101
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Kombrink A, Rovenich H, Shi‐Kunne X, Rojas‐Padilla E, van den Berg GCM, Domazakis E, de Jonge R, Valkenburg D, Sánchez‐Vallet A, Seidl MF, Thomma BPHJ. Verticillium dahliae LysM effectors differentially contribute to virulence on plant hosts. MOLECULAR PLANT PATHOLOGY 2017; 18:596-608. [PMID: 27911046 PMCID: PMC6638240 DOI: 10.1111/mpp.12520] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Chitin-binding lysin motif (LysM) effectors contribute to the virulence of various plant-pathogenic fungi that are causal agents of foliar diseases. Here, we report the LysM effectors of the soil-borne fungal vascular wilt pathogen Verticillium dahliae. Comparative genomics revealed three core LysM effectors that are conserved in a collection of V. dahliae strains. Remarkably, and in contrast with the previously studied LysM effectors of other plant pathogens, no expression of core LysM effectors was monitored in planta in a taxonomically diverse panel of host plants. Moreover, targeted deletion of the individual LysM effector genes in V. dahliae strain JR2 did not compromise virulence in infections on Arabidopsis, tomato or Nicotiana benthamiana. Interestingly, an additional lineage-specific LysM effector is encoded in the genome of V. dahliae strain VdLs17, but not in any other V. dahliae strain sequenced to date. Remarkably, this lineage-specific effector is expressed in planta and contributes to the virulence of V. dahliae strain VdLs17 on tomato, but not on Arabidopsis or N. benthamiana. Functional analysis revealed that this LysM effector binds chitin, is able to suppress chitin-induced immune responses and protects fungal hyphae against hydrolysis by plant hydrolytic enzymes. Thus, in contrast with the core LysM effectors of V. dahliae, this lineage-specific LysM effector of strain VdLs17 contributes to virulence in planta.
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Affiliation(s)
- Anja Kombrink
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Hanna Rovenich
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Xiaoqian Shi‐Kunne
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Eduardo Rojas‐Padilla
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Grardy C. M. van den Berg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Emmanouil Domazakis
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Ronnie de Jonge
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Dirk‐Jan Valkenburg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Andrea Sánchez‐Vallet
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Michael F. Seidl
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 1WageningenPB 6708the Netherlands
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102
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Complete genome sequence of Bacillus velezensis LM2303, a biocontrol strain isolated from the dung of wild yak inhabited Qinghai-Tibet plateau. J Biotechnol 2017; 251:124-127. [PMID: 28461206 DOI: 10.1016/j.jbiotec.2017.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 11/20/2022]
Abstract
Bacillus velezensis LM2303 is a biocontrol strain with a broad inhibitory spectrum against plant pathogens, isolated from the dung of wild yak inhabited Qinghai-Tibet plateau, China. Here we present its complete genome sequence, which consists of a single, circular chromosome of 3,989,393bp with a 46.68% G+C content. Genome analysis revealed genes encoding specialized functions for the biosynthesis of antifungal metabolites and antibacterial metabolites, the promotion of plant growth, the alleviation of oxidative stress and nutrient utilization. And the biosynthesis of antimicrobial metabolites in strain LM2303 was confirmed by biochemical analysis, while its plant growth promoting traits were confirmed by inoculation tests. Our results will establish a better foundation for further studies and biocontrol application of B. velezensis LM2303.
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103
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017. [PMID: 28417959 DOI: 10.1038/srep4655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture &Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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104
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Yin L, An Y, Qu J, Li X, Zhang Y, Dry I, Wu H, Lu J. Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism. Sci Rep 2017; 7:46553. [PMID: 28417959 PMCID: PMC5394536 DOI: 10.1038/srep46553] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/22/2017] [Indexed: 12/17/2022] Open
Abstract
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome. In the secretome, 261 potential pathogenicity genes and 95 carbohydrate-active enzymes were predicted. Transcriptional analysis revealed that most of the RXLR effectors, pathogenicity genes and carbohydrate-active enzymes were significantly up-regulated during infection. Comparative genomic analysis revealed that P. viticola evolved independently from the Arabidopsis downy mildew pathogen Hyaloperonospora arabidopsidis. The availability of the P. viticola genome provides a valuable resource not only for comparative genomic analysis and evolutionary studies among oomycetes, but also enhance our knowledge on the mechanism of interactions between this biotrophic pathogen and its host.
