mycoparasitic interactions. Such interactions depend on signal exchange between both participants and can be mediated by effector proteins that alter the host cell structure and function, allowing the establishment of the relationship. The main purpose of this work was to identify, using computational methods, candidates of effector proteins from T. virens, T. atroviride and T. reesei, validate the expression of some of the genes during a beneficial interaction and mycoparasitism and to define the biological function for one of them. RESULTS We defined a catalogue of putative effector proteins from T. virens, T. atroviride and T. reesei. We further validated the expression of 16 genes encoding putative effector proteins from T. virens and T. atroviride during the interaction with the plant Arabidopsis thaliana, and with two anastomosis groups of the phytopathogenic fungus Rhizoctonia solani. We found genes which transcript levels are modified in response to the presence of both plant fungi, as well as genes that respond only to either a plant or a fungal host. Further, we show that overexpression of the gene tvhydii1, a Class II hydrophobin family member, enhances the antagonistic activity of T. virens against R. solani AG2. Further, deletion of tvhydii1 results in reduced colonization of plant roots, while its overexpression increases it. CONCLUSIONS Our results show that Trichoderma is able to respond in different ways to the presence of a plant or a fungal host, and it can even distinguish between different strains of fungi of a given species. The putative effector proteins identified here may play roles in preventing perception of the fungus by its hosts, favoring host colonization or protecting it from the host's defense response. Finally, the novel effector protein TVHYDII1 plays a role in plant root colonization by T, virens, and participates in its antagonistic activity against R. solani.
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Affiliation(s)
- Paulina Guzmán-Guzmán
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Gto, Mexico
| | - Mario Iván Alemán-Duarte
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto, Mexico
- Unidad Irapuato, Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto, Mexico
| | - Luis Delaye
- Unidad Irapuato, Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Gto, Mexico
| | - Vianey Olmedo-Monfil
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Gto, Mexico
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Species delimitation in Pythium species complexes: the case of Pythium myriotylum Drechsler and Pythium zingiberis Takahashi. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1272-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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120
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Kamel L, Tang N, Malbreil M, San Clemente H, Le Marquer M, Roux C, Frei dit Frey N. The Comparison of Expressed Candidate Secreted Proteins from Two Arbuscular Mycorrhizal Fungi Unravels Common and Specific Molecular Tools to Invade Different Host Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:124. [PMID: 28223991 PMCID: PMC5293756 DOI: 10.3389/fpls.2017.00124] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/20/2017] [Indexed: 05/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF), belonging to the fungal phylum Glomeromycota, form mutualistic symbioses with roots of almost 80% of land plants. The release of genomic data from the ubiquitous AMF Rhizophagus irregularis revealed that this species possesses a large set of putative secreted proteins (RiSPs) that could be of major importance for establishing the symbiosis. In the present study, we aimed to identify SPs involved in the establishment of AM symbiosis based on comparative gene expression analyses. We first curated the secretome of the R. irregularis DAOM 197198 strain based on two available genomic assemblies. Then we analyzed the expression patterns of the putative RiSPs obtained from the fungus in symbiotic association with three phylogenetically distant host plants-a monocot, a dicot and a liverwort-in comparison with non-symbiotic stages. We found that 33 out of 84 RiSPs induced in planta were commonly up-regulated in these three hosts. Most of these common RiSPs are small proteins of unknown function that may represent putative host non-specific effector proteins. We further investigated the expressed secretome of Gigaspora rosea, an AM fungal species phylogenetically distant from R. irregularis. G. rosea also presents original symbiotic features, a narrower host spectrum and a restrictive geographic distribution compared to R. irregularis. Interestingly, when analyzing up-regulated G. rosea SPs (GrSPs) in different hosts, a higher ratio of host-specific GrSPs was found compared to RiSPs. Such difference of expression patterns may mirror the restrained host spectrum of G. rosea compared to R. irregularis. Finally, we identified a set of conserved SPs, commonly up-regulated by both fungi in all hosts tested, that could correspond to common keys of AMF to colonize host plants. Our data thus highlight the specificities of two distant AM fungi and help in understanding their conserved and specific strategies to invade different hosts.
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Affiliation(s)
- Laurent Kamel
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
- Agronutrition, Laboratoire de BiotechnologiesLabege, France
| | - Nianwu Tang
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Mathilde Malbreil
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Morgane Le Marquer
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
| | - Nicolas Frei dit Frey
- Laboratoire de Recherche en Sciences Végétales, Université Paul Sabatier - Université de Toulouse, Centre National de la Recherche ScientifiqueCastanet-Tolosan, France
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Derevnina L, Petre B, Kellner R, Dagdas YF, Sarowar MN, Giannakopoulou A, De la Concepcion JC, Chaparro-Garcia A, Pennington HG, van West P, Kamoun S. Emerging oomycete threats to plants and animals. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150459. [PMID: 28080985 PMCID: PMC5095538 DOI: 10.1098/rstb.2015.0459] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2016] [Indexed: 12/31/2022] Open
Abstract
Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans, Phytophthora palmivora, Phytophthora ramorum, Plasmopara obducens, and the animal pathogens Aphanomyces invadans, Saprolegnia parasitica and Halioticida noduliformans For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Lida Derevnina
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Benjamin Petre
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ronny Kellner
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Yasin F Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
| | - Mohammad Nasif Sarowar
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | | | | | | | | | - Pieter van West
- International Centre for Aquaculture Research and Development, Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, UK
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Wang XW, Guo LY, Han M, Shan K. Diversity, evolution and expression profiles of histone acetyltransferases and deacetylases in oomycetes. BMC Genomics 2016; 17:927. [PMID: 27852223 PMCID: PMC5112689 DOI: 10.1186/s12864-016-3285-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/09/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Oomycetes are a group of fungus-like eukaryotes with diverse microorganisms living in marine, freshwater and terrestrial environments. Many of them are important pathogens of plants and animals, causing severe economic losses. Based on previous study, gene expression in eukaryotic cells is regulated by epigenetic mechanisms such as DNA methylation and histone modification. However, little is known about epigenetic mechanisms of oomycetes. RESULTS In this study, we investigated the candidate genes in regulating histone acetylation in oomycetes genomes through bioinformatics approaches and identified a group of diverse histone acetyltransferases (HATs) and histone deacetylases (HDACs), along with three putative novel HATs. Phylogenetic analyses suggested that most of these oomycetes HATs and HDACs derived from distinct evolutionary ancestors. Phylogenetic based analysis revealed the complex and distinct patterns of duplications and losses of HATs and HDACs in oomycetes. Moreover, gene expression analysis unveiled the specific expression patterns of the 33 HATs and 11 HDACs of Phytophthora infestans during the stages of development, infection and stress response. CONCLUSIONS In this study, we reveal the structure, diversity and the phylogeny of HATs and HDACs of oomycetes. By analyzing the expression data, we provide an overview of the specific biological stages of these genes involved. Our datasets provide useful inputs to help explore the epigenetic mechanisms and the relationship between genomes and phenotypes of oomycetes.
