101
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Gay EJ, Soyer JL, Lapalu N, Linglin J, Fudal I, Da Silva C, Wincker P, Aury JM, Cruaud C, Levrel A, Lemoine J, Delourme R, Rouxel T, Balesdent MH. Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant. BMC Biol 2021; 19:55. [PMID: 33757516 PMCID: PMC7986464 DOI: 10.1186/s12915-021-00989-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/19/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of "two-speed" genome organisms in the genome of which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field. RESULTS We performed RNA-seq on samples corresponding to all stages of the interaction of L. maculans with its host plant, either alive or dead (stem residues after harvest) in controlled conditions or in field experiments under natural inoculum pressure, over periods of time ranging from a few days to months or years. A total of 102 biological samples corresponding to 37 sets of conditions were analyzed. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are enriched in heterochromatin regions associated with H3K9me3 or H3K27me3 repressive marks. These findings provide support for the hypothesis that part of the fungal genes involved in niche adaptation is located in heterochromatic regions of the genome, conferring an extreme plasticity of expression. CONCLUSION This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.
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Affiliation(s)
- Elise J Gay
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Jessica L Soyer
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Juliette Linglin
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, 91057, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Anne Levrel
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Jocelyne Lemoine
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Regine Delourme
- INRAE, Institut Agro, Univ Rennes, IGEPP, 35653, Le Rheu, France
| | - Thierry Rouxel
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.
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102
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Duan G, Bao J, Chen X, Xie J, Liu Y, Chen H, Zheng H, Tang W, Wang Z. Large-Scale Genome Scanning within Exonic Regions Revealed the Contributions of Selective Sweep Prone Genes to Host Divergence and Adaptation in Magnaporthe oryzae Species Complex. Microorganisms 2021; 9:562. [PMID: 33803140 PMCID: PMC8000120 DOI: 10.3390/microorganisms9030562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 11/30/2022] Open
Abstract
Magnaporthe oryzae, one of the most notorious plant pathogens in the agronomic ecosystem, causes a destructive rice blast disease around the world. The blast fungus infects wide arrays of cultivated and non-cultivated plants within the Poaceae. Studies have shown that host speciation exerts selection pressure that drives the evolution and divergence of the M. oryzae population. Population genetic relationship deducted by genome-wide single nucleotide polymorphisms showed that M. oryzae differentiation is highly consistent with the host speciation process. In particular, the rice-infecting population of M. oryzae is distinct from populations from other hosts. However, how genome regions prone to host-mediated selection pressures associated with speciation in M. oryzae, especially at a large-scale population level, has not been extensively characterized. Here, we detected strong evidence of sweep selection throughout the genomes of rice and non-rice pathotypes of M. oryzae population using integrated haplotype score (iHS), cross population extended haplotype homozygosity (XPEHH), and cross population composite likelihood ratio (XPCLR) tests. Functional annotation analyses of the genes associated with host-mediated selection pressure showed that 14 pathogenicity-related genes are under positive selection pressure. Additionally, we showed that 17 candidate effector proteins are under positive and divergent selection among the blast fungus population through sweep selection analysis. Specifically, we find that a divergent selective gene, MGG_13871, is experiencing host-directed mutation in two amino acid residues in rice and non-rice infecting populations. These results provide a crucial insight into the impact of selective sweeping on the differentiation of M. oryzae populations and the dynamic influences of genomic regions in promoting host adaptation and speciation among M. oryzae species.
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Affiliation(s)
- Guohua Duan
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiandong Bao
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Xiaomin Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiahui Xie
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuchan Liu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Huiquan Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Huakun Zheng
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Tang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
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103
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Garcia-Ceron D, Dawson CS, Faou P, Bleackley MR, Anderson MA. Size-exclusion chromatography allows the isolation of EVs from the filamentous fungal plant pathogen Fusarium oxysporum f. sp. vasinfectum (Fov). Proteomics 2021; 21:e2000240. [PMID: 33609009 DOI: 10.1002/pmic.202000240] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EVs) are nano-sized compartments involved in cell communication and macromolecule transport that are well characterized in mammalian organisms. Fungal EVs transport virulence-related cargo and modulate the host immune response, but most work has been focused on human yeast pathogens. Additionally, the study of EVs from filamentous fungi has been hindered by the lack of protein markers and efficient isolation methods. In this study we performed the isolation and proteomic characterization of EVs from the filamentous cotton pathogen Fusarium oxysporum f. sp. vasinfectum (Fov). EVs were recovered from two different growth media, Czapek Dox and Saboraud's dextrose broth, and purified by size-exclusion chromatography. Our results show that the EV proteome changes depending on the growth medium but EV production remains constant. EVs contained proteins involved in polyketide synthesis, cell wall modifications, proteases and potential effectors. These results support a role in modulation of host-pathogen interactions for Fov EVs.
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Affiliation(s)
- Donovan Garcia-Ceron
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Charlotte S Dawson
- Cambridge Centre for Proteomics, Department of Biochemistry, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Pierre Faou
- La Trobe Comprehensive Proteomics Platform, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Mark R Bleackley
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Marilyn A Anderson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
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104
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Comparative analysis of extracellular proteomes reveals putative effectors of the boxwood blight pathogens, Calonectria henricotiae and C. pseudonaviculata. Biosci Rep 2021; 41:227917. [PMID: 33619567 PMCID: PMC7937907 DOI: 10.1042/bsr20203544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/20/2021] [Accepted: 02/05/2021] [Indexed: 01/25/2023] Open
Abstract
Calonectria henricotiae (Che) and C. pseudonaviculata (Cps) are destructive fungal pathogens causing boxwood blight, a persistent threat to horticultural production, landscape industries, established gardens, and native ecosystems. Although extracellular proteins including effectors produced by fungal pathogens are known to play a fundamental role in pathogenesis, the composition of Che and Cps extracellular proteins has not been examined. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatics prediction tools, 630 extracellular proteins and 251 cell membrane proteins of Che and Cps were identified in the classical secretion pathway in the present study. In the non-classical secretion pathway, 79 extracellular proteins were identified. The cohort of proteins belonged to 364 OrthoMCL clusters, with the majority (62%) present in both species, and a subset unique to Che (19%) and Cps (20%). These extracellular proteins were predicted to play important roles in cell structure, regulation, metabolism, and pathogenesis. A total of 124 proteins were identified as putative effectors. Many of them are orthologs of proteins with documented roles in suppressing host defense and facilitating infection processes in other pathosystems, such as SnodProt1-like proteins in the OrthoMCL cluster OG5_152723 and PhiA-like cell wall proteins in the cluster OG5_155754. This exploratory study provides a repository of secreted proteins and putative effectors that can provide insights into the virulence mechanisms of the boxwood blight pathogens.
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105
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Han Z, Xiong D, Xu Z, Liu T, Tian C. The Cytospora chrysosperma Virulence Effector CcCAP1 Mainly Localizes to the Plant Nucleus To Suppress Plant Immune Responses. mSphere 2021; 6:e00883-20. [PMID: 33627507 PMCID: PMC8544888 DOI: 10.1128/msphere.00883-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/01/2021] [Indexed: 01/07/2023] Open
Abstract
Canker disease is caused by the fungus Cytospora chrysosperma and damages a wide range of woody plants, causing major losses to crops and native plants. Plant pathogens secrete virulence-related effectors into host cells during infection to regulate plant immunity and promote colonization. However, the functions of C. chrysosperma effectors remain largely unknown. In this study, we used Agrobacterium tumefaciens-mediated transient expression system in Nicotiana benthamiana and confocal microscopy to investigate the immunoregulation roles and subcellular localization of CcCAP1, a virulence-related effector identified in C. chrysosperma CcCAP1 was significantly induced in the early stages of infection and contains cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) superfamily domain with four cysteines. CcCAP1 suppressed the programmed cell death triggered by Bcl-2-associated X protein (BAX) and the elicitin infestin1 (INF1) in transient expression assays with Nicotiana benthamiana The CAP superfamily domain was sufficient for its cell death-inhibiting activity and three of the four cysteines in the CAP superfamily domain were indispensable for its activity. Pathogen challenge assays in N. benthamiana demonstrated that transient expression of CcCAP1 promoted Botrytis cinerea infection and restricted reactive oxygen species accumulation, callose deposition, and defense-related gene expression. In addition, expression of green fluorescent protein-labeled CcCAP1 in N. benthamiana showed that it localized to both the plant nucleus and the cytoplasm, but the nuclear localization was essential for its full immune inhibiting activity. These results suggest that this virulence-related effector of C. chrysosperma modulates plant immunity and functions mainly via its nuclear localization and the CAP domain.IMPORTANCE The data presented in this study provide a key resource for understanding the biology and molecular basis of necrotrophic pathogen responses to Nicotiana benthamiana resistance utilizing effector proteins, and CcCAP1 may be used in future studies to understand effector-triggered susceptibility processes in the Cytospora chrysosperma-poplar interaction system.
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Affiliation(s)
- Zhu Han
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Dianguang Xiong
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Zhiye Xu
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
| | - Tingli Liu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China
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106
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He X, Yuan Z. Near-Chromosome-Level Genome Assembly of the Dark Septate Endophyte Laburnicola rhizohalophila: A Model for Investigating Root-Fungus Symbiosis. Genome Biol Evol 2021; 13:6133230. [PMID: 33570561 PMCID: PMC7936028 DOI: 10.1093/gbe/evab026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2021] [Indexed: 11/14/2022] Open
Abstract
The novel DSE Laburnicola rhizohalophila (Pleosporales, Ascomycota) is frequently found in the halophytic seepweed (Suaeda salsa). In this article, we report a near-chromosome-level hybrid assembly of this fungus using a combination of short-read Illumina data to polish assemblies generated from long-read Nanopore data. The reference genome for L. rhizohalophila was assembled into 26 scaffolds with a total length of 64.0 Mb and a N50 length of 3.15 Mb. Of them, 17 scaffolds approached the length of intact chromosomes, and 5 had telomeres at one end only. A total of 10,891 gene models were predicted. Intriguingly, 27.5 Mb of repeat sequences that accounted for 42.97% of the genome was identified, and long terminal repeat retrotransposons were the most frequent known transposable elements, indicating that transposable element proliferation contributes to its increased genome size. BUSCO analyses using the Fungi_odb10 data set showed that 95.0% of genes were complete. In addition, 292 carbohydrate active enzymes, 33 secondary metabolite clusters, and 84 putative effectors were identified in silico. The resulting high-quality assembly and genome features are not only an important resource for further research on understanding the mechanism of root-fungi symbiotic interactions but will also contribute to comparative analyses of genome biology and evolution within Pleosporalean species.
