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Chen ECH, Morin E, Beaudet D, Noel J, Yildirir G, Ndikumana S, Charron P, St-Onge C, Giorgi J, Krüger M, Marton T, Ropars J, Grigoriev IV, Hainaut M, Henrissat B, Roux C, Martin F, Corradi N. High intraspecific genome diversity in the model arbuscular mycorrhizal symbiont Rhizophagus irregularis. THE NEW PHYTOLOGIST 2018; 220:1161-1171. [PMID: 29355972 DOI: 10.1111/nph.14989] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/03/2017] [Indexed: 05/20/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are known to improve plant fitness through the establishment of mycorrhizal symbioses. Genetic and phenotypic variations among closely related AMF isolates can significantly affect plant growth, but the genomic changes underlying this variability are unclear. To address this issue, we improved the genome assembly and gene annotation of the model strain Rhizophagus irregularis DAOM197198, and compared its gene content with five isolates of R. irregularis sampled in the same field. All isolates harbor striking genome variations, with large numbers of isolate-specific genes, gene family expansions, and evidence of interisolate genetic exchange. The observed variability affects all gene ontology terms and PFAM protein domains, as well as putative mycorrhiza-induced small secreted effector-like proteins and other symbiosis differentially expressed genes. High variability is also found in active transposable elements. Overall, these findings indicate a substantial divergence in the functioning capacity of isolates harvested from the same field, and thus their genetic potential for adaptation to biotic and abiotic changes. Our data also provide a first glimpse into the genome diversity that resides within natural populations of these symbionts, and open avenues for future analyses of plant-AMF interactions that link AMF genome variation with plant phenotype and fitness.
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Affiliation(s)
- Eric C H Chen
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Emmanuelle Morin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Denis Beaudet
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jessica Noel
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Steve Ndikumana
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Philippe Charron
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Camille St-Onge
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - John Giorgi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Manuela Krüger
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Timea Marton
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Jeanne Ropars
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRA, USC 1408 AFMB, Marseille, F-13288, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Christophe Roux
- Laboratoire de Recherche en Sciences Végétales, UPS, CNRS 24 Chemin de Borde Rouge-Auzeville, Université de Toulouse, Castanet-Tolosan, 31326, France
| | - Francis Martin
- Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire D'excellence Recherches Avancées sur la Biologie de l'Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Grand Est-Nancy, Champenoux, 54280, France
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, ON, K1N9A7, Canada
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152
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Stam R, Münsterkötter M, Pophaly SD, Fokkens L, Sghyer H, Güldener U, Hückelhoven R, Hess M. A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni. Genome Biol Evol 2018; 10:3243-3249. [PMID: 30371775 PMCID: PMC6301796 DOI: 10.1093/gbe/evy240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2018] [Indexed: 01/17/2023] Open
Abstract
Ramularia leaf spot has recently emerged as a major threat to barley production world-wide, causing 25% yield loss in many barley growing regions. Here, we provide a new reference genome of the causal agent, the Dothideomycete Ramularia collo-cygni. The assembly of 32 Mb consists of 78 scaffolds. We used RNA-seq to identify 11,622 genes of which 1,303 and 282 are coding for predicted secreted proteins and putative effectors respectively. The pathogen separated from its nearest sequenced relative, Zymoseptoria tritici ∼27 Ma. We calculated the divergence of the two species on protein level and see remarkably high synonymous and nonsynonymous divergence. Unlike in many other plant pathogens, the comparisons of transposable elements and gene distributions, show a very homogeneous genome for R. collo-cygni. We see no evidence for higher selective pressure on putative effectors or other secreted proteins and repetitive sequences are spread evenly across the scaffolds. These findings could be associated to the predominantly endophytic life-style of the pathogen. We hypothesize that R. collo-cygni only recently became pathogenic and that therefore its genome does not yet show the typical pathogen characteristics. Because of its high scaffold length and improved CDS annotations, our new reference sequence provides a valuable resource for the community for future comparative genomics and population genetics studies.
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Affiliation(s)
- Remco Stam
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Martin Münsterkötter
- Functional Genomics and Bioinformatics, Research Centre for Forestry and Wood Industry, University of Sopron, Hungary.,Institute of Bioinformatics and Systems Biology, Helmholtz Centre Munich, Germany
| | - Saurabh Dilip Pophaly
- Section of Population Genetics, School of Life Sciences Weihenstephan, Technische Universität München, Germany.,Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden and Division of Evolutionary Biology, Faculty of Biology II, Ludwig-Maximilians-Universität München, Germany
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Hind Sghyer
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Ulrich Güldener
- Department of Bioinformatics, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
| | - Michael Hess
- Chair of Phytopathology, School of Life Sciences Weihenstephan, Technische University Munich, Germany
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153
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Derbyshire MC, Gohari AM, Mehrabi R, Kilaru S, Steinberg G, Ali S, Bailey A, Hammond-Kosack K, Kema GHJ, Rudd JJ. Phosphopantetheinyl transferase (Ppt)-mediated biosynthesis of lysine, but not siderophores or DHN melanin, is required for virulence of Zymoseptoria tritici on wheat. Sci Rep 2018; 8:17069. [PMID: 30459352 PMCID: PMC6244202 DOI: 10.1038/s41598-018-35223-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/30/2018] [Indexed: 12/19/2022] Open
Abstract
Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB) disease of wheat. Z. tritici is an apoplastic fungal pathogen, which does not penetrate plant cells at any stage of infection, and has a long initial period of symptomless leaf colonisation. During this phase it is unclear to what extent the fungus can access host plant nutrients or communicate with plant cells. Several important primary and secondary metabolite pathways in fungi are regulated by the post-translational activator phosphopantetheinyl transferase (Ppt) which provides an essential co-factor for lysine biosynthesis and the activities of non-ribosomal peptide synthases (NRPS) and polyketide synthases (PKS). To investigate the relative importance of lysine biosynthesis, NRPS-based siderophore production and PKS-based DHN melanin biosynthesis, we generated deletion mutants of ZtPpt. The ∆ZtPpt strains were auxotrophic for lysine and iron, non-melanised and non-pathogenic on wheat. Deletion of the three target genes likely affected by ZtPpt loss of function (Aar- lysine; Nrps1-siderophore and Pks1- melanin), highlighted that lysine auxotrophy was the main contributing factor for loss of virulence, with no reduction caused by loss of siderophore production or melanisation. This reveals Ppt, and the lysine biosynthesis pathway, as potential targets for fungicides effective against Z. tritici.