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Affiliation(s)
- Ling Yin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Yunhe An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Junjie Qu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Xinlong Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yali Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ian Dry
- CSIRO Agriculture & Food, Wine Innovation West Building, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Huijuan Wu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | - Jiang Lu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200024, China
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105
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Santhanam P, Boshoven JC, Salas O, Bowler K, Islam MT, Saber MK, van den Berg GCM, Bar‐Peled M, Thomma BPHJ. Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae. MOLECULAR PLANT PATHOLOGY 2017; 18:347-362. [PMID: 26996832 PMCID: PMC6638212 DOI: 10.1111/mpp.12401] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/17/2016] [Accepted: 03/17/2016] [Indexed: 05/05/2023]
Abstract
The initial interaction of a pathogenic fungus with its host is complex and involves numerous metabolic pathways and regulatory proteins. Considerable attention has been devoted to proteins that play a crucial role in these interactions, with an emphasis on so-called effector molecules that are secreted by the invading microbe to establish the symbiosis. However, the contribution of other types of molecules, such as glycans, is less well appreciated. Here, we present a random genetic screen that enabled us to identify 58 novel candidate genes that are involved in the pathogenic potential of the fungal pathogen Verticillium dahliae, which causes vascular wilt diseases in over 200 dicotyledonous plant species, including economically important crops. One of the candidate genes that was identified concerns a putative biosynthetic gene involved in nucleotide sugar precursor formation, as it encodes a putative nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER). This enzyme has homology to bacterial enzymes involved in the biosynthesis of the nucleotide sugar deoxy-thymidine diphosphate (dTDP)-rhamnose, a precursor of L-rhamnose, which has been shown to be required for virulence in several human pathogenic bacteria. Rhamnose is known to be a minor cell wall glycan in fungi and has therefore not been suspected as a crucial molecule in fungal-host interactions. Nevertheless, our study shows that deletion of the VdNRS/ER gene from the V. dahliae genome results in complete loss of pathogenicity on tomato and Nicotiana benthamiana plants, whereas vegetative growth and sporulation are not affected. We demonstrate that VdNRS/ER is a functional enzyme in the biosynthesis of uridine diphosphate (UDP)-rhamnose, and further analysis has revealed that VdNRS/ER deletion strains are impaired in the colonization of tomato roots. Collectively, our results demonstrate that rhamnose, although only a minor cell wall component, is essential for the pathogenicity of V. dahliae.
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Affiliation(s)
- Parthasarathy Santhanam
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Jordi C. Boshoven
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Omar Salas
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Kyle Bowler
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Md Tohidul Islam
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Mojtaba Keykha Saber
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Grardy C. M. van den Berg
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Maor Bar‐Peled
- Complex Carbohydrate Research Center, University of GeorgiaAthensGA30602USA
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
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106
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Feehan JM, Scheibel KE, Bourras S, Underwood W, Keller B, Somerville SC. Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing. J Vis Exp 2017. [PMID: 28448006 DOI: 10.3791/55463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.
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Affiliation(s)
- Joanna M Feehan
- Department of Plant and Microbial Biology, University of California Berkeley; John Innes Centre, Norwich Research Park
| | | | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich
| | | | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich
| | - Shauna C Somerville
- Department of Plant and Microbial Biology, University of California Berkeley;
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107
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Derbyshire M, Denton-Giles M, Hegedus D, Seifbarghy S, Rollins J, van Kan J, Seidl MF, Faino L, Mbengue M, Navaud O, Raffaele S, Hammond-Kosack K, Heard S, Oliver R. The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens. Genome Biol Evol 2017; 9:593-618. [PMID: 28204478 PMCID: PMC5381539 DOI: 10.1093/gbe/evx030] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/16/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022] Open
Abstract
Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale.