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Affiliation(s)
- Xiao-Wen Wang
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Li-Yun Guo
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, China.
| | - Miao Han
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Kun Shan
- Department of Plant Pathology and the Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing, 100193, China
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Makkonen J, Vesterbacka A, Martin F, Jussila J, Diéguez-Uribeondo J, Kortet R, Kokko H. Mitochondrial genomes and comparative genomics of Aphanomyces astaci and Aphanomyces invadans. Sci Rep 2016; 6:36089. [PMID: 27808238 PMCID: PMC5093560 DOI: 10.1038/srep36089] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/10/2016] [Indexed: 11/11/2022] Open
Abstract
The genus Aphanomyces (Saprolegniales, Oomycetes) includes species with a variety of ecologies from saprotrophs to plant and animal parasites. Two important species in this genus are A. astaci, the cause of crayfish plague and its close relative, A. invadans, which causes the epizootic ulcerative syndrome on fish. In this study, we have assembled and annotated the mitochondrial (mt) genomes of A. astaci and A. invadans from the whole genome shotgun sequence reads (PRJNA187372; PRJNA258292, respectively). The assembly was generated from A. astaci Pc-genotype strain APO3 and A. invadans strain NJM9701. The sizes of the mtDNAs were 49,489 bp and 49,061 bp for A. astaci and A. invadans, respectively. The species shared similar genetic content and organization encoding 35 proteins, two ribosomal RNAs, three putative open reading frames and 33 transfer RNAs of 19 amino acids for peptide synthesis. Both species also had a large inverted repeat region (LIR) of approximately 12 kb, the LIR contained large and small ribosomal RNAs and eight protein coding genes. These annotated mt genomes serve as a valuable genetic backbone for further development of diagnostic methods and phylogenetic and migration studies of the animal parasitic species of Aphanomyces.
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Affiliation(s)
- Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Arto Vesterbacka
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | - Frank Martin
- United States Department of Agriculture, ARS, 1636 E. Alisal St., CA-93905 Salinas, USA
| | - Japo Jussila
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
| | | | - Raine Kortet
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Department of Biology, Biological & Geological Sciences, University of Western Ontario, 1151 Richmond St N, London, Ontario N6A 5B7, Canada
| | - Harri Kokko
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland
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Toh SS, Perlin MH. Resurgence of Less-Studied Smut Fungi as Models of Phytopathogenesis in the Omics Age. PHYTOPATHOLOGY 2016; 106:1244-1254. [PMID: 27111800 DOI: 10.1094/phyto-02-16-0075-rvw] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The smut fungi form a large, diverse, and nonmonophyletic group of plant pathogens that have long served as both important pests of human agriculture and, also, as fertile organisms of scientific investigation. As modern techniques of molecular genetic analysis became available, many previously studied species that proved refractive to these techniques fell by the wayside and were neglected. Now, as the advent of rapid and affordable next-generation sequencing provides genomic and transcriptomic resources for even these "forgotten" fungi, several species are making a comeback and retaking prominent places in phytopathogenic research. In this review, we highlight several of these smut fungi, with special emphasis on Microbotryum lychnidis-dioicae, an anther smut whose molecular genetic tools have finally begun to catch up with its historical importance in classical genetics and now provide mechanistic insights for ecological studies, evolution of host-pathogen interaction, and investigations of emerging infectious disease.
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Affiliation(s)
- Su San Toh
- First and second authors: Department of Biology and Program on Disease Evolution, University of Louisville, Kentucky; and first author: Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore
| | - Michael H Perlin
- First and second authors: Department of Biology and Program on Disease Evolution, University of Louisville, Kentucky; and first author: Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore
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Chen JY, Xiao HL, Gui YJ, Zhang DD, Li L, Bao YM, Dai XF. Characterization of the Verticillium dahliae Exoproteome Involves in Pathogenicity from Cotton-Containing Medium. Front Microbiol 2016; 7:1709. [PMID: 27840627 PMCID: PMC5083787 DOI: 10.3389/fmicb.2016.01709] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/12/2016] [Indexed: 12/31/2022] Open
Abstract
Verticillium wilt, caused by the Verticillium dahliae phytopathogen, is a devastating disease affecting many economically important crops. Previous studies have shown that the exoproteome of V. dahliae plays a significant role in this pathogenic process, but the components and mechanisms that underlie this remain unclear. In this study, the exoproteome of V. dahliae was induced in a cotton-containing C’zapek-Dox (CCD) medium and quantified using the high-throughput isobaric tag technique for relative and absolute quantification (iTRAQ). Results showed that the abundance of 271 secreted proteins was affected by the CCD medium, of which 172 contain typical signal peptides generally produced by the Golgi/endoplasmic reticulum (ER). These enhanced abundance proteins were predominantly enriched in carbohydrate hydrolases; 126 were classified as carbohydrate-active (CAZymes) and almost all were significantly up-regulated in the CCD medium. Results showed that CAZymes proteins 30 and 22 participate in pectin and cellulose degradation pathways, corresponding with the transcription levels of several genes encoded plant cell wall degradation enzyme activated significantly during cotton infection. In addition, targeted deletion of two pectin lyase genes (VdPL3.1 and VdPL3.3) impaired wilt virulence to cotton. This study demonstrates that the V. dahliae exoproteome plays a crucial role in the development of symptoms of wilting and necrosis, predominantly via the pathogenic mechanisms of plant cell wall degradation as part of host plant infection.