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Affiliation(s)
- Mark C Derbyshire
- BioIntercations and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK.,Centre for Crop and Disease Management, Curtin University, Perth, Australia
| | - Amir Mirzadi Gohari
- Department of Plant Pathology, Faculty of Agricultural Sciences and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran.,Wageningen University and Research, Wageningen Plant Research, PO Box 16, 6700AA, Wageningen, The Netherlands
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | | | | | - Solaf Ali
- Technical College of Health, Sulaimani Polytechnic University, Qrga, Wrme Street, Mardin 327, Alley 76, Sulaimaniyah, Kurdistan Region of Iraq, Sulaimani Governorate, Iraq
| | - Andy Bailey
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, UK
| | - Kim Hammond-Kosack
- BioIntercations and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Gert H J Kema
- Wageningen University and Research, Wageningen Plant Research, PO Box 16, 6700AA, Wageningen, The Netherlands. .,Wageningen University and Research, Laboratory of Phytopathology, PO box 16, 6700AA, Wageningen, The Netherlands.
| | - Jason J Rudd
- BioIntercations and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire, UK.
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154
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155
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Winter DJ, Ganley ARD, Young CA, Liachko I, Schardl CL, Dupont PY, Berry D, Ram A, Scott B, Cox MP. Repeat elements organise 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae. PLoS Genet 2018; 14:e1007467. [PMID: 30356280 PMCID: PMC6218096 DOI: 10.1371/journal.pgen.1007467] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/05/2018] [Accepted: 08/27/2018] [Indexed: 11/18/2022] Open
Abstract
Structural features of genomes, including the three-dimensional arrangement of DNA in the nucleus, are increasingly seen as key contributors to the regulation of gene expression. However, studies on how genome structure and nuclear organisation influence transcription have so far been limited to a handful of model species. This narrow focus limits our ability to draw general conclusions about the ways in which three-dimensional structures are encoded, and to integrate information from three-dimensional data to address a broader gamut of biological questions. Here, we generate a complete and gapless genome sequence for the filamentous fungus, Epichloë festucae. We use Hi-C data to examine the three-dimensional organisation of the genome, and RNA-seq data to investigate how Epichloë genome structure contributes to the suite of transcriptional changes needed to maintain symbiotic relationships with the grass host. Our results reveal a genome in which very repeat-rich blocks of DNA with discrete boundaries are interspersed by gene-rich sequences that are almost repeat-free. In contrast to other species reported to date, the three-dimensional structure of the genome is anchored by these repeat blocks, which act to isolate transcription in neighbouring gene-rich regions. Genes that are differentially expressed in planta are enriched near the boundaries of these repeat-rich blocks, suggesting that their three-dimensional orientation partly encodes and regulates the symbiotic relationship formed by this organism.
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Affiliation(s)
- David J. Winter
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Austen R. D. Ganley
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Carolyn A. Young
- Noble Research Institute, LLC, Ardmore, Oklahoma, United States of America
| | - Ivan Liachko
- Phase Genomics Inc, Seattle, Washington, United States of America
| | - Christopher L. Schardl
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
| | - Pierre-Yves Dupont
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Daniel Berry
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Arvina Ram
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Barry Scott
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- Genetics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Murray P. Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- The Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
- * E-mail:
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156
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Möller M, Habig M, Freitag M, Stukenbrock EH. Extraordinary Genome Instability and Widespread Chromosome Rearrangements During Vegetative Growth. Genetics 2018; 210:517-529. [PMID: 30072376 PMCID: PMC6216587 DOI: 10.1534/genetics.118.301050] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/18/2018] [Indexed: 12/27/2022] Open
Abstract
The haploid genome of the pathogenic fungus Zymoseptoria tritici is contained on "core" and "accessory" chromosomes. While 13 core chromosomes are found in all strains, as many as eight accessory chromosomes show presence/absence variation and rearrangements among field isolates. The factors influencing these presence/absence polymorphisms are so far unknown. We investigated chromosome stability using experimental evolution, karyotyping, and genome sequencing. We report extremely high and variable rates of accessory chromosome loss during mitotic propagation in vitro and in planta Spontaneous chromosome loss was observed in 2 to >50% of cells during 4 weeks of incubation. Similar rates of chromosome loss in the closely related Zymoseptoria ardabiliae suggest that this extreme chromosome dynamic is a conserved phenomenon in the genus. Elevating the incubation temperature greatly increases instability of accessory and even core chromosomes, causing severe rearrangements involving telomere fusion and chromosome breakage. Chromosome losses do not affect the fitness of Zymoseptoria tritici in vitro, but some lead to increased virulence, suggesting an adaptive role of this extraordinary chromosome instability.
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Affiliation(s)
- Mareike Möller
- Environmental Genomics, Christian-Albrechts University, D-24118 Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, D-24306 Plön, Germany
| | - Michael Habig
- Environmental Genomics, Christian-Albrechts University, D-24118 Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, D-24306 Plön, Germany
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University, D-24118 Kiel, Germany
- Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, D-24306 Plön, Germany
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157
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Syme RA, Tan KC, Rybak K, Friesen TL, McDonald BA, Oliver RP, Hane JK. Pan-Parastagonospora Comparative Genome Analysis-Effector Prediction and Genome Evolution. Genome Biol Evol 2018; 10:2443-2457. [PMID: 30184068 PMCID: PMC6152946 DOI: 10.1093/gbe/evy192] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2018] [Indexed: 01/01/2023] Open
Abstract
We report a fungal pan-genome study involving Parastagonospora spp., including 21 isolates of the wheat (Triticum aestivum) pathogen Parastagonospora nodorum, 10 of the grass-infecting Parastagonospora avenae, and 2 of a closely related undefined sister species. We observed substantial variation in the distribution of polymorphisms across the pan-genome, including repeat-induced point mutations, diversifying selection and gene gains and losses. We also discovered chromosome-scale inter and intraspecific presence/absence variation of some sequences, suggesting the occurrence of one or more accessory chromosomes or regions that may play a role in host-pathogen interactions. The presence of known pathogenicity effector loci SnToxA, SnTox1, and SnTox3 varied substantially among isolates. Three P. nodorum isolates lacked functional versions for all three loci, whereas three P. avenae isolates carried one or both of the SnTox1 and SnTox3 genes, indicating previously unrecognized potential for discovering additional effectors in the P. nodorum-wheat pathosystem. We utilized the pan-genomic comparative analysis to improve the prediction of pathogenicity effector candidates, recovering the three confirmed effectors among our top-ranked candidates. We propose applying this pan-genomic approach to identify the effector repertoire involved in other host-microbe interactions involving necrotrophic pathogens in the Pezizomycotina.