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Affiliation(s)
- Mark Derbyshire
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
| | - Matthew Denton-Giles
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
| | - Dwayne Hegedus
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | | | - Jeffrey Rollins
- Department of Plant Pathology, University of Florida, Gainesville, FL
| | - Jan van Kan
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Luigi Faino
- Laboratory of Phytopathology, Wageningen University, The Netherlands
| | - Malick Mbengue
- LIPM Université de Toulouse INRA CNRS, Castanet-Tolosan, France
| | - Olivier Navaud
- LIPM Université de Toulouse INRA CNRS, Castanet-Tolosan, France
| | | | - Kim Hammond-Kosack
- Department of Plant Biology and Crop Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Stephanie Heard
- Department of Plant Pathology, University of Florida, Gainesville, FL
- Department of Plant Biology and Crop Sciences, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Richard Oliver
- Centre for Crop and Disease Management Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia, Australia
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108
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Song Y, Zhang Z, Seidl MF, Majer A, Jakse J, Javornik B, Thomma BPHJ. Broad taxonomic characterization of Verticillium wilt resistance genes reveals an ancient origin of the tomato Ve1 immune receptor. MOLECULAR PLANT PATHOLOGY 2017; 18:195-209. [PMID: 26946045 PMCID: PMC6638226 DOI: 10.1111/mpp.12390] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/12/2016] [Accepted: 03/01/2016] [Indexed: 05/02/2023]
Abstract
Plant-pathogenic microbes secrete effector molecules to establish themselves on their hosts, whereas plants use immune receptors to try and intercept such effectors in order to prevent pathogen colonization. The tomato cell surface-localized receptor Ve1 confers race-specific resistance against race 1 strains of the soil-borne vascular wilt fungus Verticillium dahliae which secrete the Ave1 effector. Here, we describe the cloning and characterization of Ve1 homologues from tobacco (Nicotiana glutinosa), potato (Solanum tuberosum), wild eggplant (Solanum torvum) and hop (Humulus lupulus), and demonstrate that particular Ve1 homologues govern resistance against V. dahliae race 1 strains through the recognition of the Ave1 effector. Phylogenetic analysis shows that Ve1 homologues are widely distributed in land plants. Thus, our study suggests an ancient origin of the Ve1 immune receptor in the plant kingdom.
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Affiliation(s)
- Yin Song
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Zhao Zhang
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Michael F. Seidl
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Aljaz Majer
- Biotechnical Faculty, Agronomy Department, Centre for Plant Biotechnology and Breeding, University of LjubljanaJamnikarieva 1011000LjubljanaSlovenia
| | - Jernej Jakse
- Biotechnical Faculty, Agronomy Department, Centre for Plant Biotechnology and Breeding, University of LjubljanaJamnikarieva 1011000LjubljanaSlovenia
| | - Branka Javornik
- Biotechnical Faculty, Agronomy Department, Centre for Plant Biotechnology and Breeding, University of LjubljanaJamnikarieva 1011000LjubljanaSlovenia
| | - Bart P. H. J. Thomma
- Laboratory of PhytopathologyWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
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109
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Schuster M, Schweizer G, Kahmann R. Comparative analyses of secreted proteins in plant pathogenic smut fungi and related basidiomycetes. Fungal Genet Biol 2017; 112:21-30. [PMID: 28089076 DOI: 10.1016/j.fgb.2016.12.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 12/13/2016] [Accepted: 12/15/2016] [Indexed: 12/28/2022]
Abstract
In the ten years since the genome sequence of the basidiomycete corn smut fungus Ustilago maydis was published, additional genomes of smut species infecting different hosts became available. In addition, the genomes of related Malassezia species causing skin diseases and of Pseudozyma species not known to infect plants were determined. As secreted proteins are critical virulence determinants in U. maydis we compare here the secretomes of 12 basidiomycete species to gain information about their composition and conservation. For this we classify secreted proteins into those with and without domains using InterPro scans. Homology among proteins is inferred by building clusters based on pairwise similarities and cluster presence is then assessed in the different species. We detect in particular a strong correspondence between the secretomes of Pseudozyma species and plant infecting smuts. Furthermore, we identify a high proportion of secreted proteins to be part of gene families and present an advancement of the CRISPR-Cas9 technology for simultaneous disruption of multiple genes in U. maydis using five genes of the eff1 family as example.
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Affiliation(s)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany
| | - Gabriel Schweizer
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany.
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110
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Friedman S, Freitag M. Centrochromatin of Fungi. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:85-109. [PMID: 28840234 DOI: 10.1007/978-3-319-58592-5_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The centromere is an essential chromosomal locus that dictates the nucleation point for assembly of the kinetochore and subsequent attachment of spindle microtubules during chromosome segregation. Research over the last decades demonstrated that centromeres are defined by a combination of genetic and epigenetic factors. Recent work showed that centromeres are quite diverse and flexible and that many types of centromere sequences and centromeric chromatin ("centrochromatin") have evolved. The kingdom of the fungi serves as an outstanding example of centromere plasticity, including organisms with centromeres as diverse as 0.15-300 kb in length, and with different types of chromatin states for most species examined thus far. Some of the species in the less familiar taxa provide excellent opportunities to help us better understand centromere biology in all eukaryotes, which may improve treatment options against fungal infection, and biotechnologies based on fungi. This review summarizes the current knowledge of fungal centromeres and centrochromatin, including an outlook for future research.
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Affiliation(s)
- Steven Friedman
- Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS Bldg, Corvallis, OR, 97331, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, 2011 ALS Bldg, Corvallis, OR, 97331, USA.