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Affiliation(s)
- Xinghua He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Nanjing Forestry University, Nanjing, China.,Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.,Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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107
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Karki SJ, Reilly A, Zhou B, Mascarello M, Burke J, Doohan F, Douchkov D, Schweizer P, Feechan A. A small secreted protein from Zymoseptoria tritici interacts with a wheat E3 ubiquitin ligase to promote disease. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:733-746. [PMID: 33095257 PMCID: PMC7853600 DOI: 10.1093/jxb/eraa489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/15/2020] [Indexed: 05/05/2023]
Abstract
Septoria tritici blotch (STB), caused by the ascomycete fungus Zymoseptoria tritici, is a major threat to wheat production worldwide. The Z. tritici genome encodes many small secreted proteins (ZtSSPs) that are likely to play a key role in the successful colonization of host tissues. However, few of these ZtSSPs have been functionally characterized for their role during infection. In this study, we identified and characterized a small, conserved cysteine-rich secreted effector from Z. tritici which has homologues in other plant pathogens in the Dothideomycetes. ZtSSP2 was expressed throughout Z. tritici infection in wheat, with the highest levels observed early during infection. A yeast two-hybrid assay revealed an interaction between ZtSSP2 and wheat E3 ubiquitin ligase (TaE3UBQ) in yeast, and this was further confirmed in planta using bimolecular fluorescence complementation and co-immunoprecipitation. Down-regulation of this wheat E3 ligase using virus-induced gene silencing increased the susceptibility of wheat to STB. Together, these results suggest that TaE3UBQ is likely to play a role in plant immunity to defend against Z. tritici.
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Affiliation(s)
- Sujit Jung Karki
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Aisling Reilly
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Binbin Zhou
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Maurizio Mascarello
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Ecology, Evolution and Biodiversity Conservation, Charles Deberiotstraat 8 32, 3000 Leuven, Belgium
| | - James Burke
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Fiona Doohan
- School of Biology and Environmental Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Dimitar Douchkov
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Patrick Schweizer
- Institute of Plant Genetics and Crop Plant Research (IPK), Cytogenetics, Gatersleben, Germany
| | - Angela Feechan
- School of Agriculture & Food Science and UCD Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Correspondence:
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108
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Wang R, Luo S, Clarke BB, Belanger FC. The Epichloë
festucae Antifungal Protein Efe-AfpA Is also a Possible Effector Protein Required for the Interaction of the Fungus with Its Host Grass Festuca rubra subsp. rubra. Microorganisms 2021; 9:140. [PMID: 33435432 PMCID: PMC7827515 DOI: 10.3390/microorganisms9010140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/18/2020] [Accepted: 01/07/2021] [Indexed: 01/08/2023] Open
Abstract
Strong creeping red fescue (Festuca rubra subsp. rubra) is a commercially important low-maintenance turfgrass and is often naturally infected with the fungal endophyte Epichloë festucae. Epichloë spp. are endophytes of several cool-season grass species, often conferring insect resistance to the grass hosts due to the production of toxic alkaloids. In addition to insect resistance, a unique feature of the strong creeping red fescue/E. festucae symbiosis is the endophyte-mediated disease resistance to the fungal pathogen Clarireedia jacksonii, the causal agent of dollar spot disease. Such disease resistance is not a general feature of other grass/ Epichloë interactions. E. festucae isolates infecting red fescue have an antifungal protein gene Efe-afpA, whereas most other Epichloë spp. do not have a similar gene. The uniqueness of this gene suggests it may, therefore, be a component of the unique disease resistance seen in endophyte-infected red fescue. Here, we report the generation of CRISPR-Cas9 Efe-afpA gene knockouts with the goal of determining if absence of the protein in endophyte-infected Festuca rubra leads to disease susceptibility. However, it was not possible to infect plants with the knockout isolates, although infection was possible with the wild type E. festucae and with complemented isolates. This raises the interesting possibility that, in addition to having antifungal activity, the protein is required for the symbiotic interaction. The antifungal protein is a small secreted protein with high expression in planta relative to its expression in culture, all characteristics consistent with effector proteins. If Efe-AfpA is an effector protein it must be specific to certain interactions, since most Epichloë spp. do not have such a gene in their genomes.
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Affiliation(s)
- Ruying Wang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (R.W.); (S.L.); (B.B.C.)
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Simin Luo
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (R.W.); (S.L.); (B.B.C.)
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Bruce B. Clarke
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (R.W.); (S.L.); (B.B.C.)
| | - Faith C. Belanger
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (R.W.); (S.L.); (B.B.C.)
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109
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Lukito Y, Lee K, Noorifar N, Green KA, Winter DJ, Ram A, Hale TK, Chujo T, Cox MP, Johnson LJ, Scott B. Regulation of host-infection ability in the grass-symbiotic fungus Epichloë festucae by histone H3K9 and H3K36 methyltransferases. Environ Microbiol 2020; 23:2116-2131. [PMID: 33350014 DOI: 10.1111/1462-2920.15370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/02/2020] [Accepted: 12/19/2020] [Indexed: 01/30/2023]
Abstract
Recent studies have identified key genes that control the symbiotic interaction between Epichloë festucae and Lolium perenne. Here we report on the identification of specific E. festucae genes that control host infection. Deletion of setB, which encodes a homologue of the H3K36 histone methyltransferase Set2/KMT3, reduced histone H3K36 trimethylation and led to severe defects in colony growth and hyphal development. The E. festucae ΔclrD mutant, which lacks the gene encoding the homologue of the H3K9 methyltransferase KMT1, displays similar developmental defects. Both mutants are completely defective in their ability to infect L. perenne. Alleles that complement the culture and plant phenotypes of both mutants also complement the histone methylation defects. Co-inoculation of either ΔsetB or ΔclrD with the wild-type strain enables these mutants to colonize the host. However, successful colonization by the mutants resulted in death or stunting of the host plant. Transcriptome analysis at the early infection stage identified four fungal candidate genes, three of which encode small-secreted proteins, that are differentially regulated in these mutants compared to wild type. Deletion of crbA, which encodes a putative carbohydrate binding protein, resulted in significantly reduced host infection rates by E. festucae.
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Affiliation(s)
- Yonathan Lukito
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand.,Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Kate Lee
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Nazanin Noorifar
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Kimberly A Green
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - David J Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Arvina Ram
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Tracy K Hale
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Tetsuya Chujo
- Research and Development Center, Mayekawa Mfg. Co., Ltd, Tokyo, Japan
| | - Murray P Cox
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Linda J Johnson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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110
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In-depth secretome analysis of Puccinia striiformis f. sp. tritici in infected wheat uncovers effector functions. Biosci Rep 2020; 40:226968. [PMID: 33275764 PMCID: PMC7724613 DOI: 10.1042/bsr20201188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 11/17/2022] Open
Abstract
The importance of wheat yellow rust disease, caused by Puccinia striiformis f. sp. tritici (Pst), has increased substantially due to the emergence of aggressive new Pst races in the last couple of decades. In an era of escalating human populations and climate change, it is vital to understand the infection mechanism of Pst in order to develop better strategies to combat wheat yellow disease. The present study focuses on the identification of small secreted proteins (SSPs) and candidate-secreted effector proteins (CSEPs) that are used by the pathogen to support infection and control disease development. We generated de novo assembled transcriptomes of Pst collected from wheat fields in central Anatolia. We inoculated both susceptible and resistant seedlings with Pst and analyzed haustoria formation. At 10 days post-inoculation (dpi), we analyzed the transcriptomes and identified 10550 Differentially Expressed Unigenes (DEGs), of which 6072 were Pst-mapped. Among those Pst-related genes, 227 were predicted as PstSSPs. In silico characterization was performed using an approach combining the transcriptomic data and data mining results to provide a reliable list to narrow down the ever-expanding repertoire of predicted effectorome. The comprehensive analysis detected 14 Differentially Expressed Small-Secreted Proteins (DESSPs) that overlapped with the genes in available literature data to serve as the best CSEPs for experimental validation. One of the CSEPs was cloned and studied to test the reliability of the presented data. Biological assays show that the randomly selected CSEP, Unigene17495 (PSTG_10917), localizes in the chloroplast and is able to suppress cell death induced by INF1 in a Nicotiana benthamiana heterologous expression system.
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111
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Zaccaron AZ, Stergiopoulos I. First Draft Genome Resource for the Tomato Black Leaf Mold Pathogen Pseudocercospora fuligena. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1441-1445. [PMID: 33044124 DOI: 10.1094/mpmi-06-20-0139-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pseudocercospora fuligena is a fungus that causes black leaf mold, an important disease of tomato in tropical and subtropical regions of the world. Despite its economic importance, genomic resources for this pathogen are scarce and no reference genome was available thus far. Here, we report a 50.6-Mb genome assembly for P. fuligena, consisting of 348 contigs with an N50 value of 0.407 Mb. In total, 13,764 protein-coding genes were predicted with an estimated BUSCO completeness of 98%. Among the predicted genes there were 179 candidate effectors, 445 carbohydrate-active enzymes, and 30 secondary metabolite gene clusters. The resources presented in this study will allow genome-wide comparative analyses and population genomic studies of this pathogen, ultimately improving management strategies for black leaf mold of tomato.
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Affiliation(s)
- Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA 95616-8751, U.S.A
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA 95616-8751, U.S.A
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112
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Ingram TW, Oh Y, Adhikari TB, Louws FJ, Dean RA. Comparative Genome Analyses of 18 Verticillium dahliae Tomato Isolates Reveals Phylogenetic and Race Specific Signatures. Front Microbiol 2020; 11:573755. [PMID: 33329432 PMCID: PMC7734093 DOI: 10.3389/fmicb.2020.573755] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/11/2020] [Indexed: 12/03/2022] Open
Abstract
Host resistance is one of the few strategies available to combat the soil borne pathogenic fungus Verticillium dahliae. Understanding pathogen diversity in populations is key to successfully deploying host resistance. In this study the genomes of 18 V. dahliae isolates of races 1 (n = 2), 2 (n = 4), and 3 (n = 12) from Japan, California, and North Carolina were sequenced and mapped to the reference genome of JR2 (from tomato). The genomes were analyzed for phylogenetic and pathogen specific signatures to classify specific strains or genes for future research. Four highly clonal lineages/groups were discovered, including a lineage unique to North Carolina isolates, which had the rare MAT1-1 mating type. No evidence for recombination between isolates of different mating types was observed, even in isolates of different mating types discovered in the same field. By mapping these 18 isolates genomes to the JR2 reference genome, 193 unique candidate effectors were found using SignalP and EffectorP. Within these effectors, 144 highly conserved effectors, 42 mutable effectors (truncated or present in some isolates but absent in others), and 7 effectors present in highly variable regions of the chromosomes were discovered. Of the 144 core effectors, 21 were highly conserved in V. alfalfae and V. longisporum, 7 of which have no known function. Within the non-core effectors 30 contained large numbers of non-synonymous mutations, while 15 of them contained indels, frameshift mutations, or were present on highly variable regions of the chromosome. Two of these highly variable region effectors (HVREs) were only present in race 2 isolates, but not in race 3 isolates. The race 1 effector Ave1 was also present in a highly variable region. These data may suggest that these highly variable regions are enriched in race determinant genes, consistent with the two-speed genome hypothesis.