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Affiliation(s)
- Robert A Syme
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Kar-Chun Tan
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Kasia Rybak
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Timothy L Friesen
- Cereal Crops Research Unit, USDA-ARS Red River Valley Agricultural Research Center, Fargo, North Dakota
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Richard P Oliver
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - James K Hane
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Bentley, Western Australia, Australia
- Curtin Institute for Computation, Curtin University, Bentley, Western Australia, Australia
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158
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Siah A, Bomble M, Tisserant B, Cadalen T, Holvoet M, Hilbert JL, Halama P, Reignault P. Genetic Structure of Zymoseptoria tritici in Northern France at Region, Field, Plant, and Leaf Layer Scales. PHYTOPATHOLOGY 2018; 108:1114-1123. [PMID: 29658841 DOI: 10.1094/phyto-09-17-0322-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Population genetic structure of the worldwide-distributed wheat pathogen Zymoseptoria tritici has been extensively studied at large geographical scales, but to a much less extent at small or local spatial scales. A total of 627 single-conidial fungal isolates were sampled from several locations in northern France (Hauts-de-France Region) to assess fungal genetic structure at region, field, plant, and leaf layer scales, using highly polymorphic microsatellite markers and mating type idiomorphs. Important and overall similar levels of both gene and genotype diversities (gene diversity values of ≥0.44 and haplotype frequencies of ≥94%) were found at all the examined scales. Such rates of diversity are likely due to an active sexual recombination in the investigated areas, as revealed by equal proportions of the two mating types scored in all sampled populations. Interestingly, a rare occurrence of clones among lesions from a same leaf, as well as among leaves from different plant leaf layers (e.g., upper versus lower leaves), was highlighted, indicating that ascospores contribute much more than expected to Z. tritici epidemics, compared with pycnidiospores. Population structure and analyses of molecular variance revealed significant genetic differentiation at the regional scale (GST = 0.23) and, as expected, not at the other more local scales (GST ≤ 0.01). Further analyses using Bayesian and unweighted neighbor-joining statistical methods detected six genetic clusters within the regional population, overall distributed according to the locations from which the isolates were sampled. Neither clear directional relative migration linked to the geographical distribution of the locations, nor isolation by distance, were observed. Separate evolutionary trajectories caused by selection and adaptations to habitat heterogeneity could be the main forces shaping such structuration. This study provides new insights into the epidemiology and the genetic structure of Z. tritici at small local and, for the first time, at single plant and leaf layer scales. Such findings would be helpful in implementing effective control strategies.
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Affiliation(s)
- Ali Siah
- First, second, fourth, fifth, sixth, and seventh authors: Institut Charles Viollette (ICV-EA 7394), ISA, Université de Lille, SFR Condorcet FR CNRS 3417, 48 bd Vauban, BP 41290, F-59014 Lille Cedex, France; and third and eighth authors: Univ. Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais Cedex, France
| | - Myriam Bomble
- First, second, fourth, fifth, sixth, and seventh authors: Institut Charles Viollette (ICV-EA 7394), ISA, Université de Lille, SFR Condorcet FR CNRS 3417, 48 bd Vauban, BP 41290, F-59014 Lille Cedex, France; and third and eighth authors: Univ. Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais Cedex, France
| | - Benoit Tisserant
- First, second, fourth, fifth, sixth, and seventh authors: Institut Charles Viollette (ICV-EA 7394), ISA, Université de Lille, SFR Condorcet FR CNRS 3417, 48 bd Vauban, BP 41290, F-59014 Lille Cedex, France; and third and eighth authors: Univ. Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais Cedex, France
| | - Thierry Cadalen
- First, second, fourth, fifth, sixth, and seventh authors: Institut Charles Viollette (ICV-EA 7394), ISA, Université de Lille, SFR Condorcet FR CNRS 3417, 48 bd Vauban, BP 41290, F-59014 Lille Cedex, France; and third and eighth authors: Univ. Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais Cedex, France
| | - Maxime Holvoet
- First, second, fourth, fifth, sixth, and seventh authors: Institut Charles Viollette (ICV-EA 7394), ISA, Université de Lille, SFR Condorcet FR CNRS 3417, 48 bd Vauban, BP 41290, F-59014 Lille Cedex, France; and third and eighth authors: Univ. Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais Cedex, France
| | - Jean-Louis Hilbert
- First, second, fourth, fifth, sixth, and seventh authors: Institut Charles Viollette (ICV-EA 7394), ISA, Université de Lille, SFR Condorcet FR CNRS 3417, 48 bd Vauban, BP 41290, F-59014 Lille Cedex, France; and third and eighth authors: Univ. Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais Cedex, France
| | - Patrice Halama
- First, second, fourth, fifth, sixth, and seventh authors: Institut Charles Viollette (ICV-EA 7394), ISA, Université de Lille, SFR Condorcet FR CNRS 3417, 48 bd Vauban, BP 41290, F-59014 Lille Cedex, France; and third and eighth authors: Univ. Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais Cedex, France
| | - Philippe Reignault
- First, second, fourth, fifth, sixth, and seventh authors: Institut Charles Viollette (ICV-EA 7394), ISA, Université de Lille, SFR Condorcet FR CNRS 3417, 48 bd Vauban, BP 41290, F-59014 Lille Cedex, France; and third and eighth authors: Univ. Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (UCEIV-EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais Cedex, France
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159
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Sperschneider J, Dodds PN, Gardiner DM, Singh KB, Taylor JM. Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0. MOLECULAR PLANT PATHOLOGY 2018; 19:2094-2110. [PMID: 29569316 PMCID: PMC6638006 DOI: 10.1111/mpp.12682] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 05/14/2023]
Abstract
Plant-pathogenic fungi secrete effector proteins to facilitate infection. We describe extensive improvements to EffectorP, the first machine learning classifier for fungal effector prediction. EffectorP 2.0 is now trained on a larger set of effectors and utilizes a different approach based on an ensemble of classifiers trained on different subsets of negative data, offering different views on classification. EffectorP 2.0 achieves an accuracy of 89%, compared with 82% for EffectorP 1.0 and 59.8% for a small size classifier. Important features for effector prediction appear to be protein size, protein net charge as well as the amino acids serine and cysteine. EffectorP 2.0 decreases the number of predicted effectors in secretomes of fungal plant symbionts and saprophytes by 40% when compared with EffectorP 1.0. However, EffectorP 1.0 retains value, and combining EffectorP 1.0 and 2.0 results in a stringent classifier with a low false positive rate of 9%. EffectorP 2.0 predicts significant enrichments of effectors in 12 of 13 sets of infection-induced proteins from diverse fungal pathogens, whereas a small cysteine-rich classifier detects enrichment in only seven of 13. EffectorP 2.0 will fast track the prioritization of high-confidence effector candidates for functional validation and aid in improving our understanding of effector biology. EffectorP 2.0 is available at http://effectorp.csiro.au.