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111
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Van Kan JAL, Stassen JHM, Mosbach A, Van Der Lee TAJ, Faino L, Farmer AD, Papasotiriou DG, Zhou S, Seidl MF, Cottam E, Edel D, Hahn M, Schwartz DC, Dietrich RA, Widdison S, Scalliet G. A gapless genome sequence of the fungus Botrytis cinerea. MOLECULAR PLANT PATHOLOGY 2017; 18:75-89. [PMID: 26913498 PMCID: PMC6638203 DOI: 10.1111/mpp.12384] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 05/03/2023]
Abstract
Following earlier incomplete and fragmented versions of a genome sequence for the grey mould Botrytis cinerea, a gapless, near-finished genome sequence for B. cinerea strain B05.10 is reported. The assembly comprised 18 chromosomes and was confirmed by an optical map and a genetic map based on approximately 75 000 single nucleotide polymorphism (SNP) markers. All chromosomes contained fully assembled centromeric regions, and 10 chromosomes had telomeres on both ends. The genetic map consisted of 4153 cM and a comparison of the genetic distances with the physical distances identified 40 recombination hotspots. The linkage map also identified two mutations, located in the previously described genes Bos1 and BcsdhB, that conferred resistance to the fungicides boscalid and iprodione. The genome was predicted to encode 11 701 proteins. RNAseq data from >20 different samples were used to validate and improve gene models. Manual curation of chromosome 1 revealed interesting features, such as the occurrence of a dicistronic transcript and fully overlapping genes in opposite orientations, as well as many spliced antisense transcripts. Manual curation also revealed that the untranslated regions (UTRs) of genes can be complex and long, with many UTRs exceeding lengths of 1 kb and possessing multiple introns. Community annotation is in progress.
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MESH Headings
- Base Pairing/genetics
- Base Sequence
- Botrytis/cytology
- Botrytis/drug effects
- Botrytis/genetics
- Chromosome Mapping
- Chromosomes, Fungal/genetics
- Drug Resistance, Fungal/drug effects
- Drug Resistance, Fungal/genetics
- Evolution, Molecular
- Fungicides, Industrial/pharmacology
- Genes, Fungal
- Genetic Linkage
- Genetic Loci
- Genome, Fungal
- Meiosis/drug effects
- Molecular Sequence Annotation
- Open Reading Frames/genetics
- Optogenetics
- Polymorphism, Single Nucleotide/genetics
- Proteome/metabolism
- Proteomics
- Recombination, Genetic/drug effects
- Recombination, Genetic/genetics
- Reproducibility of Results
- Sequence Analysis, DNA
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Affiliation(s)
- Jan A. L. Van Kan
- Laboratory of PhytopathologyWageningen University6708 PB, Wageningenthe Netherlands
| | - Joost H. M. Stassen
- Laboratory of PhytopathologyWageningen University6708 PB, Wageningenthe Netherlands
- Present address:
University of Sheffield, Department of Animal and Plant Sciences, S10 2TN SheffieldUK
| | - Andreas Mosbach
- Syngenta Crop Protection Münchwilen AG, Crop Protection ResearchCH‐4332SteinSwitzerland
| | | | - Luigi Faino
- Laboratory of PhytopathologyWageningen University6708 PB, Wageningenthe Netherlands
| | - Andrew D. Farmer
- National Center for Genome ResourcesSanta FeNM87505, USA
- Syngenta Biotechnology Inc., Research Triangle ParkNC27709, USA
| | | | - Shiguo Zhou
- Department of Chemistry, Laboratory of Genetics and Laboratory for Molecular and Computational Genomics, UW Biotechnology CenterUniversity of WisconsinMadisonWI53706USA
| | - Michael F. Seidl
- Laboratory of PhytopathologyWageningen University6708 PB, Wageningenthe Netherlands
| | - Eleanor Cottam
- General Bioinformatics, Jealotts Hill International Research CentreBracknellBerkshireRG42 6EYUK
| | - Dominique Edel
- Syngenta Crop Protection Münchwilen AG, Crop Protection ResearchCH‐4332SteinSwitzerland
| | - Matthias Hahn
- Faculty of BiologyTechnical University Kaiserslautern67653 KaiserslauternGermany
| | - David C. Schwartz
- Department of Chemistry, Laboratory of Genetics and Laboratory for Molecular and Computational Genomics, UW Biotechnology CenterUniversity of WisconsinMadisonWI53706USA
| | | | - Stephanie Widdison
- General Bioinformatics, Jealotts Hill International Research CentreBracknellBerkshireRG42 6EYUK
| | - Gabriel Scalliet
- Syngenta Crop Protection Münchwilen AG, Crop Protection ResearchCH‐4332SteinSwitzerland
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112
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Gibriel HAY, Thomma BPHJ, Seidl MF. The Age of Effectors: Genome-Based Discovery and Applications. PHYTOPATHOLOGY 2016; 106:1206-1212. [PMID: 27050568 DOI: 10.1094/phyto-02-16-0110-fi] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Microbial pathogens cause devastating diseases on economically and ecologically important plant species, threatening global food security, and causing billions of dollars of losses annually. During the infection process, pathogens secrete so-called effectors that support host colonization, often by deregulating host immune responses. Over the last decades, much of the research on molecular plant-microbe interactions has focused on the identification and functional characterization of such effectors. The increasing availability of sequenced plant pathogen genomes has enabled genomics-based discovery of effector candidates. Nevertheless, identification of full plant pathogen effector repertoires is often hampered by erroneous gene annotation and the localization effector genes in genomic regions that are notoriously difficult to assemble. Here, we argue that recent advances in genome sequencing technologies, genome assembly, gene annotation, as well as effector identification methods hold promise to disclose complete and correct effector repertoires. This allows to exploit complete effector repertoires, and knowledge of their diversity within pathogen populations, to develop durable and sustainable resistance breeding strategies, disease control, and management of plant pathogens.