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Affiliation(s)
- Thomas W Ingram
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Yeonyee Oh
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Tika B Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Frank J Louws
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States.,Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - Ralph A Dean
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
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113
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Dubrulle G, Picot A, Madec S, Corre E, Pawtowski A, Baroncelli R, Zivy M, Balliau T, Le Floch G, Pensec F. Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis. Microorganisms 2020; 8:microorganisms8101621. [PMID: 33096724 PMCID: PMC7589765 DOI: 10.3390/microorganisms8101621] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/07/2023] Open
Abstract
The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection.
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Affiliation(s)
- Guillaume Dubrulle
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
| | - Adeline Picot
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
| | - Stéphanie Madec
- CNRS, IRD, Ifremer, LEMAR, Université de Brest, F-29280 Plouzané, France;
| | - Erwan Corre
- Station Biologique de Roscoff, FR2424 CNRS Sorbonne Université, Place Georges Teissier, 29680 Roscoff, France;
| | - Audrey Pawtowski
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
| | - Riccardo Baroncelli
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca, Calle del Duero 12, 37185 Villamayor (Salamanca), Spain;
| | - Michel Zivy
- INRAE le Moulon, Plateforme PAPPSO, ferme du Moulon, 91190 Gif-sur-Yvette, France; (M.Z.); (T.B.)
| | - Thierry Balliau
- INRAE le Moulon, Plateforme PAPPSO, ferme du Moulon, 91190 Gif-sur-Yvette, France; (M.Z.); (T.B.)
| | - Gaétan Le Floch
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
| | - Flora Pensec
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, ESIAB, Université de Brest, F-29280 Plouzané, France; (G.D.); (A.P.); (A.P.); (G.L.F.)
- Correspondence: ; Tel.: +33-(0)298-017-200
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114
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Valero-Jiménez CA, Steentjes MBF, Slot JC, Shi-Kunne X, Scholten OE, van Kan JAL. Dynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis. Genome Biol Evol 2020; 12:2491-2507. [PMID: 33283866 PMCID: PMC7719232 DOI: 10.1093/gbe/evaa218] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2020] [Indexed: 02/05/2023] Open
Abstract
Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8-39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.
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Affiliation(s)
| | | | - Jason C Slot
- Department of Plant Pathology, The Ohio State University
| | | | - Olga E Scholten
- Plant Breeding, Wageningen University & Research, The Netherlands
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, The Netherlands
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115
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Chromatin Dynamics Contribute to the Spatiotemporal Expression Pattern of Virulence Genes in a Fungal Plant Pathogen. mBio 2020; 11:mBio.02343-20. [PMID: 33024042 PMCID: PMC7542367 DOI: 10.1128/mbio.02343-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fungal plant pathogens possess a large repertoire of genes encoding putative effectors, which are crucial for infection. Many of these genes are expressed at low levels in the absence of the host but are strongly induced at specific stages of the infection. The mechanisms underlying this transcriptional reprogramming remain largely unknown. We investigated the role of the genomic environment and associated chromatin modifications of effector genes in controlling their expression pattern in the fungal wheat pathogen Zymoseptoria tritici. Depending on their genomic location, effector genes are epigenetically repressed in the absence of the host and during the initial stages of infection. Derepression of effector genes occurs mainly during and after penetration of plant leaves and is associated with changes in histone modifications. Our work demonstrates the role of chromatin in shaping the expression of virulence components and, thereby, the interaction between fungal pathogens and their plant hosts. Dynamic changes in transcription profiles are key for the success of pathogens in colonizing their hosts. In many pathogens, genes associated with virulence, such as effector genes, are located in regions of the genome that are rich in transposable elements and heterochromatin. The contribution of chromatin modifications to gene expression in pathogens remains largely unknown. Using a combination of a reporter gene-based approach and chromatin immunoprecipitation, we show that the heterochromatic environment of effector genes in the fungal plant pathogen Zymoseptoria tritici is a key regulator of their specific spatiotemporal expression patterns. Enrichment in trimethylated lysine 27 of histone H3 dictates the repression of effector genes in the absence of the host. Chromatin decondensation during host colonization, featuring a reduction in this repressive modification, indicates a major role for epigenetics in effector gene induction. Our results illustrate that chromatin modifications triggered during host colonization determine the specific expression profile of effector genes at the cellular level and, hence, provide new insights into the regulation of virulence in fungal plant pathogens.
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116
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Sperschneider J. Machine learning in plant-pathogen interactions: empowering biological predictions from field scale to genome scale. THE NEW PHYTOLOGIST 2020; 228:35-41. [PMID: 30834534 DOI: 10.1111/nph.15771] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/21/2019] [Indexed: 05/25/2023]
Abstract
Machine learning (ML) encompasses statistical methods that learn to identify patterns in complex datasets. Here, I review application areas in plant-pathogen interactions that have recently benefited from ML, such as disease monitoring, the discovery of gene regulatory networks, genomic selection for disease resistance and prediction of pathogen effectors. However, achieving robust performance from ML is not trivial and requires knowledge of both the methodology and the biology. I discuss common pitfalls and challenges in using ML approaches. Finally, I highlight future opportunities for ML as a tool for dissecting plant-pathogen interactions using high-throughput data, for example, through integration of diverse data sources and the analysis with higher resolution, such as from individual cells or on elaborate spatial and temporal scales.
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Affiliation(s)
- Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2600, Australia
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
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117
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Zhang Y, Wei J, Qi Y, Li J, Amin R, Yang W, Liu D. Predicating the Effector Proteins Secreted by Puccinia triticina Through Transcriptomic Analysis and Multiple Prediction Approaches. Front Microbiol 2020; 11:538032. [PMID: 33072007 PMCID: PMC7536266 DOI: 10.3389/fmicb.2020.538032] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/26/2020] [Indexed: 11/17/2022] Open
Abstract
Wheat leaf rust caused by Puccinia triticina is one of the most common and serious diseases in wheat production. The constantly changing pathogens overcome the plant resistance to P. triticina. Plant pathogens secrete effector proteins that alter the structure of the host cell, interfere plant defenses, or modify the physiology of plant cells. Therefore, the identification of effector proteins is critical to reveal the pathogenic mechanism. We used SignalP v4.1, TargetP v1.1, TMHMM v2.0, and EffectorP v2.0 to screen the candidate effector proteins in P. triticina isolates – KHTT, JHKT, and THSN. As a result, a total of 635 candidate effector proteins were obtained. Structural analysis showed that effector proteins were small in size (50AA to 422AA) and of diverse sequences, and the conserved sequential elements or clear common elements were not involved, regardless of their secretion from the pathogen to the host. There were 427 candidate effector proteins that contain more than or equal to 4 cysteine residues, and 339 candidate effector proteins contained the known motifs. Sixteen families, 9 domains, and 53 other known functional types were found in 186 candidate effector proteins using the Pfam search. Three novel motifs were found by MEME. Heterogeneous expression system was performed to verify the functions of 30 candidate effectors by inhibiting the programmed cell death (PCD) induced by BAX (the mouse-apoptotic gene elicitor) on Nicotiana benthamiana. Hypersensitive response (HR) can be induced by the six effectors in the wheat leaf rust resistance near isogenic lines, and this would be shown by the method of transient expression through Agrobacterium tumefaciens infiltration. The quantitative reverse transcription PCR (qRT-PCR) analysis of 14 candidate effector proteins secreted after P. triticina inoculation showed that the tested effectors displayed different expression patterns in different stages, suggesting that they may be involved in the wheat–P. triticina interaction. The results showed that the prediction of P. triticina effector proteins based on transcriptomic analysis and multiple bioinformatics software is effective and more accurate, laying the foundation of revealing the pathogenic mechanism of Pt and controlling disease.
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Affiliation(s)
- Yue Zhang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Jie Wei
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Yue Qi
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Jianyuan Li
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China.,College of Biological Sciences and Engineering, Hebei Xingtai College, Xingtai, China
| | - Raheela Amin
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Wenxiang Yang
- College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Daqun Liu
- Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China
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118
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Abdelsalam SSH, Kouzai Y, Watanabe M, Inoue K, Matsui H, Yamamoto M, Ichinose Y, Toyoda K, Tsuge S, Mochida K, Noutoshi Y. Identification of effector candidate genes of Rhizoctonia solani AG-1 IA expressed during infection in Brachypodium distachyon. Sci Rep 2020; 10:14889. [PMID: 32913311 PMCID: PMC7483729 DOI: 10.1038/s41598-020-71968-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/24/2020] [Indexed: 11/23/2022] Open
Abstract
Rhizoctonia solani is a necrotrophic phytopathogen belonging to basidiomycetes. It causes rice sheath blight which inflicts serious damage in rice production. The infection strategy of this pathogen remains unclear. We previously demonstrated that salicylic acid-induced immunity could block R. solani AG-1 IA infection in both rice and Brachypodium distachyon. R. solani may undergo biotrophic process using effector proteins to suppress host immunity before necrotrophic stage. To identify pathogen genes expressed at the early infection process, here we developed an inoculation method using B. distachyon which enables to sample an increased amount of semi-synchronous infection hyphae. Sixty-one R. solani secretory effector-like protein genes (RsSEPGs) were identified using in silico approach with the publicly available gene annotation of R. solani AG-1 IA genome and our RNA-sequencing results obtained from hyphae grown on agar medium. Expression of RsSEPGs was analyzed at 6, 10, 16, 24, and 32 h after inoculation by a quantitative reverse transcription-polymerase chain reaction and 52 genes could be detected at least on a single time point tested. Their expressions showed phase-specific patterns which were classified into 6 clusters. The 23 RsSEPGs in the cluster 1–3 and 29 RsSEPGs in the cluster 4–6 are expected to be involved in biotrophic and necrotrophic interactions, respectively.