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Affiliation(s)
- Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and FoodPerth, WA 6014Australia
| | - Peter N. Dodds
- Black Mountain Laboratories, CSIRO Agriculture and FoodCanberra, ACT 2601Australia
| | - Donald M. Gardiner
- CSIRO Agriculture and FoodQueensland Bioscience PrecinctBrisbane, Qld 4067Australia
| | - Karam B. Singh
- Centre for Environment and Life Sciences, CSIRO Agriculture and FoodPerth, WA 6014Australia
- Department of Environment and Agriculture, Centre for Crop and Disease ManagementCurtin UniversityBentley, WA 6102Australia
| | - Jennifer M. Taylor
- Black Mountain Laboratories, CSIRO Agriculture and FoodCanberra, ACT 2601Australia
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160
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Bertazzoni S, Williams AH, Jones DA, Syme RA, Tan KC, Hane JK. Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:779-788. [PMID: 29664319 DOI: 10.1094/mpmi-06-17-0135-fi] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Fungal pathogen genomes can often be divided into core and accessory regions. Accessory regions ARs) may be comprised of either ARs (within core chromosomes (CCs) or wholly dispensable (accessory) chromosomes (ACs). Fungal ACs and ARs typically accumulate mutations and structural rearrangements more rapidly over time than CCs and many harbor genes relevant to host-pathogen interactions. These regions are of particular interest in plant pathology and include host-specific virulence factors and secondary metabolite synthesis gene clusters. This review outlines known ACs and ARs in fungal genomes, methods used for their detection, their common properties that differentiate them from the core genome, and what is currently known of their various roles in pathogenicity. Reports on the evolutionary processes generating and shaping AC and AR compartments are discussed, including repeat induced point mutation and breakage fusion bridge cycles. Previously ACs have been studied extensively within key genera, including Fusarium, Zymoseptoria, and Alternaria, but are growing in frequency of observation and perceived importance across a wider range of fungal species. Recent advances in sequencing technologies permit affordable genome assembly and resequencing of populations that will facilitate further discovery and routine screening of ACs.
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Affiliation(s)
- Stefania Bertazzoni
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Angela H Williams
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Darcy A Jones
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Robert A Syme
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - Kar-Chun Tan
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
| | - James K Hane
- 1 Centre for Crop & Disease Management, Curtin University, Perth, Western Australia, Australia; and
- 2 Curtin Institute for Computation, Curtin University, Perth, Western Australia, Australia
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161
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Meile L, Croll D, Brunner PC, Plissonneau C, Hartmann FE, McDonald BA, Sánchez‐Vallet A. A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch. THE NEW PHYTOLOGIST 2018; 219:1048-1061. [PMID: 29693722 PMCID: PMC6055703 DOI: 10.1111/nph.15180] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/20/2018] [Indexed: 05/11/2023]
Abstract
Cultivar-strain specificity in the wheat-Zymoseptoria tritici pathosystem determines the infection outcome and is controlled by resistance genes on the host side, many of which have been identified. On the pathogen side, however, the molecular determinants of specificity remain largely unknown. We used genetic mapping, targeted gene disruption and allele swapping to characterise the recognition of the new avirulence factor Avr3D1. We then combined population genetic and comparative genomic analyses to characterise the evolutionary trajectory of Avr3D1. Avr3D1 is specifically recognised by wheat cultivars harbouring the Stb7 resistance gene, triggering a strong defence response without preventing pathogen infection and reproduction. Avr3D1 resides in a cluster of putative effector genes located in a genome region populated by independent transposable element insertions. The gene was present in all 132 investigated strains and is highly polymorphic, with 30 different protein variants identified. We demonstrated that specific amino acid substitutions in Avr3D1 led to evasion of recognition. These results demonstrate that quantitative resistance and gene-for-gene interactions are not mutually exclusive. Localising avirulence genes in highly plastic genomic regions probably facilitates accelerated evolution that enables escape from recognition by resistance proteins.
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Affiliation(s)
- Lukas Meile
- Plant PathologyInstitute of Integrative BiologyETH ZürichCH‐8092ZürichSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary GeneticsInstitute of BiologyUniversity of NeuchâtelCH‐2000NeuchâtelSwitzerland
| | - Patrick C. Brunner
- Plant PathologyInstitute of Integrative BiologyETH ZürichCH‐8092ZürichSwitzerland
| | - Clémence Plissonneau
- Plant PathologyInstitute of Integrative BiologyETH ZürichCH‐8092ZürichSwitzerland
- UMR BIOGERINRAAgroParisTechUniversité Paris‐SaclayAvenue Lucien Bretignières, BP 01Thiverval‐GrignonF‐78850France
| | - Fanny E. Hartmann
- Ecologie Systématique EvolutionUniversite Paris‐SudAgroParisTechCNRSUniversité Paris‐Saclay91400OrsayFrance
| | - Bruce A. McDonald
- Plant PathologyInstitute of Integrative BiologyETH ZürichCH‐8092ZürichSwitzerland
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162
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Luo H, Cai Q, Lüli Y, Li X, Sinha R, Hallen-Adams HE, Yang ZL. The MSDIN family in amanitin-producing mushrooms and evolution of the prolyl oligopeptidase genes. IMA Fungus 2018; 9:225-242. [PMID: 30622880 PMCID: PMC6317590 DOI: 10.5598/imafungus.2018.09.02.01] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/24/2018] [Indexed: 12/18/2022] Open
Abstract
The biosynthetic pathway for amanitins and related cyclic peptides in deadly Amanita (Amanitaceae) mushrooms represents the first known ribosomal cyclic peptide pathway in the Fungi. Amanitins are found outside of the genus in distantly related agarics Galerina (Strophariaceae) and Lepiota (Agaricaceae). A long-standing question in the field persists: why is this pathway present in these phylogenetically disjunct agarics? Two deadly mushrooms, A. pallidorosea and A. subjunquillea, were deep sequenced, and sequences of biosynthetic genes encoding MSDINs (cyclic peptide precursor) and prolyl oligopeptidases (POPA and POPB) were obtained. The two Amanita species yielded 29 and 18 MSDINs, respectively. In addition, two MSDIN sequences were cloned from L. brunneoincarnata basidiomes. The toxin MSDIN genes encoding amatoxins or phallotoxins from the three genera were compared, and a phylogenetic tree constructed. Prolyl oligopeptidase B (POPB), a key enzyme in the biosynthetic pathway, was used in phylogenetic reconstruction to infer the evolutionary history of the genes. Phylogenies of POPB and POPA based on both coding and amino acid sequences showed very different results: while POPA genes clearly reflected the phylogeny of the host species, POPB did not; strikingly, it formed a well-supported monophyletic clade, despite that the species belong to different genera in disjunct families. POPA, a known house-keeping gene, was shown to be restricted in a branch containing only Amanita species and the phylogeny resembled that of those Amanita species. Phylogenetic analyses of MSDIN and POPB genes showed tight coordination and disjunct distribution. A POPB gene tree was compared with a corresponding species tree, and distances and substitution rates were compared. The result suggested POPB genes have significant smaller distances and rates than the house-keeping rpb2, discounting massive gene loss. Under this assumption, the incongruency between the gene tree and species tree was shown with strong support. Additionally, k-mer analyses consistently cluster Galerina and Amanita POPB genes, while Lepiota POPB is distinct. Our result suggests that horizontal gene transfer (HGT), at least between Amanita and Galerina, was involved in the acquisition of POPB genes, which may shed light on the evolution of the α-amanitin biosynthetic pathway.