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Affiliation(s)
- Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Hong-Li Xiao
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Yue-Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Lei Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Yu-Ming Bao
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences Beijing, China
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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] [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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127
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Abstract
We examine exon junctions near apparent amino acid insertions and deletions in alignments of orthologous protein-coding genes. In 1,917 ortholog families across nine oomycete genomes, 10–20% of introns are near an alignment gap, indicating at first sight that splice-site displacements are frequent. We designed a robust algorithmic procedure for the delineation of intron-containing homologous regions, and combined it with a parsimony-based reconstruction of intron loss, gain, and splice-site shift events on a phylogeny. The reconstruction implies that 12% of introns underwent an acceptor-site shift, and 10% underwent a donor-site shift. In order to offset gene annotation problems, we amended the procedure with the reannotation of intron boundaries using alignment evidence. The corresponding reconstruction involves much fewer intron gain and splice-site shift events. The frequency of acceptor- and donor-side shifts drops to 4% and 3%, respectively, which are not much different from what one would expect by random codon insertions and deletions. In other words, gaps near exon junctions are mostly artifacts of gene annotation rather than evidence of sliding intron boundaries. Our study underscores the importance of using well-supported gene structure annotations in comparative studies. When transcription evidence is not available, we propose a robust ancestral reconstruction procedure that corrects misannotated intron boundaries using sequence alignments. The results corroborate the view that boundary shifts and complete intron sliding are only accidental in eukaryotic genome evolution and have a negligible impact on protein diversity.
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Affiliation(s)
- Steven Sêton Bocco
- Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, Canada
| | - Miklós Csűrös
- Department of Computer Science and Operations Research, University of Montréal, Montréal, Canada Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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128
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Fletcher KIG, van West P, Gachon CMM. Nonagonal cadherins: A new protein family found within the Stramenopiles. Gene 2016; 593:64-75. [PMID: 27498181 DOI: 10.1016/j.gene.2016.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/30/2016] [Accepted: 08/03/2016] [Indexed: 12/21/2022]
Abstract
Cadherins, a group of molecules typically associated with planar cell polarity and Wnt signalling, have been little reported outside of the animal kingdom. Here, we identify a new family of cadherins in the Stramenopiles, termed Nonagonal after their 9 transmembrane passes, which contrast to the one or seven passes found in other known cadherin families. Manual curation and experimental validation reveal two subclasses of nonagonal cadherins, depending on the number of uninterrupted extracellular cadherin (EC) modules presented. Firstly, shorter mono-exonic, unimodular, protein models, with 3 to 12 EC domains occur as duplicate paralogs in the saprotrophic Labyrinthulomycetes Aurantiochytrium limanicum and Schizochytrium aggregatum, the gastrointestinal Blastocystis hominis (Blastocystae) and as a single copy gene in the autotrophic Pelagophyte Aureococcus anophagefferens. Larger, single copy, multi-exonal, tri-modular protein models, with up to 72 EC domain in total, are found in the Oomycete genera Albugo, Phytophthora, Pythium and Eurychasma. No homolog was found in the closely related autotrophic Phaeophyceae (brown algae) or Bacillariophyceae (diatoms), nor in several genera of plant and animal pathogenic oomycetes (Aphanomyces, Saprolegnia and Hyaloperonospora). This potential absence was further investigated by synteny analysis of the genome regions flanking the cadherin gene models, which are found to be highly variable. Novel to this new cadherin family is the presence of intercalated laminin and putative carbohydrate binding in tri-modular oomycete cadherins and at the N-terminus of thraustochytrid proteins. As we were unable to detect any homologs of proteins involved in signalling pathways where other cadherin families are involved, we present a conceptual hypothesis on the function of nonagonal cadherin based around the presence of putative carbohydrate binding domains.
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Affiliation(s)
- Kyle I G Fletcher
- Oceanlab, University of Aberdeen, Newburgh, Aberdeenshire AB41 6AA, United Kingdom; Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom; Culture Collection for Algae and Protozoa, Scottish Marine Institute, Scottish Association for Marine Science, Dunstaffnage, Oban, Argyll PA37 1QA, United Kingdom.
| | - Pieter van West
- Aberdeen Oomycete Laboratory, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom.
| | - Claire M M Gachon
- Culture Collection for Algae and Protozoa, Scottish Marine Institute, Scottish Association for Marine Science, Dunstaffnage, Oban, Argyll PA37 1QA, United Kingdom.
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129
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Whitham SA, Qi M, Innes RW, Ma W, Lopes-Caitar V, Hewezi T. Molecular Soybean-Pathogen Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:443-68. [PMID: 27359370 DOI: 10.1146/annurev-phyto-080615-100156] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Soybean hosts a wide variety of pathogens that cause significant yield losses. The importance of soybean as a major oilseed crop has led to research focused on its interactions with pathogens, such as Soybean mosaic virus, Pseudomonas syringae, Phytophthora sojae, Phakopsora pachyrhizi, and Heterodera glycines. Pioneering work on soybean's interactions with these organisms, which represent the five major pathogen groups (viruses, bacteria, oomycetes, fungi, and nematodes), has contributed to our understanding of the molecular mechanisms underlying virulence and immunity. These mechanisms involve conserved and unique features that validate the need for research in both soybean and homologous model systems. In this review, we discuss identification of effectors and their functions as well as resistance gene-mediated recognition and signaling. We also point out areas in which model systems and recent advances in resources and tools have provided opportunities to gain deeper insights into soybean-pathogen interactions.
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Affiliation(s)
- Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405;
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
| | - Valéria Lopes-Caitar
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
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130
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Ye W, Wang Y, Shen D, Li D, Pu T, Jiang Z, Zhang Z, Zheng X, Tyler BM, Wang Y. Sequencing of the Litchi Downy Blight Pathogen Reveals It Is a Phytophthora Species With Downy Mildew-Like Characteristics. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:573-83. [PMID: 27183038 DOI: 10.1094/mpmi-03-16-0056-r] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
On the basis of its downy mildew-like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently, however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLR, 30 necrosis-and-ethylene-inducing protein-like, and 14 crinkler proteins. The typical motifs, phylogenies, and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preferences of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew-like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens.