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Affiliation(s)
- Sobhy S H Abdelsalam
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.,Plant Pathology Department, Faculty of Agriculture, Alexandria University, El-Shatby, Egypt
| | - Yusuke Kouzai
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Megumi Watanabe
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Komaki Inoue
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yuki Ichinose
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Seiji Tsuge
- Graduate School of Agriculture, Kyoto Prefectural University, Kyoto, Japan
| | - Keiichi Mochida
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.,Institute for Plant Science and Resources (IPSR), Okayama University, Okayama, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
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119
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Jaswal R, Kiran K, Rajarammohan S, Dubey H, Singh PK, Sharma Y, Deshmukh R, Sonah H, Gupta N, Sharma TR. Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospects. Microbiol Res 2020; 241:126567. [PMID: 33080488 DOI: 10.1016/j.micres.2020.126567] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 07/21/2020] [Accepted: 07/25/2020] [Indexed: 12/13/2022]
Abstract
The interaction of fungal pathogens with their host requires a novel invading mechanism and the presence of various virulence-associated components responsible for promoting the infection. The small secretory proteins, explicitly known as effector proteins, are one of the prime mechanisms of host manipulation utilized by the pathogen to disarm the host. Several effector proteins are known to translocate from fungus to the plant cell for host manipulation. Many fungal effectors have been identified using genomic, transcriptomic, and bioinformatics approaches. Most of the effector proteins are devoid of any conserved signatures, and their prediction based on sequence homology is very challenging, therefore by combining the sequence consensus based upon machine learning features, multiple tools have also been developed for predicting apoplastic and cytoplasmic effectors. Various post-genomics approaches like transcriptomics of virulent isolates have also been utilized for identifying active consortia of effectors. Significant progress has been made in understanding biotrophic effectors; however, most of it is underway due to their complex interaction with host and complicated recognition and signaling networks. This review discusses advances, and challenges in effector identification and highlighted various features of the potential effector proteins and approaches for understanding their genetics and strategies for regulation.
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Affiliation(s)
- Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India; Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India
| | - Kanti Kiran
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | | | - Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology, Pusa Campus New Delhi, 110012, India
| | - Pankaj Kumar Singh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Yogesh Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Naveen Gupta
- Department of Microbiology, Panjab University, Chandigarh, Punjab, 160014, India.
| | - T R Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India.
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120
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Rocafort M, Fudal I, Mesarich CH. Apoplastic effector proteins of plant-associated fungi and oomycetes. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:9-19. [PMID: 32247857 DOI: 10.1016/j.pbi.2020.02.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/08/2020] [Accepted: 02/14/2020] [Indexed: 05/23/2023]
Abstract
The outcome of an interaction between a plant and a fungus or an oomycete, whether compatibility or incompatibility, is often determined in the hostile extracellular spaces and matrices of the apoplast. Indeed, for compatibility to occur, many plant-associated fungi and oomycetes must first neutralize the apoplast, which is both monitored by plant cell-surface immune receptors, and enriched in plant (and frequently, competitor)-derived antimicrobial compounds. Research is highlighting the diverse roles that fungal and oomycete effector proteins play in the apoplast to promote compatibility, with most recent progress made towards understanding the role of these proteins in evading chitin-triggered immunity. Research is also showcasing the ability of apoplastic effector proteins to bring about incompatibility upon recognition by diverse plant cell-surface immune receptors, and the use of effectoromics to rapidly identify apoplastic effector protein-cell-surface immune receptor interactions.
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Affiliation(s)
- Mercedes Rocafort
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Isabelle Fudal
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France
| | - Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand; Bio-Protection Research Centre, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand.
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Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14. G3-GENES GENOMES GENETICS 2020; 10:2131-2140. [PMID: 32345704 PMCID: PMC7341154 DOI: 10.1534/g3.120.401265] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ascochyta rabiei is the causal organism of ascochyta blight of chickpea and is present in chickpea crops worldwide. Here we report the release of a high-quality PacBio genome assembly for the Australian A. rabiei isolate ArME14. We compare the ArME14 genome assembly with an Illumina assembly for Indian A. rabiei isolate, ArD2. The ArME14 assembly has gapless sequences for nine chromosomes with telomere sequences at both ends and 13 large contig sequences that extend to one telomere. The total length of the ArME14 assembly was 40,927,385 bp, which was 6.26 Mb longer than the ArD2 assembly. Division of the genome by OcculterCut into GC-balanced and AT-dominant segments reveals 21% of the genome contains gene-sparse, AT-rich isochores. Transposable elements and repetitive DNA sequences in the ArME14 assembly made up 15% of the genome. A total of 11,257 protein-coding genes were predicted compared with 10,596 for ArD2. Many of the predicted genes missing from the ArD2 assembly were in genomic regions adjacent to AT-rich sequence. We compared the complement of predicted transcription factors and secreted proteins for the two A. rabiei genome assemblies and found that the isolates contain almost the same set of proteins. The small number of differences could represent real differences in the gene complement between isolates or possibly result from the different sequencing methods used. Prediction pipelines were applied for carbohydrate-active enzymes, secondary metabolite clusters and putative protein effectors. We predict that ArME14 contains between 450 and 650 CAZymes, 39 putative protein effectors and 26 secondary metabolite clusters.
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Zhao S, Shang X, Bi W, Yu X, Liu D, Kang Z, Wang X, Wang X. Genome-Wide Identification of Effector Candidates With Conserved Motifs From the Wheat Leaf Rust Fungus Puccinia triticina. Front Microbiol 2020; 11:1188. [PMID: 32582112 PMCID: PMC7283542 DOI: 10.3389/fmicb.2020.01188] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
Rust fungi secrete various specialized effectors into host cells to manipulate the plant defense response. Conserved motifs, including RXLR, LFLAK-HVLVxxP (CRN), Y/F/WxC, CFEM, LysM, EAR, [SG]-P-C-[KR]-P, DPBB_1 (PNPi), and ToxA, have been identified in various oomycete and fungal effectors and are reported to be crucial for effector translocation or function. However, little is known about potential effectors containing any of these conserved motifs in the wheat leaf rust fungus (Puccinia triticina, Pt). In this study, sequencing was performed on RNA samples collected from the germ tubes (GT) of uredospores of an epidemic Pt pathotype PHTT(P) and Pt-infected leaves of a susceptible wheat cultivar "Chinese Spring" at 4, 6, and 8 days post-inoculation (dpi). The assembled transcriptome data were compared to the reference genome of "Pt 1-1 BBBD Race 1." A total of 17,976 genes, including 2,284 "novel" transcripts, were annotated. Among all these genes, we identified 3,149 upregulated genes upon Pt infection at all time points compared to GT, whereas 1,613 genes were more highly expressed in GT. A total of 464 secreted proteins were encoded by those upregulated genes, with 79 of them also predicted as possible effectors by EffectorP. Using hmmsearch and Regex, we identified 719 RXLR-like, 19 PNPi-like, 19 CRN-like, 138 Y/F/WxC, and 9 CFEM effector candidates from the deduced protein database including data based on the "Pt 1-1 BBBD Race 1" genome and the transcriptome data collected here. Four of the PNPi-like effector candidates with DPBB_1 conserved domain showed physical interactions with wheat NPR1 protein in yeast two-hybrid assay. Nine Y/F/WxC and seven CFEM effector candidates were transiently expressed in Nicotiana benthamiana. None of these effector candidates showed induction or suppression of cell death triggered by BAX protein, but the expression of one CFEM effector candidate, PTTG_08198, accelerated the progress of cell death and promoted the accumulation of reactive oxygen species (ROS). In conclusion, we profiled genes associated with the infection process of the Pt pathotype PHTT(P). The identified effector candidates with conserved motifs will help guide the investigation of virulent mechanisms of leaf rust fungus.
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Affiliation(s)
- Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Xiaofeng Shang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Weishuai Bi
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Xiumei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Daqun Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang, China
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Technological Innovation Center for Biological Control of Crop Diseases and Insect Pests of Hebei Province, Hebei Agricultural University, Baoding, China
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Jeffress S, Arun-Chinnappa K, Stodart B, Vaghefi N, Tan YP, Ash G. Genome mining of the citrus pathogen Elsinoë fawcettii; prediction and prioritisation of candidate effectors, cell wall degrading enzymes and secondary metabolite gene clusters. PLoS One 2020; 15:e0227396. [PMID: 32469865 PMCID: PMC7259788 DOI: 10.1371/journal.pone.0227396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/17/2020] [Indexed: 11/22/2022] Open
Abstract
Elsinoë fawcettii, a necrotrophic fungal pathogen, causes citrus scab on numerous citrus varieties around the world. Known pathotypes of E. fawcettii are based on host range; additionally, cryptic pathotypes have been reported and more novel pathotypes are thought to exist. E. fawcettii produces elsinochrome, a non-host selective toxin which contributes to virulence. However, the mechanisms involved in potential pathogen-host interactions occurring prior to the production of elsinochrome are unknown, yet the host-specificity observed among pathotypes suggests a reliance upon such mechanisms. In this study we have generated a whole genome sequencing project for E. fawcettii, producing an annotated draft assembly 26.01 Mb in size, with 10,080 predicted gene models and low (0.37%) coverage of transposable elements. A small proportion of the assembly showed evidence of AT-rich regions, potentially indicating genomic regions with increased plasticity. Using a variety of computational tools, we mined the E. fawcettii genome for potential virulence genes as candidates for future investigation. A total of 1,280 secreted proteins and 276 candidate effectors were predicted and compared to those of other necrotrophic (Botrytis cinerea, Parastagonospora nodorum, Pyrenophora tritici-repentis, Sclerotinia sclerotiorum and Zymoseptoria tritici), hemibiotrophic (Leptosphaeria maculans, Magnaporthe oryzae, Rhynchosporium commune and Verticillium dahliae) and biotrophic (Ustilago maydis) plant pathogens. Genomic and proteomic features of known fungal effectors were analysed and used to guide the prioritisation of 120 candidate effectors of E. fawcettii. Additionally, 378 carbohydrate-active enzymes were predicted and analysed for likely secretion and sequence similarity with known virulence genes. Furthermore, secondary metabolite prediction indicated nine additional genes potentially involved in the elsinochrome biosynthesis gene cluster than previously described. A further 21 secondary metabolite clusters were predicted, some with similarity to known toxin producing gene clusters. The candidate virulence genes predicted in this study provide a comprehensive resource for future experimental investigation into the pathogenesis of E. fawcettii.