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Affiliation(s)
- Hong Luo
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Qing Cai
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Yunjiao Lüli
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Li
- Department of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650091, Yunnan, China
| | | | - Heather E Hallen-Adams
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Zhu L Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
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163
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Yan Y, Yuan Q, Tang J, Huang J, Hsiang T, Wei Y, Zheng L. Colletotrichum higginsianum as a Model for Understanding Host⁻Pathogen Interactions: A Review. Int J Mol Sci 2018; 19:E2142. [PMID: 30041456 PMCID: PMC6073530 DOI: 10.3390/ijms19072142] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 11/16/2022] Open
Abstract
Colletotrichum higginsianum is a hemibiotrophic ascomycetous fungus that causes economically important anthracnose diseases on numerous monocot and dicot crops worldwide. As a model pathosystem, the Colletotrichum⁻Arabidopsis interaction has the significant advantage that both organisms can be manipulated genetically. The goal of this review is to provide an overview of the system and to point out recent significant studies that update our understanding of the pathogenesis of C. higginsianum and resistance mechanisms of Arabidopsis against this hemibiotrophic fungus. The genome sequence of C. higginsianum has provided insights into how genome structure and pathogen genetic variability has been shaped by transposable elements, and allows systematic approaches to longstanding areas of investigation, including infection structure differentiation and fungal⁻plant interactions. The Arabidopsis-Colletotrichum pathosystem provides an integrated system, with extensive information on the host plant and availability of genomes for both partners, to illustrate many of the important concepts governing fungal⁻plant interactions, and to serve as an excellent starting point for broad perspectives into issues in plant pathology.
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Affiliation(s)
- Yaqin Yan
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qinfeng Yuan
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jintian Tang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Junbin Huang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada.
| | - Lu Zheng
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China.
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164
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Chang HX, Noel ZA, Sang H, Chilvers MI. Annotation resource of tandem repeat-containing secretory proteins in sixty fungi. Fungal Genet Biol 2018; 119:7-19. [PMID: 30026018 DOI: 10.1016/j.fgb.2018.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/06/2018] [Accepted: 07/15/2018] [Indexed: 11/17/2022]
Abstract
Fungal secretory proteins that interact with host plants are regarded as effectors. Because fungal effectors rarely contain conserved sequence features, identification and annotation of fungal effectors from predicted secretory proteins are difficult using outward comparison methods such as BLAST or hidden Markov model. In desire of more sequence features to prioritize research interests of fungal secretory proteins, this study developed a pipeline to identify tandem repeat (TR) domain within putative secretory proteins and tested a hypothesis that at least one type of TR domain in non-orthologous secretory proteins has emerged from convergent evolution for plant pathogenicity. There were 2804 types of TR domains and a total of 2925 TR-containing secretory proteins found from 60 fungi. There was no conserved type of TR domain shared only by plant pathogens, indicating functional divergence for different types of TR domain and TR-containing secretory proteins. The annotation resource of putative fungal TR-containing secretory proteins provides new sequence features that will be useful for the community interested in fungal effector biology.
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Affiliation(s)
- Hao-Xun Chang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Zachary A Noel
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Hyunkyu Sang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing 48824, MI, United States.
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165
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Krishnan P, Meile L, Plissonneau C, Ma X, Hartmann FE, Croll D, McDonald BA, Sánchez-Vallet A. Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat. BMC Biol 2018; 16:78. [PMID: 30012138 PMCID: PMC6047131 DOI: 10.1186/s12915-018-0543-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Fungal plant pathogens pose major threats to crop yield and sustainable food production if they are highly adapted to their host and the local environment. Variation in gene expression contributes to phenotypic diversity within fungal species and affects adaptation. However, very few cases of adaptive regulatory changes have been reported in fungi and the underlying mechanisms remain largely unexplored. Fungal pathogen genomes are highly plastic and harbor numerous insertions of transposable elements, which can potentially contribute to gene expression regulation. In this work, we elucidated how transposable elements contribute to variation in melanin accumulation, a quantitative trait in fungi that affects survival under stressful conditions. RESULTS We demonstrated that differential transcriptional regulation of the gene encoding the transcription factor Zmr1, which controls expression of the genes in the melanin biosynthetic gene cluster, is responsible for variation in melanin accumulation in the fungal plant pathogen Zymoseptoria tritici. We show that differences in melanin levels between two strains of Z. tritici are due to two levels of transcriptional regulation: (1) variation in the promoter sequence of Zmr1 and (2) an insertion of transposable elements upstream of the Zmr1 promoter. Remarkably, independent insertions of transposable elements upstream of Zmr1 occurred in 9% of Z. tritici strains from around the world and negatively regulated Zmr1 expression, contributing to variation in melanin accumulation. CONCLUSIONS Our studies identified two levels of transcriptional control that regulate the synthesis of melanin. We propose that these regulatory mechanisms evolved to balance the fitness costs associated with melanin production against its positive contribution to survival in stressful environments.