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Affiliation(s)
- Wenwu Ye
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Wang
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Danyu Shen
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Delong Li
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianhuizi Pu
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zide Jiang
- 3 Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Zhengguang Zhang
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaobo Zheng
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Brett M Tyler
- 2 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A.; and
| | - Yuanchao Wang
- 1 Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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131
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van Hooff JJE, Snel B, Seidl MF. Small homologous blocks in phytophthora genomes do not point to an ancient whole-genome duplication. Genome Biol Evol 2016; 6:1079-85. [PMID: 24760277 PMCID: PMC4040989 DOI: 10.1093/gbe/evu081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomes of the plant-pathogenic genus Phytophthora are characterized by small duplicated blocks consisting of two consecutive genes (2HOM blocks) and by an elevated abundance of similarly aged gene duplicates. Both properties, in particular the presence of 2HOM blocks, have been attributed to a whole-genome duplication (WGD) at the last common ancestor of Phytophthora. However, large intraspecies synteny—compelling evidence for a WGD—has not been detected. Here, we revisited the WGD hypothesis by deducing the age of 2HOM blocks. Two independent timing methods reveal that the majority of 2HOM blocks arose after divergence of the Phytophthora lineages. In addition, a large proportion of the 2HOM block copies colocalize on the same scaffold. Therefore, the presence of 2HOM blocks does not support a WGD at the last common ancestor of Phytophthora. Thus, genome evolution of Phytophthora is likely driven by alternative mechanisms, such as bursts of transposon activity.
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Affiliation(s)
- Jolien J E van Hooff
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, The Netherlands
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Chen XR, Li YP, Li QY, Xing YP, Liu BB, Tong YH, Xu JY. SCR96, a small cysteine-rich secretory protein of Phytophthora cactorum, can trigger cell death in the Solanaceae and is important for pathogenicity and oxidative stress tolerance. MOLECULAR PLANT PATHOLOGY 2016; 17:577-87. [PMID: 26307454 PMCID: PMC6638419 DOI: 10.1111/mpp.12303] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Peptides and small molecules produced by both the plant pathogen Phytophthora and host plants in the apoplastic space mediate the relationship between the interplaying organisms. Various Phytophthora apoplastic effectors, including small cysteine-rich (SCR) secretory proteins, have been identified, but their roles during interaction remain to be determined. Here, we identified an SCR effector encoded by scr96, one of three novel genes encoding SCR proteins in P. cactorum with similarity to the P. cactorum phytotoxic protein PcF. Together with the other two genes, scr96 was transcriptionally induced throughout the developmental and infection stages of the pathogen. These genes triggered plant cell death (PCD) in the Solanaceae, including Nicotiana benthamiana and tomato. The scr96 gene did not show single nucleotide polymorphisms in a collection of P. cactorum isolates from different countries and host plants, suggesting that its role is essential and non-redundant during infection. Homologues of SCR96 were identified only in oomycetes, but not in fungi and other organisms. A stable protoplast transformation protocol was adapted for P. cactorum using green fluorescent protein as a marker. The silencing of scr96 in P. cactorum caused gene-silenced transformants to lose their pathogenicity on host plants and these transformants were significantly more sensitive to oxidative stress. Transient expression of scr96 partially recovered the virulence of gene-silenced transformants on plants. Overall, our results indicate that the P. cactorum scr96 gene encodes an important virulence factor that not only causes PCD in host plants, but is also important for pathogenicity and oxidative stress tolerance.
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Affiliation(s)
- Xiao-Ren Chen
- College of Horticulture and Plant Protection, Yangzhou University, Wenhui Eastern Road 48, Yangzhou, 225009, Jiangsu Province, China
| | - Yan-Peng Li
- College of Horticulture and Plant Protection, Yangzhou University, Wenhui Eastern Road 48, Yangzhou, 225009, Jiangsu Province, China
| | - Qi-Yuan Li
- College of Horticulture and Plant Protection, Yangzhou University, Wenhui Eastern Road 48, Yangzhou, 225009, Jiangsu Province, China
| | - Yu-Ping Xing
- College of Horticulture and Plant Protection, Yangzhou University, Wenhui Eastern Road 48, Yangzhou, 225009, Jiangsu Province, China
| | - Bei-Bei Liu
- College of Horticulture and Plant Protection, Yangzhou University, Wenhui Eastern Road 48, Yangzhou, 225009, Jiangsu Province, China
| | - Yun-Hui Tong
- College of Horticulture and Plant Protection, Yangzhou University, Wenhui Eastern Road 48, Yangzhou, 225009, Jiangsu Province, China
| | - Jing-You Xu
- College of Horticulture and Plant Protection, Yangzhou University, Wenhui Eastern Road 48, Yangzhou, 225009, Jiangsu Province, China
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133
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Draft Genome Sequence of Biocontrol Agent Pythium oligandrum Strain Po37, an Oomycota. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00215-16. [PMID: 27081125 PMCID: PMC4832153 DOI: 10.1128/genomea.00215-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The oomycotaPythium oligandrumPo37 is used as a biocontrol agent of plant diseases. Here, we present the first draft of theP. oligandrumPo37 genome sequence, which comprises 725 scaffolds with a total length of 35.9 Mb and 11,695 predicted protein-coding genes.