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Affiliation(s)
- Sarah Jeffress
- Centre for Crop Health, Institute for Life Sciences and the Environment, Research and Innovation Division, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Kiruba Arun-Chinnappa
- Centre for Crop Health, Institute for Life Sciences and the Environment, Research and Innovation Division, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Ben Stodart
- Graham Centre for Agricultural Innovation, (Charles Sturt University and NSW Department of Primary Industries), School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Niloofar Vaghefi
- Centre for Crop Health, Institute for Life Sciences and the Environment, Research and Innovation Division, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Yu Pei Tan
- Department of Agriculture and Fisheries, Queensland Government, Brisbane, QLD, Australia
| | - Gavin Ash
- Centre for Crop Health, Institute for Life Sciences and the Environment, Research and Innovation Division, University of Southern Queensland, Toowoomba, QLD, Australia
- Graham Centre for Agricultural Innovation, (Charles Sturt University and NSW Department of Primary Industries), School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
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MacWilliams JR, Dingwall S, Chesnais Q, Sugio A, Kaloshian I. AcDCXR Is a Cowpea Aphid Effector With Putative Roles in Altering Host Immunity and Physiology. FRONTIERS IN PLANT SCIENCE 2020; 11:605. [PMID: 32499809 PMCID: PMC7243947 DOI: 10.3389/fpls.2020.00605] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/21/2020] [Indexed: 06/01/2023]
Abstract
Cowpea, Vigna unguiculata, is a crop that is essential to semiarid areas of the world like Sub-Sahara Africa. Cowpea is highly susceptible to cowpea aphid, Aphis craccivora, infestation that can lead to major yield losses. Aphids feed on their host plant by inserting their hypodermal needlelike flexible stylets into the plant to reach the phloem sap. During feeding, aphids secrete saliva, containing effector proteins, into the plant to disrupt plant immune responses and alter the physiology of the plant to their own advantage. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to identify the salivary proteome of the cowpea aphid. About 150 candidate proteins were identified including diacetyl/L-xylulose reductase (DCXR), a novel enzyme previously unidentified in aphid saliva. DCXR is a member of short-chain dehydrogenases/reductases with dual enzymatic functions in carbohydrate and dicarbonyl metabolism. To assess whether cowpea aphid DCXR (AcDCXR) has similar functions, recombinant AcDCXR was purified and assayed enzymatically. For carbohydrate metabolism, the oxidation of xylitol to xylulose was tested. The dicarbonyl reaction involved the reduction of methylglyoxal, an α-β-dicarbonyl ketoaldehyde, known as an abiotic and biotic stress response molecule causing cytotoxicity at high concentrations. To assess whether cowpea aphids induce methylglyoxal in plants, we measured methylglyoxal levels in both cowpea and pea (Pisum sativum) plants and found them elevated transiently after aphid infestation. Agrobacterium-mediated transient overexpression of AcDCXR in pea resulted in an increase of cowpea aphid fecundity. Taken together, our results indicate that AcDCXR is an effector with a putative ability to generate additional sources of energy to the aphid and to alter plant defense responses. In addition, this work identified methylglyoxal as a potential novel aphid defense metabolite adding to the known repertoire of plant defenses against aphid pests.
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Affiliation(s)
- Jacob R. MacWilliams
- Graduate Program in Biochemistry and Molecular Biology, University of California, Riverside, Riverside, CA, United States
| | - Stephanie Dingwall
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | | | - Akiko Sugio
- INRAE, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Isgouhi Kaloshian
- Graduate Program in Biochemistry and Molecular Biology, University of California, Riverside, Riverside, CA, United States
- Department of Nematology, University of California Riverside, Riverside, CA, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
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125
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Pelgrom AJE, Meisrimler CN, Elberse J, Koorman T, Boxem M, Van den Ackerveken G. Host interactors of effector proteins of the lettuce downy mildew Bremia lactucae obtained by yeast two-hybrid screening. PLoS One 2020; 15:e0226540. [PMID: 32396563 PMCID: PMC7217486 DOI: 10.1371/journal.pone.0226540] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/24/2020] [Indexed: 12/26/2022] Open
Abstract
Plant pathogenic bacteria, fungi and oomycetes secrete effector proteins to manipulate host cell processes to establish a successful infection. Over the last decade the genomes and transcriptomes of many agriculturally important plant pathogens have been sequenced and vast candidate effector repertoires were identified using bioinformatic analyses. Elucidating the contribution of individual effectors to pathogenicity is the next major hurdle. To advance our understanding of the molecular mechanisms underlying lettuce susceptibility to the downy mildew Bremia lactucae, we mapped physical interactions between B. lactucae effectors and lettuce candidate target proteins. Using a lettuce cDNA library-based yeast-two-hybrid system, 61 protein-protein interactions were identified, involving 21 B. lactucae effectors and 46 unique lettuce proteins. The top ten interactors based on the number of independent colonies identified in the Y2H and two interactors that belong to gene families involved in plant immunity, were further characterized. We determined the subcellular localization of the fluorescently tagged lettuce proteins and their interacting effectors. Importantly, relocalization of effectors or their interactors to the nucleus was observed for four protein-pairs upon their co-expression, supporting their interaction in planta.
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Affiliation(s)
- Alexandra J. E. Pelgrom
- Plant–Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | | | - Joyce Elberse
- Plant–Microbe Interactions, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Thijs Koorman
- Developmental Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Mike Boxem
- Developmental Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
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Genome Sequence of Fusarium graminearum Strain CML3066, Isolated from a Wheat Spike in Southern Brazil. Microbiol Resour Announc 2020; 9:9/19/e00157-20. [PMID: 32381606 PMCID: PMC7206484 DOI: 10.1128/mra.00157-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fusarium graminearum is a global fungal pathogen of wheat and other small grains, causing Fusarium head blight (FHB) disease, also known as wheat scab. We report here the annotated genome of a deoxynivalenol/15-acetyl-deoxynivalenol-producing Brazilian strain called CML3066, isolated from FHB-symptomatic wheat spikes collected in 2009. Fusarium graminearum is a global fungal pathogen of wheat and other small grains, causing Fusarium head blight (FHB) disease, also known as wheat scab. We report here the annotated genome of a deoxynivalenol/15-acetyl-deoxynivalenol-producing Brazilian strain called CML3066, isolated from FHB-symptomatic wheat spikes collected in 2009.
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127
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Carreón-Anguiano KG, Islas-Flores I, Vega-Arreguín J, Sáenz-Carbonell L, Canto-Canché B. EffHunter: A Tool for Prediction of Effector Protein Candidates in Fungal Proteomic Databases. Biomolecules 2020; 10:biom10050712. [PMID: 32375409 PMCID: PMC7277995 DOI: 10.3390/biom10050712] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/17/2020] [Accepted: 03/21/2020] [Indexed: 11/16/2022] Open
Abstract
Pathogens are able to deliver small-secreted, cysteine-rich proteins into plant cells to enable infection. The computational prediction of effector proteins remains one of the most challenging areas in the study of plant fungi interactions. At present, there are several bioinformatic programs that can help in the identification of these proteins; however, in most cases, these programs are managed independently. Here, we present EffHunter, an easy and fast bioinformatics tool for the identification of effectors. This predictor was used to identify putative effectors in 88 proteomes using characteristics such as size, cysteine residue content, secretion signal and transmembrane domains.
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Affiliation(s)
- Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Julio Vega-Arreguín
- Laboratorio de Ciencias AgroGenómicas, Escuela Nacional de Estudios Superiores-UNAM, León, México
| | - Luis Sáenz-Carbonell
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 X 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205 Mérida, México
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Wang D, Tian L, Zhang D, Song J, Song S, Yin C, Zhou L, Liu Y, Wang B, Kong Z, Klosterman SJ, Li J, Wang J, Li T, Adamu S, Subbarao KV, Chen J, Dai X. Functional analyses of small secreted cysteine-rich proteins identified candidate effectors in Verticillium dahliae. MOLECULAR PLANT PATHOLOGY 2020; 21:667-685. [PMID: 32314529 PMCID: PMC7170778 DOI: 10.1111/mpp.12921] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 05/09/2023]
Abstract
Secreted small cysteine-rich proteins (SCPs) play a critical role in modulating host immunity in plant-pathogen interactions. Bioinformatic analyses showed that the fungal pathogen Verticillium dahliae encodes more than 100 VdSCPs, but their roles in host-pathogen interactions have not been fully characterized. Transient expression of 123 VdSCP-encoding genes in Nicotiana benthamiana identified three candidate genes involved in host-pathogen interactions. The expression of these three proteins, VdSCP27, VdSCP113, and VdSCP126, in N. benthamiana resulted in cell death accompanied by a reactive oxygen species burst, callose deposition, and induction of defence genes. The three VdSCPs mainly localized to the periphery of the cell. BAK1 and SOBIR1 (associated with receptor-like protein) were required for the immunity triggered by these three VdSCPs in N. benthamiana. Site-directed mutagenesis showed that cysteine residues that form disulphide bonds are essential for the functioning of VdSCP126, but not VdSCP27 and VdSCP113. VdSCP27, VdSCP113, and VdSCP126 individually are not essential for V. dahliae infection of N. benthamiana and Gossypium hirsutum, although there was a significant reduction of virulence on N. benthamiana and G. hirsutum when inoculated with the VdSCP27/VdSCP126 double deletion strain. These results illustrate that the SCPs play a critical role in the V. dahliae-plant interaction via an intrinsic virulence function and suppress immunity following infection.
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Affiliation(s)
- Dan Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Li Tian
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Dan‐Dan Zhang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport ProcessMinistry of AgricultureBeijingChina
| | - Jian Song
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | | | - Chun‐Mei Yin
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Lei Zhou
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport ProcessMinistry of AgricultureBeijingChina
| | - Yan Liu
- College of Life ScienceQufu Normal UniversityQufuChina
| | - Bao‐Li Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Zhi‐Qiang Kong
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Steven J. Klosterman
- United States Department of AgricultureAgricultural Research ServiceSalinasCAUSA
| | - Jun‐Jiao Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Jie Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Ting‐Gang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Sabiu Adamu
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Krishna V. Subbarao
- Department of Plant PathologyUniversity of CaliforniaDavis, c/o United States Agricultural Research StationSalinasCAUSA
| | - Jie‐Yin Chen
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport ProcessMinistry of AgricultureBeijingChina
| | - Xiao‐Feng Dai
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
- Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport ProcessMinistry of AgricultureBeijingChina
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129
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Schwessinger B, Chen YJ, Tien R, Vogt JK, Sperschneider J, Nagar R, McMullan M, Sicheritz-Ponten T, Sørensen CK, Hovmøller MS, Rathjen JP, Justesen AF. Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat. Genome Biol Evol 2020; 12:597-617. [PMID: 32271913 DOI: 10.1101/859728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 05/27/2023] Open
Abstract
Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.