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Affiliation(s)
- Parvathy Krishnan
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Lukas Meile
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Xin Ma
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris Saclay, Orsay, France
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
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166
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Wang B, Liang X, Gleason ML, Zhang R, Sun G. Comparative genomics of Botryosphaeria dothidea and B. kuwatsukai, causal agents of apple ring rot, reveals both species expansion of pathogenicity-related genes and variations in virulence gene content during speciation. IMA Fungus 2018; 9:243-257. [PMID: 30622881 PMCID: PMC6317582 DOI: 10.5598/imafungus.2018.09.02.02] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 08/10/2018] [Indexed: 12/25/2022] Open
Abstract
Ring rot, one of the most destructive diseases of apple worldwide, is caused primarily by Botryosphaeria dothidea and B. kuwatsukai. Here, we sequenced the genomes of B. dothidea strain PG45 (44.3 Mb with 5.12 % repeat rate) and B. kuwatsukai epitype strain PG2 (48.0 Mb with 13.02 % repeat rate), and conducted a comparative analysis of these two genomes, as well as other sequenced fungal genomes, in order to understand speciation and distinctive patterns of evolution of pathogenicity-related genes. Pair-wise genome alignments revealed that the two species are highly syntenic (96.74 % average sequence identity). Both species encode a significant number of pathogenicity-related genes, e.g. carbohydrate active enzymes (CAZYs), plant cell wall degrading enzymes (PCWDEs), secondary metabolites (SMs) biosynthetic enzymes, cytochrome P450 enzymes (CYPs), and secreted peptidases, in comparison to all additional sequenced fungal species involved in various life-styles. The number of pathogenicity-related genes in B. dothidea and B. kuwatsukai is higher than other genomes of Botryosphaeriaceae pathogens (Macrophomina phaseolina and Neofusicoccum parvum), suggesting a secondary round of Botryosphaeria-lineage expansion in the family. There were, however, also significant differences in the genomes of the two Botryosphaeria species. Botryosphaeria kuwatsukai, which infects only apple and pear, apparently lost a set of SMs genes, CAZYs and PCWDEs, possibly as a result of host specialization. Botryosphaeria kuwatsukai contained significantly more transposable elements and higher value of repeat induced point (RIP) index than B. dothidea. Our results will be instrumental in understanding how both phytopathogens interact with their plant hosts and in designing efficient strategies for disease control and molecular breeding to help ensure global apple production and food security.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100, China
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167
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Wang J, Tian L, Zhang DD, Short DPG, Zhou L, Song SS, Liu Y, Wang D, Kong ZQ, Cui WY, Ma XF, Klosterman SJ, Subbarao KV, Chen JY, Dai XF. SNARE-Encoding Genes VdSec22 and VdSso1 Mediate Protein Secretion Required for Full Virulence in Verticillium dahliae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:651-664. [PMID: 29419372 DOI: 10.1094/mpmi-12-17-0289-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Proteins that mediate cellular and subcellular membrane fusion are key factors in vesicular trafficking in all eukaryotic cells, including the secretion and transport of plant pathogen virulence factors. In this study, we identified vesicle-fusion components that included 22 soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), four Sec1/Munc18 (SM) family proteins, and 10 Rab GTPases encoded in the genome of the vascular wilt pathogen Verticillium dahliae Vd991. Targeted deletion of two SNARE-encoding genes in V. dahliae, VdSec22 and VdSso1, significantly reduced virulence of both mutants on cotton, relative to the wild-type Vd991 strain. Comparative analyses of the secreted protein content (exoproteome) revealed that many enzymes involved in carbohydrate hydrolysis were regulated by VdSec22 or VdSso1. Consistent with a role of these enzymes in plant cell-wall degradation, pectin, cellulose, and xylan utilization were reduced in the VdSec22 or VdSso1 mutant strains along with a loss of exoproteome cytotoxic activity on cotton leaves. Comparisons with a pathogenicity-related exoproteome revealed that several known virulence factors were not regulated by VdSec22 or VdSso1, but some of the proteins regulated by VdSec22 or VdSso1 displayed different characteristics, including the lack of a typical signal peptide, suggesting that V. dahliae employs more than one secretory route to transport proteins to extracellular sites during infection.
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Affiliation(s)
- Jie Wang
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Li Tian
- 3 College of Life Science, Qufu Normal University, Qufu, 273165, Shandong, China; and
| | - Dan-Dan Zhang
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dylan P G Short
- 2 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, U.S.A
| | - Lei Zhou
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shuang-Shuang Song
- 3 College of Life Science, Qufu Normal University, Qufu, 273165, Shandong, China; and
| | - Yan Liu
- 3 College of Life Science, Qufu Normal University, Qufu, 273165, Shandong, China; and
| | - Dan Wang
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhi-Qiang Kong
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Wei-Ye Cui
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xue-Feng Ma
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Steven J Klosterman
- 4 United States Department of Agriculture, Agricultural Research Service, Salinas, CA, U.S.A
| | - Krishna V Subbarao
- 2 Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, U.S.A
| | - Jie-Yin Chen
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiao-Feng Dai
- 1 Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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168
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Fouché S, Plissonneau C, McDonald BA, Croll D. Meiosis Leads to Pervasive Copy-Number Variation and Distorted Inheritance of Accessory Chromosomes of the Wheat Pathogen Zymoseptoria tritici. Genome Biol Evol 2018; 10:1416-1429. [PMID: 29850789 PMCID: PMC6007412 DOI: 10.1093/gbe/evy100] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
Meiosis is one of the most conserved molecular processes in eukaryotes. The fidelity of pairing and segregation of homologous chromosomes has a major impact on the proper transmission of genetic information. Aberrant chromosomal transmission can have major phenotypic consequences, yet the mechanisms are poorly understood. Fungi are excellent models to investigate processes of chromosomal transmission, because many species have highly polymorphic genomes that include accessory chromosomes. Inheritance of accessory chromosomes is often unstable and chromosomal losses have little impact on fitness. We analyzed chromosomal inheritance in 477 progeny coming from two crosses of the fungal wheat pathogen Zymoseptoria tritici. For this, we developed a high-throughput screening method based on restriction site-associated DNA sequencing that generated dense coverage of genetic markers along each chromosome. We identified rare instances of chromosomal duplications (disomy) in core chromosomes. Accessory chromosomes showed high overall frequencies of disomy. Chromosomal rearrangements were found exclusively on accessory chromosomes and were more frequent than disomy. Accessory chromosomes present in only one of the parents in an analyzed cross were inherited at significantly higher rates than the expected 1:1 segregation ratio. Both the chromosome and the parental background had significant impacts on the rates of disomy, losses, rearrangements, and distorted inheritance. We found that chromosomes with higher sequence similarity and lower repeat content were inherited more faithfully. The large number of rearranged progeny chromosomes identified in this species will enable detailed analyses of the mechanisms underlying chromosomal rearrangement.
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Affiliation(s)
- Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Switzerland
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
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169
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Van Wyk S, Wingfield BD, De Vos L, Santana QC, Van der Merwe NA, Steenkamp ET. Multiple independent origins for a subtelomeric locus associated with growth rate in Fusarium circinatum. IMA Fungus 2018; 9:27-36. [PMID: 30018870 PMCID: PMC6048564 DOI: 10.5598/imafungus.2018.09.01.03] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 02/19/2018] [Indexed: 12/28/2022] Open
Abstract
Fusarium is a diverse assemblage that includes a large number of species of considerable medical and agricultural importance. Not surprisingly, whole genome sequences for many Fusarium species have been published or are in the process of being determined, the availability of which is invaluable for deciphering the genetic basis of key phenotypic traits. Here we investigated the distribution, genic composition, and evolutionary history of a locus potentially determining growth rate in the pitch canker pathogen F. circinatum. We found that the genomic region underlying this locus is highly conserved amongst F. circinatum and its close relatives, except for the presence of a 12 000 base pair insertion in all of the examined isolates of F. circinatum. This insertion encodes for five genes and our phylogenetic analyses revealed that each was most likely acquired through horizontal gene transfer from polyphyletic origins. Our data further showed that this region is located in a region low in G+C content and enriched for repetitive sequences and transposable elements, which is situated near the telomere of Chromosome 3 of F. circinatum. As have been shown for other fungi, these findings thus suggest that the emergence of the unique 12 000 bp region in F. circinatum is linked to the dynamic evolutionary processes associated with subtelomeres that, in turn, have been implicated in the ecological adaptation of fungal pathogens.