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134
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Ramirez-Garcés D, Camborde L, Pel MJC, Jauneau A, Martinez Y, Néant I, Leclerc C, Moreau M, Dumas B, Gaulin E. CRN13 candidate effectors from plant and animal eukaryotic pathogens are DNA-binding proteins which trigger host DNA damage response. THE NEW PHYTOLOGIST 2016; 210:602-17. [PMID: 26700936 DOI: 10.1111/nph.13774] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/21/2015] [Indexed: 05/20/2023]
Abstract
To successfully colonize their host, pathogens produce effectors that can interfere with host cellular processes. Here we investigated the function of CRN13 candidate effectors produced by plant pathogenic oomycetes and detected in the genome of the amphibian pathogenic chytrid fungus Batrachochytrium dendrobatidis (BdCRN13). When expressed in Nicotiana, AeCRN13, from the legume root pathogen Aphanomyces euteiches, increases the susceptibility of the leaves to the oomycete Phytophthora capsici. When transiently expressed in amphibians or plant cells, AeCRN13 and BdCRN13 localize to the cell nuclei, triggering aberrant cell development and eventually causing cell death. Using Förster resonance energy transfer experiments in plant cells, we showed that both CRN13s interact with nuclear DNA and trigger plant DNA damage response (DDR). Mutating key amino acid residues in a predicted HNH-like endonuclease motif abolished the interaction of AeCRN13 with DNA, the induction of DDR and the enhancement of Nicotiana susceptibility to P. capsici. Finally, H2AX phosphorylation, a marker of DNA damage, and enhanced expression of genes involved in the DDR were observed in A. euteiches-infected Medicago truncatula roots. These results show that CRN13 from plant and animal eukaryotic pathogens promotes host susceptibility by targeting nuclear DNA and inducing DDR.
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Affiliation(s)
- Diana Ramirez-Garcés
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Laurent Camborde
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Michiel J C Pel
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Alain Jauneau
- CNRS, Plateforme Imagerie-Microscopie Plateforme Imagerie-Microscopie, F-31326, Castanet-Tolosan, France
| | - Yves Martinez
- CNRS, Plateforme Imagerie-Microscopie Plateforme Imagerie-Microscopie, F-31326, Castanet-Tolosan, France
| | - Isabelle Néant
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Catherine Leclerc
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Marc Moreau
- Centre de Biologie du Développement, Université Toulouse 3, Toulouse, F31062, France
- CNRS UMR5547, Toulouse, F31062, France
| | - Bernard Dumas
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
| | - Elodie Gaulin
- Laboratoire de Recherche en Sciences Végétales, UPS, Université Toulouse 3, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales, CNRS, 24 chemin de Borde Rouge, BP42617, Auzeville, F-31326, Castanet-Tolosan, France
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135
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Wibberg D, Andersson L, Tzelepis G, Rupp O, Blom J, Jelonek L, Pühler A, Fogelqvist J, Varrelmann M, Schlüter A, Dixelius C. Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes. BMC Genomics 2016; 17:245. [PMID: 26988094 PMCID: PMC4794925 DOI: 10.1186/s12864-016-2561-1] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/29/2016] [Indexed: 11/25/2022] Open
Abstract
Background Sugar beet (Beta vulgaris) is a crop cultivated for its high content in sugar, but it is vulnerable to many soil-borne pathogens. One of them is the basidiomycete Rhizoctonia solani. This fungal species has a compatibility system regulating hyphal fusions (anastomosis). Consequently, R. solani species are categorized in anastomosis groups (AGs). AG2-2IIIB isolates are most aggressive on sugar beet. In the present study, we report on the draft genome of R. solani AG2-2IIIB using the Illumina technology. Genome analysis, interpretation and comparative genomics of five sequenced R. solani isolates were carried out. Results The draft genome of R. solani AG2-2IIIB has an estimated size of 56.02 Mb. In addition, two normalized EST libraries were sequenced. In total 20,790 of 21,980 AG2-2IIIB isotigs (transcript isoforms) were mapped on the genome with more than 95 % sequence identity. The genome of R. solani AG2-2IIIB was predicted to harbor 11,897 genes and 4908 were found to be isolate-specific. R. solani AG2-2IIIB was predicted to contain 1142 putatively secreted proteins and 473 of them were found to be unique for this isolate. The R. solani AG2-2IIIB genome encodes a high number of carbohydrate active enzymes. The highest numbers were observed for the polysaccharide lyases family 1 (PL-1), glycoside hydrolase family 43 (GH-43) and carbohydrate estarase family 12 (CE-12). Transcription analysis of selected genes representing different enzyme clades revealed a mixed pattern of up- and down-regulation six days after infection on sugar beets featuring variable levels of resistance compared to mycelia of the fungus grown in vitro. Conclusions The established R. solani AG2-2IIIB genome and EST sequences provide important information on the gene content, gene structure and transcriptional activity for this sugar beet pathogen. The enriched genomic platform provides an important platform to enhance our understanding of R. solani biology. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2561-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Wibberg
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany
| | - Louise Andersson
- Syngenta Seeds AB, Säbyholmsvägen 24, 26191, Landskrona, Sweden.,Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | - Georgios Tzelepis
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Lukas Jelonek
- Bioinformatics and Systems Biology, Gießen University, D-35392, Gießen, Germany
| | - Alfred Pühler
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany
| | - Johan Fogelqvist
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden
| | | | - Andreas Schlüter
- Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, D-33501, Bielefeld, Germany.
| | - Christina Dixelius
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007, Uppsala, Sweden.
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136
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Oomycete interactions with plants: infection strategies and resistance principles. Microbiol Mol Biol Rev 2016; 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] [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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137
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Ascunce MS, Huguet-Tapia JC, Braun EL, Ortiz-Urquiza A, Keyhani NO, Goss EM. Whole genome sequence of the emerging oomycete pathogen Pythium insidiosum strain CDC-B5653 isolated from an infected human in the USA. GENOMICS DATA 2016; 7:60-1. [PMID: 26981361 PMCID: PMC4778604 DOI: 10.1016/j.gdata.2015.11.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 11/22/2015] [Indexed: 11/30/2022]
Abstract
Pythium insidiosum ATCC 200269 strain CDC-B5653, an isolate from necrotizing lesions on the mouth and eye of a 2-year-old boy in Memphis, Tennessee, USA, was sequenced using a combination of Illumina MiSeq (300 bp paired-end, 14 millions reads) and PacBio (10 Kb fragment library, 356,001 reads). The sequencing data were assembled using SPAdes version 3.1.0, yielding a total genome size of 45.6 Mb contained in 8992 contigs, N50 of 13 Kb, 57% G + C content, and 17,867 putative protein-coding genes. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession JRHR00000000.