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Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Yan-Jun Chen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Richard Tien
- School of Dentistry, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Josef Korbinian Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Ramawatar Nagar
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Mark McMullan
- Earlham Institute, Norwich Research Park, United Kingdom
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | | | - John P Rathjen
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Annemarie Fejer Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
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130
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Schwessinger B, Chen YJ, Tien R, Vogt JK, Sperschneider J, Nagar R, McMullan M, Sicheritz-Ponten T, Sørensen CK, Hovmøller MS, Rathjen JP, Justesen AF. Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat. Genome Biol Evol 2020; 12:597-617. [PMID: 32271913 PMCID: PMC7250506 DOI: 10.1093/gbe/evaa071] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 12/12/2022] Open
Abstract
Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.
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Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Yan-Jun Chen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Richard Tien
- School of Dentistry, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Josef Korbinian Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Ramawatar Nagar
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Mark McMullan
- Earlham Institute, Norwich Research Park, United Kingdom
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | | | - John P Rathjen
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Annemarie Fejer Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
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131
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Queiroz CBD, Santana MF. Prediction of the secretomes of endophytic and nonendophytic fungi reveals similarities in host plant infection and colonization strategies. Mycologia 2020; 112:491-503. [PMID: 32286912 DOI: 10.1080/00275514.2020.1716566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Endophytic fungi are microorganisms that inhabit internal plant tissues without causing apparent damage. During the infection process, both endophytic and phytopathogenic fungi secrete proteins to resist or supplant the plant's defense mechanisms. This study analyzed the predicted secretomes of six species of endophytic fungi and compared them with predicted secretomes of eight fungal species with different lifestyles: saprophytic, necrotrophic, hemibiotrophic, and biotrophic. The sizes of the predicted secretomes varied from 260 to 1640 proteins, and the predicted secretomes have a wide diversity of CAZymes, proteases, and conserved domains. Regarding the CAZymes in the secretomes of the analyzed fungi, the most abundant CAZyme families were glycosyl hydrolase and serine proteases. Several predicted proteins have characteristics similar to those found in small, secreted proteins with effector characteristics (SSPEC). The most abundant conserved domains, besides those found in the SSPEC, have oxidation activities, indicating that these proteins can protect the fungus against oxidative stress, against domains with protease activity, which may be involved in the mechanisms of nutrition, or against lytic enzymes secreted by the host plant. This study demonstrates that secretomes of endophytic and nonendophytic fungi share an arsenal of proteins important in the process of infection and colonization of host plants.
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Affiliation(s)
- Casley Borges de Queiroz
- Laboratório de Biologia Molecular, Embrapa Amazônia Ocidental , Rodovia AM 10, km 29, s/n, CEP: 69010-970, Manaus, Amazonas, Brazil
| | - Mateus Ferreira Santana
- Departamento de Microbiologia (BIOAGRO), Universidade Federal de Viçosa , CEP: 36570-900, Viçosa, Minas Gerais, Brazil
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132
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Zhao S, An B, Guo Y, Hou X, Luo H, He C, Wang Q. Label free proteomics and systematic analysis of secretome reveals effector candidates regulated by SGE1 and FTF1 in the plant pathogen Fusarium oxysporum f. sp. cubense tropical race 4. BMC Genomics 2020; 21:275. [PMID: 32245409 PMCID: PMC7119298 DOI: 10.1186/s12864-020-6695-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Phytopathogens secreted effectors during host colonization to suppress or trigger plant immunity. Identification of new effectors is one of the research focuses in recent years. There is only a limited knowledge about effectors of Fusarium oxysporum f. sp. Cubense tropical race 4 (Foc TR4), the causal agent of wilt disease in Cavendish banana. RESULTS Two transcription factors, SGE1 and FTF1, were constitutively over-expressed in Foc TR4 to partially mimic the in-planta state. Secreted proteins with high purity were prepared through a two-round extraction method. Then the secretome were analyzed via label free proteomics method. A total of 919 non-redundant proteins were detected, of which 74 proteins were predicted to be effector candidates. Among these candidates, 29 were up-regulated and 13 down-regulated in the strain over-expressing SGE1 and FTF1, 8 were up-regulated and 4 down-regulated in either SGE1 or FTF1 over expression strain. CONCLUSIONS Through label free proteomics analysis, a series of effector candidates were identified in secretome of Foc TR4. Our work put a foundation for functional research of these effectors.
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Affiliation(s)
- Shixue Zhao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Bang An
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Yanhua Guo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Xingrong Hou
- College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, Hainan, 572022, People's Republic of China
| | - Hongli Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Chaozu He
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Qiannan Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China.
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133
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Martin A, Moolhuijzen P, Tao Y, McIlroy J, Ellwood SR, Fowler RA, Platz GJ, Kilian A, Snyman L. Genomic Regions Associated with Virulence in Pyrenophora teres f. teres Identified by Genome-Wide Association Analysis and Biparental Mapping. PHYTOPATHOLOGY 2020; 110:881-891. [PMID: 31855502 DOI: 10.1094/phyto-10-19-0372-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.
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Affiliation(s)
- Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland 4370, Australia
| | - Paula Moolhuijzen
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Yongfu Tao
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Judy McIlroy
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Simon R Ellwood
- Centre for Crop & Disease Management, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6102, Australia
| | - Ryan A Fowler
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Greg J Platz
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology, Bruce, Australian Capital Territory 2617, Australia
| | - Lisle Snyman
- Hermitage Research Facility, Department of Agriculture & Fisheries, Warwick, Queensland 4370, Australia
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134
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Feldman D, Yarden O, Hadar Y. Seeking the Roles for Fungal Small-Secreted Proteins in Affecting Saprophytic Lifestyles. Front Microbiol 2020; 11:455. [PMID: 32265881 PMCID: PMC7105643 DOI: 10.3389/fmicb.2020.00455] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/03/2020] [Indexed: 11/24/2022] Open
Abstract
Small secreted proteins (SSPs) comprise 40–60% of the total fungal secretome and are present in fungi of all phylogenetic groups, representing the entire spectrum of lifestyles. They are characteristically shorter than 300 amino acids in length and have a signal peptide. The majority of SSPs are coded by orphan genes, which lack known domains or similarities to known protein sequences. Effectors are a group of SSPs that have been investigated extensively in fungi that interact with living hosts, either pathogens or mutualistic systems. They are involved in suppressing the host defense response and altering its physiology. Here, we aim to delineate some of the potential roles of SSPs in saprotrophic fungi, that have been bioinformatically predicted as effectors, and termed in this mini-review as “effector-like” proteins. The effector-like Ssp1 from the white-rot fungus Pleurotus ostreatus is presented as a case study, and its potential role in regulating the ligninolytic system, secondary metabolism, development, and fruiting body initiation are discussed. We propose that deciphering the nature of effector-like SSPs will contribute to our understanding of development and communication in saprophytic fungi, as well as help, to elucidate the origin, regulation, and mechanisms of fungal-host, fungal-fungal, and fungal-bacterial interactions.
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Affiliation(s)
- Daria Feldman
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yitzhak Hadar
- Department of Plant Pathology and Microbiology, The R.H. Smith Faculty Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem, Israel
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135
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Human MP, Berger DK, Crampton BG. Time-Course RNAseq Reveals Exserohilum turcicum Effectors and Pathogenicity Determinants. Front Microbiol 2020; 11:360. [PMID: 32265851 PMCID: PMC7099616 DOI: 10.3389/fmicb.2020.00360] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/18/2020] [Indexed: 11/16/2022] Open
Abstract
Exserohilum turcicum (sexual stage Setosphaeria turcica) is the hemibiotrophic causal agent of northern leaf blight of maize and sorghum. This study aimed to identify the genes involved in host colonization during the biotrophic and necrotrophic phases of infection. It also aimed to identify race-specific differences in gene expression. RNAseq of maize seedlings inoculated with a race 13N or 23N E. turcicum isolate was conducted before inoculation and at 2, 5, 7, and 13 days post-inoculation (dpi). Biological replicates were pooled per time point for each race and sequenced. A bioinformatics pipeline was used to identify candidate effectors, and expression was validated for selected candidates. Fungal biomass was positively correlated with the percentages of E. turcicum reads mapped, which were low at early time points (2-7 dpi) with a significant increase at 13 dpi, indicating a lifestyle switch from biotrophy to necrotrophy between 7 and 13 dpi. AVRHt1 is the putative E. turcicum effector recognized by the maize resistance gene Ht1. Consistent with this, AVRHt1 was expressed in planta by race 23N, but transcripts were absent in race 13N. In addition, specific transposable elements were expressed in 23N only. Genes encoding the virulence-associated peptidases leupeptin-inhibiting protein 1 and fungalysin were expressed in planta. Transcriptional profiles of genes involved in secondary metabolite synthesis or cell wall degradation revealed the importance of these genes during late stages of infection (13 dpi). A total of 346 expressed candidate effectors were identified, including Ecp6 and proteins similar to the secreted in xylem (SIX) effectors common to formae speciales of Fusarium oxysporum, SIX13 and SIX5. Expression profiling of Ecp6 and SIX13-like indicated a peak in expression at 5 and 7 dpi compared to 2 and 13 dpi. Sequencing of SIX13-like from diverse isolates of E. turcicum revealed host-specific polymorphisms that were mostly non-synonymous, resulting in two groups of SIX13-like proteins that corresponded to the maize or sorghum origin of each isolate. This study suggests putative mechanisms whereby E. turcicum causes disease. Identification of the candidate effector SIX13-like is consistent with the infection mode of E. turcicum through the xylem of susceptible hosts.