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Affiliation(s)
- Stephanie Van Wyk
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Lieschen De Vos
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Quentin C Santana
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Nicolaas A Van der Merwe
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
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170
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Wu B, Macielog AI, Hao W. Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria. Genome Biol Evol 2018; 9:2658-2667. [PMID: 29048531 PMCID: PMC5647799 DOI: 10.1093/gbe/evx211] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2017] [Indexed: 12/16/2022] Open
Abstract
Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species. Within the genome, spliceosomal introns can proliferate in unrelated genes and intergenic regions. Among conspecific strains, spliceosomal introns undergo rapid turnover (gains and losses) and frequent sequence exchange between geographically distinct strains. Furthermore, spliceosomal introns could undergo introgression between distinct species, which can further promote intron invasion and proliferation. The dynamic invasion and proliferation processes of spliceosomal introns resemble the life cycles of mobile selfish (group I/II) introns, and these intron movements, at least in part, account for the dramatic processes of intron gain and intron loss during eukaryotic evolution.
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Affiliation(s)
- Baojun Wu
- Department of Biology, Clark University, Worcester, MA, USA
| | | | - Weilong Hao
- Department of Biological Sciences, Wayne State University
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171
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Odilbekov F, Armoniené R, Henriksson T, Chawade A. Proximal Phenotyping and Machine Learning Methods to Identify Septoria Tritici Blotch Disease Symptoms in Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:685. [PMID: 29875788 PMCID: PMC5974968 DOI: 10.3389/fpls.2018.00685] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 05/04/2018] [Indexed: 05/21/2023]
Abstract
Phenotyping with proximal sensors allow high-precision measurements of plant traits both in the controlled conditions and in the field. In this work, using machine learning, an integrated analysis was done from the data obtained from spectroradiometer, infrared thermometer, and chlorophyll fluorescence measurements to identify most predictive proxy measurements for studying Septoria tritici blotch (STB) disease of wheat. The random forest (RF) models for chlorosis and necrosis identified photosystem II quantum yield (QY) and vegetative indices (VIs) associated with the biochemical composition of leaves as the top predictive variables for identifying disease symptoms. The RF model for chlorosis was validated with a validation set (R2: 0.80) and in an independent test set (R2: 0.55). Based on the results, it can be concluded that the proxy measurements for photosystem II, chlorophyll content, carotenoid, and anthocyanin levels and leaf surface temperature can be successfully used to detect STB. Further validation of these results in the field will enable application of these predictive variables for detection of STB in the field.
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Affiliation(s)
- Firuz Odilbekov
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Rita Armoniené
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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172
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Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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173
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Abstract
The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute's Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.
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174
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Ma X, Keller B, McDonald BA, Palma-Guerrero J, Wicker T. Comparative Transcriptomics Reveals How Wheat Responds to Infection by Zymoseptoria tritici. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:420-431. [PMID: 29090630 DOI: 10.1094/mpmi-10-17-0245-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The fungus Zymoseptoria tritici causes septoria tritici blotch (STB) on wheat, an important disease globally and the most damaging wheat disease in Europe. Despite the global significance of STB, the molecular basis of wheat defense against Z. tritici is poorly understood. Here, we use a comparative transcriptomic study to investigate how wheat responds to infection by four distinct strains of Z. tritici. We examined the response of wheat across the entire infection cycle, identifying both shared responses to the four strains and strain-specific responses. We found that the early asymptomatic phase is characterized by strong upregulation of genes encoding receptor-like kinases and pathogenesis-related proteins, indicating the onset of a defense response. We also identified genes that were differentially expressed among the four fungal strains, including genes related to defense. Genes involved in senescence were induced during both the asymptomatic phase and at late stages of infection, suggesting manipulation of senescence processes by both the plant and the pathogen. Our findings illustrate the need, when identifying important genes affecting disease resistance in plants, to include multiple pathogen strains.
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Affiliation(s)
- Xin Ma
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
- 2 Department of Plant and Microbial Biology, University of Zurich, Zurich 8008, Switzerland
| | - Beat Keller
- 2 Department of Plant and Microbial Biology, University of Zurich, Zurich 8008, Switzerland
| | - Bruce A McDonald
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
| | - Javier Palma-Guerrero
- 1 Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland; and
| | - Thomas Wicker
- 2 Department of Plant and Microbial Biology, University of Zurich, Zurich 8008, Switzerland
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175
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Zhang W, Gui Y, Short DPG, Li T, Zhang D, Zhou L, Liu C, Bao Y, Subbarao KV, Chen J, Dai X. Verticillium dahliae transcription factor VdFTF1 regulates the expression of multiple secreted virulence factors and is required for full virulence in cotton. MOLECULAR PLANT PATHOLOGY 2018; 19:841-857. [PMID: 28520093 PMCID: PMC6638078 DOI: 10.1111/mpp.12569] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/11/2017] [Accepted: 05/13/2017] [Indexed: 05/05/2023]
Abstract
Fungal transcription factors (TFs) implicated in the regulation of virulence gene expression have been identified in a number of plant pathogens. In Verticillium dahliae, despite its agricultural importance, few regulators of transcription have been characterized. In this study, a T-DNA insertion mutant with significantly reduced virulence towards cotton was identified. The T-DNA was traced to VdFTF1, a gene encoding a TF containing a Fungal_trans domain. Transient expression in onion epidermal cells indicated that VdFTF1 is localized to the nucleus. The VdFTF1-deletion strains displayed normal vegetative growth, mycelial pigmentation and conidial morphology, but exhibited significantly reduced virulence on cotton, suggesting that VdFTF1 is required exclusively for pathogenesis. Comparisons of global transcription patterns of wild-type and VdFTF1-deletion strains indicated that VdFTF1 affected the expression of 802 genes, 233 of which were associated with catalytic processes. These genes encoded 69 potentially secreted proteins, 43 of which contained a carbohydrate enzyme domain known to participate in pathogenesis during infection of cotton. Targeted gene deletion of one VdFTF1-regulated gene resulted in significantly impaired vascular colonization, as measured by quantitative polymerase chain reaction, as well as aggressiveness and symptom severity in cotton. In conclusion, VdFTF1, which encodes a TF containing a Fungal_trans domain, regulates the gene expression of plant cell wall degradation enzymes in V. dahliae, which are required for full virulence on cotton.
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Affiliation(s)
- Wen‐Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Yue‐Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dylan P. G. Short
- Department of Plant PathologyUniversity of CaliforniaDavisCA 95616USA
| | - Ting‐Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dan‐Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Chun Liu
- BGI‐ShenzhenShenzhenGuangdong 518083China
| | - Yu‐Ming Bao
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | | | - Jie‐Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Xiao‐Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
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176
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Soyer JL, Balesdent MH, Rouxel T, Dean RA. To B or not to B: a tale of unorthodox chromosomes. Curr Opin Microbiol 2018; 46:50-57. [PMID: 29579575 DOI: 10.1016/j.mib.2018.01.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Jessica L Soyer
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France
| | | | - Thierry Rouxel
- UMR BIOGER, INRA, AgroParisTech, Paris-Saclay University, Thiverval-Grignon, France
| | - Ralph A Dean
- Center for Integrated Fungal Research, North Carolina State University & Department of Entomology and Plant Pathology, North Carolina State University, United States.