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Affiliation(s)
- Marina S. Ascunce
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Jose C. Huguet-Tapia
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Edward L. Braun
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Almudena Ortiz-Urquiza
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Nemat O. Keyhani
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Erica M. Goss
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
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138
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Liu H, Ma X, Yu H, Fang D, Li Y, Wang X, Wang W, Dong Y, Xiao B. Genomes and virulence difference between two physiological races of Phytophthora nicotianae. Gigascience 2016; 5:3. [PMID: 26823972 PMCID: PMC4730604 DOI: 10.1186/s13742-016-0108-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/06/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Black shank is a severe plant disease caused by the soil-borne pathogen Phytophthora nicotianae. Two physiological races of P. nicotianae, races 0 and 1, are predominantly observed in cultivated tobacco fields around the world. Race 0 has been reported to be more aggressive, having a shorter incubation period, and causing worse root rot symptoms, while race 1 causes more severe necrosis. The molecular mechanisms underlying the difference in virulence between race 0 and 1 remain elusive. FINDINGS We assembled and annotated the genomes of P. nicotianae races 0 and 1, which were obtained by a combination of PacBio single-molecular real-time sequencing and second-generation sequencing (both HiSeq and MiSeq platforms). Gene family analysis revealed a highly expanded ATP-binding cassette transporter gene family in P. nicotianae. Specifically, more RxLR effector genes were found in the genome of race 0 than in that of race 1. In addition, RxLR effector genes were found to be mainly distributed in gene-sparse, repeat-rich regions of the P. nicotianae genome. CONCLUSIONS These results provide not only high quality reference genomes of P. nicotianae, but also insights into the infection mechanisms of P. nicotianae and its co-evolution with the host plant. They also reveal insights into the difference in virulence between the two physiological races.
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Affiliation(s)
- Hui Liu
- />CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiao Ma
- />Yunnan Agricultural University, Kunming, 650100 China
| | - Haiqin Yu
- />Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China
| | - Dunhuang Fang
- />Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China
| | - Yongping Li
- />Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China
| | - Xiao Wang
- />CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China
- />University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wen Wang
- />CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China
| | - Yang Dong
- />Yunnan Agricultural University, Kunming, 650100 China
- />Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500 China
| | - Bingguang Xiao
- />Yunnan Academy of Tobacco Agricultural Sciences, Yuantong Street No.33, Kunming, Yunnan 650021 China
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139
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Bollmann SR, Fang Y, Press CM, Tyler BM, Grünwald NJ. Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora. FRONTIERS IN PLANT SCIENCE 2016; 7:284. [PMID: 27014308 PMCID: PMC4791657 DOI: 10.3389/fpls.2016.00284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/22/2016] [Indexed: 05/10/2023]
Abstract
Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of filamentous oomycetes, contains many devastating plant pathogens, causing multibillion-dollar damage to crops, ornamental plants, and natural environments. The genomes of several oomycetes including Phytophthora species such as the soybean pathogen P. sojae, have been sequenced, allowing evolutionary analysis of small RNA-processing enzymes. This study examined the evolutionary origins of the oomycete small RNA-related genes Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) through broad phylogenetic analyses of the key domains. Two Dicer gene homologs, DCL1 and DCL2, and one RDR homolog were cloned and analyzed from P. sojae. Gene expression analysis revealed only minor changes in transcript levels among different life stages. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs in evolutionary trees, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study that suggested the last common eukaryote ancestor possessed three RDR homologs, which were selectively retained or lost in later lineages. Our analysis clarifies the position of some Unikont and Chromalveolate RDR lineages within the tree, including oomycete homologs. Finally, we analyzed alterations in the domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain transfer of the DEAD-box helicase domain from Dicer to RDR. Implications of the oomycete domain structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed.
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Affiliation(s)
- Stephanie R. Bollmann
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
| | - Yufeng Fang
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
- Interdisciplinary Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia TechBlacksburg, VA, USA
| | - Caroline M. Press
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
| | - Brett M. Tyler
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
| | - Niklaus J. Grünwald
- Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA
- Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA
- *Correspondence: Niklaus J. Grünwald
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140
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Rajput NA, Zhang M, Shen D, Liu T, Zhang Q, Ru Y, Sun P, Dou D. Overexpression of a Phytophthora Cytoplasmic CRN Effector Confers Resistance to Disease, Salinity and Drought in Nicotiana benthamiana. PLANT & CELL PHYSIOLOGY 2015; 56:2423-35. [PMID: 26546319 DOI: 10.1093/pcp/pcv164] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
The Crinkler (CRN) effector family is produced by oomycete pathogens and may manipulate host physiological and biochemical events inside host cells. Here, PsCRN161 was identified from Phytophthora sojae based on its broad and strong cell death suppression activities. The effector protein contains two predicted nuclear localization signals and localized to nuclei of plant cells, indicating that it may target plant nuclei to modify host cell physiology and function. The chimeric gene GFP:PsCRN161 driven by the Cauliflower mosaic virus (CaMV) 35S promoter was introduced into Nicotiana benthamiana. The four independent PsCRN161-transgenic lines exhibited increased resistance to two oomycete pathogens (P. parasitica and P. capsici) and showed enhanced tolerance to salinity and drought stresses. Digital gene expression profiling analysis showed that defense-related genes, including ABC transporters, Cyt P450 and receptor-like kinases (RLKs), were significantly up-regulated in PsCRN161-transgenic plants compared with GFP (green fluorescent protein) lines, implying that PsCRN161 expression may protect plants from biotic and abiotic stresses by up-regulation of many defense-related genes. The results reveal previously unknown functions of the oomycete effectors, suggesting that the pathogen effectors could be directly used as functional genes for plant molecular breeding for enhancement of tolerance to biotic and abiotic stresses.