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Affiliation(s)
| | | | - Bridget Genevieve Crampton
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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136
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Draft Genome Sequence of the Strawberry Anthracnose Pathogen Colletotrichum fructicola. Microbiol Resour Announc 2020; 9:9/12/e01598-19. [PMID: 32193247 PMCID: PMC7082466 DOI: 10.1128/mra.01598-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Colletotrichum fructicola is a causal agent of strawberry anthracnose and a major economic pathogen of horticultural and ornamental crops worldwide. Here, we present an annotated draft genome sequence for a C. fructicola isolate previously used for transcriptomic analysis. The assembly totals 58.0 Mb in 477 contigs with 18,143 predicted genes. Colletotrichum fructicola is a causal agent of strawberry anthracnose and a major economic pathogen of horticultural and ornamental crops worldwide. Here, we present an annotated draft genome sequence for a C. fructicola isolate previously used for transcriptomic analysis. The assembly totals 58.0 Mb in 477 contigs with 18,143 predicted genes.
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137
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Ren F, Yan DH, Wu G, Sun X, Song X, Li R. Distinctive Gene Expression Profiles and Effectors Consistent With Host Specificity in Two Formae Speciales of Marssonina brunnea. Front Microbiol 2020; 11:276. [PMID: 32210930 PMCID: PMC7076119 DOI: 10.3389/fmicb.2020.00276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the host specificity of a pathogen underlying an interaction is becoming an urgent necessity for global warming. In this study, the gene expression profiles and the roles of effectors in host specificity were integrally characterized with two formae speciales, multigermtubi and monogermtubi, of a hemibiotrophic pathogen Marssonina brunnea when they were infecting respective susceptible poplar hosts. With a functional genome comparison referring to a de novo transcriptome of M. brunnea and Pathogen-Host Interaction database functional annotations, the multigermtubi strain showed abundant and significant differentially expressed unigenes (DEGs) (more than 40%) in colonizing the initial invasion stage and in the necrotrophic stage. The monogermtubi strain induced less than 10% of DEGs in the initial invasion stage but which abruptly increased to more than 80% DEGs in the necrotrophic stage. Both strains induced the least DEGs in the biotrophic stage compared to the initial invasion and necrotrophic stages. The orthologs of the effector genes Ecp6, PemG1, XEG1, ACE1, and Mg3LysM were exclusively induced by one of the two formae speciales depending on the infection stages. Some unigenes homologous to carbohydrate lytic enzyme genes, especially pectate lyases, were notably induced with multigermtubi forma specialis infection but not expressed in the monogermtubi forma specialis at an earlier infection stage. The extraordinary differences in the functional genome level between the two formae speciales of M. brunnea could be fundamental to exploring their host specificity determinant and evolution. This study also firstly provided the fungal transcriptome of the monogermtubi forma specialis for M. brunnea.
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Affiliation(s)
- Fei Ren
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
- Institute of Cereal & Oil Science and Technology, Academy of National Food and Strategic Reserves Administration, Beijing, China
| | - Dong-Hui Yan
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
| | - Guanghua Wu
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
| | - Xiaoming Sun
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
| | - Xiaoyu Song
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
| | - Ruhua Li
- Research Institute of Forest Ecology, Environment and Protection, Key Laboratory of Forest Protection Affiliated to State Forestry and Grassland Administration of China, Chinese Academy of Forestry, Beijing, China
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138
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Hybridization and introgression drive genome evolution of Dutch elm disease pathogens. Nat Ecol Evol 2020; 4:626-638. [PMID: 32123324 DOI: 10.1038/s41559-020-1133-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/29/2020] [Indexed: 11/08/2022]
Abstract
Hybridization and the resulting introgression can drive the success of invasive species via the rapid acquisition of adaptive traits. The Dutch elm disease pandemics in the past 100 years were caused by three fungal lineages with permeable reproductive barriers: Ophiostoma ulmi, Ophiostoma novo-ulmi subspecies novo-ulmi and Ophiostoma novo-ulmi subspecies americana. Using whole-genome sequences and growth phenotyping of a worldwide collection of isolates, we show that introgression has been the main driver of genomic diversity and that it impacted fitness-related traits. Introgressions contain genes involved in host-pathogen interactions and reproduction. Introgressed isolates have enhanced growth rate at high temperature and produce different necrosis sizes on an in vivo model for pathogenicity. In addition, lineages diverge in many pathogenicity-associated genes and exhibit differential mycelial growth in the presence of a proxy of a host defence compound, implying an important role of host trees in the molecular and functional differentiation of these pathogens.
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139
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Piombo E, Bosio P, Acquadro A, Abbruscato P, Spadaro D. Different Phenotypes, Similar Genomes: Three Newly Sequenced Fusarium fujikuroi Strains Induce Different Symptoms in Rice Depending on Temperature. PHYTOPATHOLOGY 2020; 110:656-665. [PMID: 31721656 DOI: 10.1094/phyto-09-19-0359-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bakanae, caused by the hemibiotrophic fungus Fusarium fujikuroi, is one of the most important diseases of rice and is attributed to up to 75% of losses, depending on the strain and environmental conditions. Some strains cause elongation and thin leaves, whereas others induce stunting and chlorotic seedlings. Differences in symptoms are attributed to genetic differences in the strains. F. fujikuroi strains Augusto2, CSV1, and I1.3 were sequenced with Illumina MiSeq, and pathogenicity trials were conducted on rice cultivar Galileo, which is susceptible to bakanae. By performing gene prediction, single nucleotide polymorphism (SNP) calling, and structural variant analysis with a reference genome, we show how an extremely limited number of polymorphisms in genes not commonly associated with bakanae disease can cause strong differences in phenotype. CSV1 and Augusto2 were particularly close, with only 21,887 SNPs between them, but they differed in virulence, reaction to temperature, induced symptoms, colony morphology and color, growth speed, fumonisin, and gibberellin production. Genes potentially involved in the shift in phenotype were identified. Furthermore, we show how temperature variation may result in different symptoms even in rice plants inoculated with the same F. fujikuroi strain. Moreover, all of the F. fujikuroi strains became more virulent at higher temperatures. Significant differences were likewise observed in gibberellic acid production and in the expression of both fungal and plant gibberellin biosynthetic genes.
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Affiliation(s)
- Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Grugliasco, Turin 10095, Italy
- Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Grugliasco, Turin 10095, Italy
| | - Pietro Bosio
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Grugliasco, Turin 10095, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Grugliasco, Turin 10095, Italy
| | | | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Grugliasco, Turin 10095, Italy
- Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, Grugliasco, Turin 10095, Italy
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140
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Mei L, Chen M, Shang Y, Tang G, Tao Y, Zeng L, Huang B, Li Z, Zhan S, Wang C. Population genomics and evolution of a fungal pathogen after releasing exotic strains to control insect pests for 20 years. ISME JOURNAL 2020; 14:1422-1434. [PMID: 32111946 PMCID: PMC7242398 DOI: 10.1038/s41396-020-0620-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/04/2020] [Accepted: 02/17/2020] [Indexed: 12/31/2022]
Abstract
Entomopathogenic fungi are one of the key regulators of insect populations in nature. Some species such as Beauveria bassiana with a wide host range have been developed as promising alternatives to chemical insecticides for the biocontrol of insect pests. However, the long-term persistence of the released strains, the effect on non-target hosts and local fungal populations remains elusive, but they are considerable concerns with respect to environmental safety. Here we report the temporal features of the Beauveria population genomics and evolution over 20 years after releasing exotic strains to control pine caterpillar pests. We found that the isolates within the biocontrol site were mostly of clonal origins. The released strains could persist in the environment for a long time but with low recovery rates. Similar to the reoccurrence of host jumping by local isolates, the infection of non-target insects by the released strains was evident to endemically occur in association with host seasonality. No obvious dilution effect on local population structure was evident by the releases. However, the population was largely replaced by genetically divergent isolates once per decade but evolved with a pattern of balancing selection and towards expansion through adaptation, non-random outcrossing and isolate migration. This study not only unveils the real-time features of entomopathogenic fungal population genomics and evolution but also provides added values to alleviate the concerns of environmental safety regarding the biocontrol application of mycoinsecticides.
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Affiliation(s)
- Lijuan Mei
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,CAS Center for Excellence in Biotic interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingjun Chen
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230031, China
| | - Yanfang Shang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Guirong Tang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ye Tao
- Biozeron Biotech Ltd., Shanghai, 201800, China
| | - Liang Zeng
- Biozeron Biotech Ltd., Shanghai, 201800, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230031, China
| | - Zengzhi Li
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, 230031, China
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Chengshu Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. .,CAS Center for Excellence in Biotic interactions, University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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141
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Lee RC, Farfan-Caceres LM, Debler JW, Syme RA. Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean ( Vicia faba L.). Front Microbiol 2020; 11:217. [PMID: 32132988 PMCID: PMC7040437 DOI: 10.3389/fmicb.2020.00217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/30/2020] [Indexed: 11/13/2022] Open
Abstract
Chocolate spot is a major fungal disease of faba bean caused by the ascomycete fungus, Botrytis fabae. B. fabae is also implicated in botrytis gray mold disease in lentils, along with B. cinerea. Here we have isolated and characterized two B. fabae isolates from chocolate spot lesions on faba bean leaves. In plant disease assays on faba bean and lentil, B. fabae was more aggressive than B. cinerea and we observed variation in susceptibility among a small set of cultivars for both plant hosts. Using light microscopy, we observed a spreading, generalized necrosis response in faba bean toward B. fabae. In contrast, the plant response to B. cinerea was localized to epidermal cells underlying germinated spores and appressoria. In addition to the species characterization of B. fabae, we produced genome assemblies for both B. fabae isolates using Illumina sequencing. Genome sequencing coverage and assembly size for B. fabae isolates, were 27x and 45x, and 43.2 and 44.5 Mb, respectively. Following genome assembly and annotation, carbohydrate-active enzyme (CAZymes) and effector genes were predicted. There were no major differences in the numbers of each of the major classes of CAZymes. We predicted 29 effector genes for B. fabae, and using the same selection criteria for B. cinerea, we predicted 34 putative effector genes. For five of the predicted effector genes, the pairwise dN/dS ratio between orthologs from B. fabae and B. cinerea was greater than 1.0, suggesting positive selection and the potential evolution of molecular mechanisms for host specificity in B. fabae. Furthermore, a homology search of secondary metabolite clusters revealed the absence of the B. cinerea phytotoxin botrydial and several other uncharacterized secondary metabolite biosynthesis genes from B. fabae. Although there were no obvious differences in the number or proportional representation of different transposable element classes, the overall proportion of AT-rich DNA sequence in B. fabae was double that of B. cinerea.