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Affiliation(s)
- Hesham A Y Gibriel
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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113
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Vanheule A, Audenaert K, Warris S, van de Geest H, Schijlen E, Höfte M, De Saeger S, Haesaert G, Waalwijk C, van der Lee T. Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen. BMC Genomics 2016; 17:670. [PMID: 27552804 PMCID: PMC4994206 DOI: 10.1186/s12864-016-2941-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 07/14/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this. RESULTS Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome. CONCLUSIONS For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A "living apart together" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.
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Affiliation(s)
- Adriaan Vanheule
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Wageningen UR, Wageningen, The Netherlands
| | - Kris Audenaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | | | | | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sarah De Saeger
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Geert Haesaert
- Department of Applied Biosciences, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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114
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Interspecific hybridization impacts host range and pathogenicity of filamentous microbes. Curr Opin Microbiol 2016; 32:7-13. [DOI: 10.1016/j.mib.2016.04.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/30/2016] [Accepted: 04/08/2016] [Indexed: 11/24/2022]
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115
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Faino L, Seidl MF, Shi-Kunne X, Pauper M, van den Berg GCM, Wittenberg AHJ, Thomma BPHJ. Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen. Genome Res 2016; 26:1091-100. [PMID: 27325116 PMCID: PMC4971763 DOI: 10.1101/gr.204974.116] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/17/2016] [Indexed: 12/29/2022]
Abstract
Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in “arms races” with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen virulence.
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Affiliation(s)
- Luigi Faino
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Xiaoqian Shi-Kunne
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Marc Pauper
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | | | | | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands
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116
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Lange A, Beier S, Steimle A, Autenrieth IB, Huson DH, Frick JS. Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk. Genome Biol Evol 2016; 8:1197-207. [PMID: 27071651 PMCID: PMC4860699 DOI: 10.1093/gbe/evw070] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota.
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Affiliation(s)
- Anna Lange
- Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Sina Beier
- Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Alex Steimle
- Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Ingo B Autenrieth
- Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Daniel H Huson
- Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Julia-Stefanie Frick
- Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
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117
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Mind the gap; seven reasons to close fragmented genome assemblies. Fungal Genet Biol 2015; 90:24-30. [PMID: 26342853 DOI: 10.1016/j.fgb.2015.08.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
Like other domains of life, research into the biology of filamentous microbes has greatly benefited from the advent of whole-genome sequencing. Next-generation sequencing (NGS) technologies have revolutionized sequencing, making genomic sciences accessible to many academic laboratories including those that study non-model organisms. Thus, hundreds of fungal genomes have been sequenced and are publically available today, although these initiatives have typically yielded considerably fragmented genome assemblies that often lack large contiguous genomic regions. Many important genomic features are contained in intergenic DNA that is often missing in current genome assemblies, and recent studies underscore the significance of non-coding regions and repetitive elements for the life style, adaptability and evolution of many organisms. The study of particular types of genetic elements, such as telomeres, centromeres, repetitive elements, effectors, and clusters of co-regulated genes, but also of phenomena such as structural rearrangements, genome compartmentalization and epigenetics, greatly benefits from having a contiguous and high-quality, preferably even complete and gapless, genome assembly. Here we discuss a number of important reasons to produce gapless, finished, genome assemblies to help answer important biological questions.
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