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Affiliation(s)
- Nasir Ahmed Rajput
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan These authors contributed equally to this work
| | - Meixiang Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China These authors contributed equally to this work
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Tingli Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Qimeng Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yanyan Ru
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Peng Sun
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
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141
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Mirzadi Gohari A, Ware SB, Wittenberg AHJ, Mehrabi R, Ben M'Barek S, Verstappen ECP, van der Lee TAJ, Robert O, Schouten HJ, de Wit PPJGM, Kema GHJ. Effector discovery in the fungal wheat pathogen Zymoseptoria tritici. MOLECULAR PLANT PATHOLOGY 2015; 16:931-45. [PMID: 25727413 PMCID: PMC6638447 DOI: 10.1111/mpp.12251] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Fungal plant pathogens, such as Zymoseptoria tritici (formerly known as Mycosphaerella graminicola), secrete repertoires of effectors to facilitate infection or trigger host defence mechanisms. The discovery and functional characterization of effectors provides valuable knowledge that can contribute to the design of new and effective disease management strategies. Here, we combined bioinformatics approaches with expression profiling during pathogenesis to identify candidate effectors of Z. tritici. In addition, a genetic approach was conducted to map quantitative trait loci (QTLs) carrying putative effectors, enabling the validation of both complementary strategies for effector discovery. In planta expression profiling revealed that candidate effectors were up-regulated in successive waves corresponding to consecutive stages of pathogenesis, contrary to candidates identified by QTL mapping that were, overall, expressed at low levels. Functional analyses of two top candidate effectors (SSP15 and SSP18) showed their dispensability for Z. tritici pathogenesis. These analyses reveal that generally adopted criteria, such as protein size, cysteine residues and expression during pathogenesis, may preclude an unbiased effector discovery. Indeed, genetic mapping of genomic regions involved in specificity render alternative effector candidates that do not match the aforementioned criteria, but should nevertheless be considered as promising new leads for effectors that are crucial for the Z. tritici-wheat pathosystem.
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Affiliation(s)
- Amir Mirzadi Gohari
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
- Department of Plant Protection, College of Agriculture, University of Tehran, Plant Pathology Building, Karaj, Iran
| | - Sarah B Ware
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Alexander H J Wittenberg
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Rahim Mehrabi
- Cereal Research Department, Seed and Plant Improvement Institute, PO Box 31585-4119, Karaj, Iran
| | - Sarrah Ben M'Barek
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
- Center of Biotechnology of Borj Cedria, BP 901, Hammam-Lif, 2050, Tunisia
| | - Els C P Verstappen
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Theo A J van der Lee
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
| | - Olivier Robert
- Bioplante, Florimond Desprez, BP41, 59242, Cappelle-en-Pévèle, France
| | - Henk J Schouten
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands
| | - Pierre P J G M de Wit
- Wageningen University and Research Centre, Laboratory of Phytopathology, P.O. Box 16, 6700, AA, Wageningen, The Netherlands
| | - Gert H J Kema
- Wageningen University and Research Centre, Plant Research International, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands
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142
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Derevnina L, Chin-Wo-Reyes S, Martin F, Wood K, Froenicke L, Spring O, Michelmore R. Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1198-215. [PMID: 26196322 DOI: 10.1094/mpmi-05-15-0112-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N50 = 79 kb) and 3,245 (55.3 Mb, N50 = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain-containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.
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Affiliation(s)
- Lida Derevnina
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | | | - Frank Martin
- 2 United States Department of Agriculture-Agricultural Research Service, Salinas, CA U.S.A
| | - Kelsey Wood
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | - Lutz Froenicke
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | - Otmar Spring
- 3 Institute of Botany, University of Hohenheim, Germany
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143
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Pedro H, Maheswari U, Urban M, Irvine AG, Cuzick A, McDowall MD, Staines DM, Kulesha E, Hammond-Kosack KE, Kersey PJ. PhytoPath: an integrative resource for plant pathogen genomics. Nucleic Acids Res 2015; 44:D688-93. [PMID: 26476449 PMCID: PMC4702788 DOI: 10.1093/nar/gkv1052] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/01/2015] [Indexed: 11/14/2022] Open
Abstract
PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species.
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Affiliation(s)
- Helder Pedro
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Uma Maheswari
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Martin Urban
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Alistair George Irvine
- Department of Computational and Systems Biology, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Alayne Cuzick
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Mark D McDowall
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Daniel M Staines
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Eugene Kulesha
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
| | | | - Paul Julian Kersey
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, Hinxton, Cambridgeshire, CB10 1SD, UK
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144
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Sharma R, Xia X, Cano LM, Evangelisti E, Kemen E, Judelson H, Oome S, Sambles C, van den Hoogen DJ, Kitner M, Klein J, Meijer HJG, Spring O, Win J, Zipper R, Bode HB, Govers F, Kamoun S, Schornack S, Studholme DJ, Van den Ackerveken G, Thines M. Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. BMC Genomics 2015; 16:741. [PMID: 26438312 PMCID: PMC4594904 DOI: 10.1186/s12864-015-1904-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/27/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. RESULTS Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. CONCLUSIONS The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,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. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany.
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,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.
| | - Liliana M Cano
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK. .,Present address: Department of Plant Pathology, North Carolina State University Raleigh, Raleigh, NC, 27695, USA.
| | | | - Eric Kemen
- Max Planck Institute for Plant Breeding Research, Carl von Linne´ Weg 10, Cologne, 50829, Germany.
| | - Howard Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.
| | - Stan Oome
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Christine Sambles
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - D Johan van den Hoogen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Miloslav Kitner
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 11, 78371, Olomouc, Czech Republic.
| | - Joël Klein
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Harold J G Meijer
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Otmar Spring
- University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany.
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Reinhard Zipper
- University of Hohenheim, Institute of Botany 210, D-70593, Stuttgart, Germany.
| | - Helge B Bode
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, NL-6708PB, Wageningen, The Netherlands.
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
| | | | - David J Studholme
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
| | - Guido Van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, NL-3584 CH, Utrecht, The Netherlands.
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,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. .,Center for Integrative Fungal Research (IPF), Georg-Voigt-Str. 14-16, 60325, Frankfurt (Main), Germany. .,Integrative Fungal Research (IPF), Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany.