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Affiliation(s)
- Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Lina M Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Johannes W Debler
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Robert A Syme
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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142
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Badet T, Oggenfuss U, Abraham L, McDonald BA, Croll D. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici. BMC Biol 2020; 18:12. [PMID: 32046716 PMCID: PMC7014611 DOI: 10.1186/s12915-020-0744-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. RESULTS Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. CONCLUSIONS Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
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Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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143
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Badet T, Oggenfuss U, Abraham L, McDonald BA, Croll D. A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici. BMC Biol 2020; 18:12. [PMID: 32046716 DOI: 10.1101/803098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/27/2020] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. RESULTS Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. CONCLUSIONS Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
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Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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144
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Depotter JRL, Doehlemann G. Target the core: durable plant resistance against filamentous plant pathogens through effector recognition. PEST MANAGEMENT SCIENCE 2020; 76:426-431. [PMID: 31713986 DOI: 10.1002/ps.5677] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/23/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Plant pathogens colonize their host through the secretion of effector proteins that modulate plant metabolism and immune responses to their benefit. Plants evolve towards effector recognition, leading to host immunity. Typically, pathogen effectors are targets for recognition through plant receptors that are encoded by resistance genes. Resistance gene mediated crop immunity puts a tremendous pressure on pathogens to adapt and alter their effector repertoire to overcome recognition. We argue that the type of effector that is recognized by the host may have considerable implications on the durability of resistance against filamentous plant pathogens. Effector genes that are conserved among pathogens and reside in core genome regions are most likely to hold indispensable virulence functions. Consequently, the cost for the pathogen to overcome recognition by the host is higher than for diversified, host-specific effectors with a quantitative impact on virulence. Consequently, resistance genes that directly target conserved effector proteins without the interception of other effector proteins are potentially excellent resistance resources. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Jasper R L Depotter
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, BioCenter, Cologne, Germany
| | - Gunther Doehlemann
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, BioCenter, Cologne, Germany
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145
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Tabima JF, Søndreli KL, Keriö S, Feau N, Sakalidis ML, Hamelin RC, LeBoldus JM. Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:189-199. [PMID: 31593527 DOI: 10.1094/mpmi-05-19-0131-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.
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Affiliation(s)
- J F Tabima
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, U.S.A
| | - K L Søndreli
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, U.S.A
| | - S Keriö
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, U.S.A
| | - N Feau
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Canada
| | - M L Sakalidis
- Department of Plant, Soil and Microbial Sciences and the Department of Forestry, College of Agriculture & Natural Resources, Michigan State University, East Lansing, U.S.A
| | - R C Hamelin
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Canada
| | - J M LeBoldus
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, U.S.A
- Department of Forest Engineering, Resources and Management, College of Forestry, Oregon State University
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146
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Winter DJ, Charlton ND, Krom N, Shiller J, Bock CH, Cox MP, Young CA. Chromosome-Level Reference Genome of Venturia effusa, Causative Agent of Pecan Scab. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:149-152. [PMID: 31631770 DOI: 10.1094/mpmi-08-19-0236-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pecan scab, caused by Venturia effusa, is a devastating disease of pecan (Carya illinoinensis), which results in economic losses on susceptible cultivars throughout the southeastern United States. To enhance our understanding of pathogenicity in V. effusa, we have generated a complete telomere-to-telomere reference genome of V. effusa isolate FRT5LL7-Albino. By combining Illumina MiSeq and Oxford Nanopore MinION data, we assembled a 45.2-Mb genome represented by 20 chromosomes and containing 10,820 putative genes, of which 7,619 have at least one functional annotation. The likely causative mutation of the albino phenotype was identified as a single base insertion and a resulting frameshift in the gene encoding the polyketide synthase ALM1. This genome represents the first full chromosome-level assembly of any Venturia sp.
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Affiliation(s)
- David J Winter
- School of Fundamental Sciences and the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Jason Shiller
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Clive H Bock
- United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008, U.S.A
| | - Murray P Cox
- School of Fundamental Sciences and the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
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147
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Wyatt NA, Richards JK, Brueggeman RS, Friesen TL. A Comparative Genomic Analysis of the Barley Pathogen Pyrenophora teres f. teres Identifies Subtelomeric Regions as Drivers of Virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:173-188. [PMID: 31502507 DOI: 10.1094/mpmi-05-19-0128-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high-quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison, resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes, examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions, consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in subtelomeric regions of chromosomes, with 10 of the 14 accessory region QTL localizing to subtelomeric regions. Comparative analysis of the subtelomeric regions of P. teres f. teres chromosomes revealed translocation events in which homology was detected between nonhomologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the subtelomeric accessory genomic compartments not only harbor most of the known virulence loci but, also, that these regions have the capacity to rapidly evolve.
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Affiliation(s)
- Nathan A Wyatt
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University
| | - Jonathan K Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, U.S.A
| | - Robert S Brueggeman
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University
| | - Timothy L Friesen
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, U.S.A
- Department of Plant Pathology, North Dakota State University
- Cereal Crops Research Unit, Red River Valley Agricultural Research Center, USDA-ARS, Fargo, ND, U.S.A
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148
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Armitage AD, Cockerton HM, Sreenivasaprasad S, Woodhall J, Lane CR, Harrison RJ, Clarkson JP. Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes. Front Microbiol 2020; 10:3124. [PMID: 32038562 PMCID: PMC6989435 DOI: 10.3389/fmicb.2019.03124] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 12/24/2019] [Indexed: 02/04/2023] Open
Abstract
The Alternaria section alternaria (Alternaria alternata species group) represents a diverse group of saprotroph, human allergens, and plant pathogens. Alternaria taxonomy has benefited from recent phylogenetic revision but the basis of differentiation between major phylogenetic clades within the group is not yet understood. Furthermore, genomic resources have been limited for the study of host-specific pathotypes. We report near complete genomes of the apple and Asian pear pathotypes as well as draft assemblies for a further 10 isolates representing Alternaria tenuissima and Alternaria arborescens lineages. These assemblies provide the first insights into differentiation of these taxa as well as allowing the description of effector and non-effector profiles of apple and pear conditionally dispensable chromosomes (CDCs). We define the phylogenetic relationship between the isolates sequenced in this study and a further 23 Alternaria spp. based on available genomes. We determine which of these genomes represent MAT1-1-1 or MAT1-2-1 idiomorphs and designate host-specific pathotypes. We show for the first time that the apple pathotype is polyphyletic, present in both the A. arborescens and A. tenuissima lineages. Furthermore, we profile a wider set of 89 isolates for both mating type idiomorphs and toxin gene markers. Mating-type distribution indicated that gene flow has occurred since the formation of A. tenuissima and A. arborescens lineages. We also developed primers designed to AMT14, a gene from the apple pathotype toxin gene cluster with homologs in all tested pathotypes. These primers allow identification and differentiation of apple, pear, and strawberry pathotypes, providing new tools for pathogen diagnostics.
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Affiliation(s)
- Andrew D. Armitage
- NIAB EMR, East Malling, United Kingdom
- Natural Resources Institute, University of Greenwich, Chatham Maritime, London, United Kingdom
| | | | | | - James Woodhall
- Parma Research and Extension Center, University of Idaho, Parma, ID, United States
| | | | | | - John P. Clarkson
- Warwick Crop Centre, University of Warwick, Warwick, United Kingdom
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149
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Rajarammohan S, Paritosh K, Pental D, Kaur J. Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae - a pathogen of the Brassicaceae family. BMC Genomics 2019; 20:1036. [PMID: 31888481 PMCID: PMC6937934 DOI: 10.1186/s12864-019-6414-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/19/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternaria brassicae, a necrotrophic pathogen, causes Alternaria Leaf Spot, one of the economically important diseases of Brassica crops. Many other Alternaria spp. such as A. brassicicola and A. alternata are known to cause secondary infections in the A. brassicae-infected Brassicas. The genome architecture, pathogenicity factors, and determinants of host-specificity of A. brassicae are unknown. In this study, we annotated and characterised the recently announced genome assembly of A. brassicae and compared it with other Alternaria spp. to gain insights into its pathogenic lifestyle. RESULTS We also sequenced the genomes of two A. alternata isolates that were co-infecting B. juncea using Nanopore MinION sequencing for additional comparative analyses within the Alternaria genus. Genome alignments within the Alternaria spp. revealed high levels of synteny between most chromosomes with some intrachromosomal rearrangements. We show for the first time that the genome of A. brassicae, a large-spored Alternaria species, contains a dispensable chromosome. We identified 460 A. brassicae-specific genes, which included many secreted proteins and effectors. Furthermore, we have identified the gene clusters responsible for the production of Destruxin-B, a known pathogenicity factor of A. brassicae. CONCLUSION The study provides a perspective into the unique and shared repertoire of genes within the Alternaria genus and identifies genes that could be contributing to the pathogenic lifestyle of A. brassicae.
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Affiliation(s)
- Sivasubramanian Rajarammohan
- Department of Genetics, University of Delhi , South Campus, New Delhi, 110021, India
- Present Address: National Agri-Food Biotechnology Institute, Mohali, India
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India
| | - Jagreet Kaur
- Department of Genetics, University of Delhi , South Campus, New Delhi, 110021, India.
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150
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Kretschmer M, Damoo D, Djamei A, Kronstad J. Chloroplasts and Plant Immunity: Where Are the Fungal Effectors? Pathogens 2019; 9:E19. [PMID: 31878153 PMCID: PMC7168614 DOI: 10.3390/pathogens9010019] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 12/12/2022] Open
Abstract
Chloroplasts play a central role in plant immunity through the synthesis of secondary metabolites and defense compounds, as well as phytohormones, such as jasmonic acid and salicylic acid. Additionally, chloroplast metabolism results in the production of reactive oxygen species and nitric oxide as defense molecules. The impact of viral and bacterial infections on plastids and chloroplasts has been well documented. In particular, bacterial pathogens are known to introduce effectors specifically into chloroplasts, and many viral proteins interact with chloroplast proteins to influence viral replication and movement, and plant defense. By contrast, clear examples are just now emerging for chloroplast-targeted effectors from fungal and oomycete pathogens. In this review, we first present a brief overview of chloroplast contributions to plant defense and then discuss examples of connections between fungal interactions with plants and chloroplast function. We then briefly consider well-characterized bacterial effectors that target chloroplasts as a prelude to discussing the evidence for fungal effectors that impact chloroplast activities.
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Affiliation(s)
- Matthias Kretschmer
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (M.K.); (D.D.)
| | - Djihane Damoo
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (M.K.); (D.D.)
| | - Armin Djamei
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) OT Gatersleben Corrensstrasse 3, D-06466 Stadt Seeland, Germany;
| | - James Kronstad
- Michael Smith Laboratories, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (M.K.); (D.D.)
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