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145
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Anderson RG, Deb D, Fedkenheuer K, McDowell JM. Recent Progress in RXLR Effector Research. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1063-72. [PMID: 26125490 DOI: 10.1094/mpmi-01-15-0022-cr] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Some of the most devastating oomycete pathogens deploy effector proteins, with the signature amino acid motif RXLR, that enter plant cells to promote virulence. Research on the function and evolution of RXLR effectors has been very active over the decade that has transpired since their discovery. Comparative genomics indicate that RXLR genes play a major role in virulence for Phytophthora and downy mildew species. Importantly, gene-for-gene resistance against these oomycete lineages is based on recognition of RXLR proteins. Comparative genomics have revealed several mechanisms through which this resistance can be broken, most notably involving epigenetic control of RXLR gene expression. Structural studies have revealed a core fold that is present in the majority of RXLR proteins, providing a foundation for detailed mechanistic understanding of virulence and avirulence functions. Finally, functional studies have demonstrated that suppression of host immunity is a major function for RXLR proteins. Host protein targets are being identified in a variety of plant cell compartments. Some targets comprise hubs that are also manipulated by bacteria and fungi, thereby revealing key points of vulnerability in the plant immune network.
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Affiliation(s)
- Ryan G Anderson
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - Devdutta Deb
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - Kevin Fedkenheuer
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - John M McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
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146
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Bourras S, McNally KE, Ben-David R, Parlange F, Roffler S, Praz CR, Oberhaensli S, Menardo F, Stirnweis D, Frenkel Z, Schaefer LK, Flückiger S, Treier G, Herren G, Korol AB, Wicker T, Keller B. Multiple Avirulence Loci and Allele-Specific Effector Recognition Control the Pm3 Race-Specific Resistance of Wheat to Powdery Mildew. THE PLANT CELL 2015; 27:2991-3012. [PMID: 26452600 PMCID: PMC4682313 DOI: 10.1105/tpc.15.00171] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 09/01/2015] [Accepted: 09/11/2015] [Indexed: 05/20/2023]
Abstract
In cereals, several mildew resistance genes occur as large allelic series; for example, in wheat (Triticum aestivum and Triticum turgidum), 17 functional Pm3 alleles confer agronomically important race-specific resistance to powdery mildew (Blumeria graminis). The molecular basis of race specificity has been characterized in wheat, but little is known about the corresponding avirulence genes in powdery mildew. Here, we dissected the genetics of avirulence for six Pm3 alleles and found that three major Avr loci affect avirulence, with a common locus_1 involved in all AvrPm3-Pm3 interactions. We cloned the effector gene AvrPm3(a2/f2) from locus_2, which is recognized by the Pm3a and Pm3f alleles. Induction of a Pm3 allele-dependent hypersensitive response in transient assays in Nicotiana benthamiana and in wheat demonstrated specificity. Gene expression analysis of Bcg1 (encoded by locus_1) and AvrPm3 (a2/f2) revealed significant differences between isolates, indicating that in addition to protein polymorphisms, expression levels play a role in avirulence. We propose a model for race specificity involving three components: an allele-specific avirulence effector, a resistance gene allele, and a pathogen-encoded suppressor of avirulence. Thus, whereas a genetically simple allelic series controls specificity in the plant host, recognition on the pathogen side is more complex, allowing flexible evolutionary responses and adaptation to resistance genes.
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Affiliation(s)
- Salim Bourras
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | | | - Roi Ben-David
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Francis Parlange
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Stefan Roffler
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | | | - Simone Oberhaensli
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Fabrizio Menardo
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Daniel Stirnweis
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Mount Carmel, 31905 Haifa, Israel
| | | | - Simon Flückiger
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Georges Treier
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Gerhard Herren
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Mount Carmel, 31905 Haifa, Israel
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
| | - Beat Keller
- Institute of Plant Biology, University of Zurich, CH-8008 Zürich, Switzerland
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147
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Sharma R, Xia X, Riess K, Bauer R, Thines M. Comparative Genomics Including the Early-Diverging Smut Fungus Ceraceosorus bombacis Reveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes. Genome Biol Evol 2015; 7:2781-98. [PMID: 26314305 PMCID: PMC4607519 DOI: 10.1093/gbe/evv162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, the genome of C. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 Mb encodes for 8,024 proteins, of which 576 are putative-secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in C. bombacis compared with other Ustilaginomycotina genomes. Metabolic pathway analyses revealed the absence of genes encoding for nitrite and nitrate reductase in the genome of the human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, while nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed for obligate biotrophic and hemi-biotrophic fungal and oomycete pathogens. Furthermore, it was found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle.
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Affiliation(s)
- Rahul Sharma
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany Cluster for Integrative Fungal Research (IPF), Frankfurt (Main), Germany
| | - Xiaojuan Xia
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany
| | - Kai Riess
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Robert Bauer
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre (BiK-F), Frankfurt (Main), Germany Department for Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt (Main), Germany Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany Cluster for Integrative Fungal Research (IPF), Frankfurt (Main), Germany
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148
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Atwell S, Corwin JA, Soltis NE, Subedy A, Denby KJ, Kliebenstein DJ. Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Front Microbiol 2015; 6:996. [PMID: 26441923 PMCID: PMC4585241 DOI: 10.3389/fmicb.2015.00996] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/07/2015] [Indexed: 01/15/2023] Open
Abstract
How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range.
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Affiliation(s)
- Susanna Atwell
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Jason A. Corwin
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Nicole E. Soltis
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Anushryia Subedy
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Katherine J. Denby
- School of Life Sciences and Warwick Systems Biology Centre, University of WarwickCoventry, UK
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149
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Blackman LM, Cullerne DP, Torreña P, Taylor J, Hardham AR. RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica. PLoS One 2015; 10:e0136899. [PMID: 26332397 PMCID: PMC4558045 DOI: 10.1371/journal.pone.0136899] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.
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Affiliation(s)
- Leila M. Blackman
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
- * E-mail:
| | - Darren P. Cullerne
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
- Agriculture Flagship, CSIRO, Canberra ACT, Australia
| | - Pernelyn Torreña
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
| | - Jen Taylor
- Agriculture Flagship, CSIRO, Canberra ACT, Australia
| | - Adrienne R. Hardham
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
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150
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Xing YM, Li XD, Liu MM, Zhang G, Wang CL, Guo SX. Morphological and Enzymatical Characterization of the Infection Process of Pythium ultimumin Dendrobium officinale(Orchidaceae). CRYPTOGAMIE MYCOL 2015. [DOI: 10.7872/crym/v36.iss3.2015.275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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