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177
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Hartmann FE, Croll D. Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen. Mol Biol Evol 2018; 34:2808-2822. [PMID: 28981698 PMCID: PMC5850472 DOI: 10.1093/molbev/msx208] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence–absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence–absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories.
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Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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178
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Stukenbrock EH, Dutheil JY. Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots. Genetics 2018; 208:1209-1229. [PMID: 29263029 PMCID: PMC5844332 DOI: 10.1534/genetics.117.300502] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 12/15/2017] [Indexed: 11/18/2022] Open
Abstract
Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species.
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Affiliation(s)
- Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118, Germany
| | - Julien Y Dutheil
- Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
- Institut des Sciences de L'Évolution de Montpellier, Centre National de la Recherche Scientifique, Université Montpellier 2, 34095, France
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179
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Feau N, Beauseigle S, Bergeron MJ, Bilodeau GJ, Birol I, Cervantes-Arango S, Dhillon B, Dale AL, Herath P, Jones SJ, Lamarche J, Ojeda DI, Sakalidis ML, Taylor G, Tsui CK, Uzunovic A, Yueh H, Tanguay P, Hamelin RC. Genome-Enhanced Detection and Identification (GEDI) of plant pathogens. PeerJ 2018; 6:e4392. [PMID: 29492338 PMCID: PMC5825881 DOI: 10.7717/peerj.4392] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Plant diseases caused by fungi and Oomycetes represent worldwide threats to crops and forest ecosystems. Effective prevention and appropriate management of emerging diseases rely on rapid detection and identification of the causal pathogens. The increase in genomic resources makes it possible to generate novel genome-enhanced DNA detection assays that can exploit whole genomes to discover candidate genes for pathogen detection. A pipeline was developed to identify genome regions that discriminate taxa or groups of taxa and can be converted into PCR assays. The modular pipeline is comprised of four components: (1) selection and genome sequencing of phylogenetically related taxa, (2) identification of clusters of orthologous genes, (3) elimination of false positives by filtering, and (4) assay design. This pipeline was applied to some of the most important plant pathogens across three broad taxonomic groups: Phytophthoras (Stramenopiles, Oomycota), Dothideomycetes (Fungi, Ascomycota) and Pucciniales (Fungi, Basidiomycota). Comparison of 73 fungal and Oomycete genomes led the discovery of 5,939 gene clusters that were unique to the targeted taxa and an additional 535 that were common at higher taxonomic levels. Approximately 28% of the 299 tested were converted into qPCR assays that met our set of specificity criteria. This work demonstrates that a genome-wide approach can efficiently identify multiple taxon-specific genome regions that can be converted into highly specific PCR assays. The possibility to easily obtain multiple alternative regions to design highly specific qPCR assays should be of great help in tackling challenging cases for which higher taxon-resolution is needed.
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Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | | | | | | | - Inanc Birol
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Sandra Cervantes-Arango
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Braham Dhillon
- Department of Plant Pathology, University of Arkansas at Fayetteville, Fayetteville, AR, United States of America
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- FPInnovations, Vancouver, BC, Canada
| | - Padmini Herath
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Steven J.M. Jones
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Josyanne Lamarche
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Dario I. Ojeda
- Department of Biology Unit of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Monique L. Sakalidis
- Department of Plant, Soil & Microbial Sciences and Department of Forestry, Michigan State University, East Lansing, MI, United States of America
| | - Greg Taylor
- BC Cancer agency, Genome Sciences Centre, Vancouver, BC, Canada
| | - Clement K.M. Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Hesther Yueh
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
| | - Philippe Tanguay
- Canadian Forest Service, Natural Resources Canada, Quebec city, Quebec, Canada
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, Forest Sciences Centre, University of British Columbia, Vancouver, BC, Canada
- Foresterie et géomatique, Institut de Biologie Intégrative des Systèmes, Laval University, Quebec city, Quebec, Canada
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180
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Schwessinger B, Sperschneider J, Cuddy WS, Garnica DP, Miller ME, Taylor JM, Dodds PN, Figueroa M, Park RF, Rathjen JP. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. mBio 2018; 9:e02275-17. [PMID: 29463659 PMCID: PMC5821087 DOI: 10.1128/mbio.02275-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies.IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
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Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - William S Cuddy
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Diana P Garnica
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
| | - John P Rathjen
- Research School of Biology, the Australian National University, Acton, ACT, Australia
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181
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Kema GHJ, Mirzadi Gohari A, Aouini L, Gibriel HAY, Ware SB, van den Bosch F, Manning-Smith R, Alonso-Chavez V, Helps J, Ben M'Barek S, Mehrabi R, Diaz-Trujillo C, Zamani E, Schouten HJ, van der Lee TAJ, Waalwijk C, de Waard MA, de Wit PJGM, Verstappen ECP, Thomma BPHJ, Meijer HJG, Seidl MF. Stress and sexual reproduction affect the dynamics of the wheat pathogen effector AvrStb6 and strobilurin resistance. Nat Genet 2018; 50:375-380. [PMID: 29434356 DOI: 10.1038/s41588-018-0052-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 01/06/2018] [Indexed: 11/09/2022]
Abstract
Host resistance and fungicide treatments are cornerstones of plant-disease control. Here, we show that these treatments allow sex and modulate parenthood in the fungal wheat pathogen Zymoseptoria tritici. We demonstrate that the Z. tritici-wheat interaction complies with the gene-for-gene model by identifying the effector AvrStb6, which is recognized by the wheat resistance protein Stb6. Recognition triggers host resistance, thus implying removal of avirulent strains from pathogen populations. However, Z. tritici crosses on wheat show that sex occurs even with an avirulent parent, and avirulence alleles are thereby retained in subsequent populations. Crossing fungicide-sensitive and fungicide-resistant isolates under fungicide pressure results in a rapid increase in resistance-allele frequency. Isolates under selection always act as male donors, and thus disease control modulates parenthood. Modeling these observations for agricultural and natural environments reveals extended durability of host resistance and rapid emergence of fungicide resistance. Therefore, fungal sex has major implications for disease control.
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Affiliation(s)
- Gerrit H J Kema
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands. .,Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands.
| | - Amir Mirzadi Gohari
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands.,Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Lamia Aouini
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Hesham A Y Gibriel
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Sarah B Ware
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands.,Department of Biological Sciences, Benedictine University, Lisle, IL, USA
| | | | | | | | | | - Sarrah Ben M'Barek
- Laboratory of Molecular Plant Physiology, Biotechnology Center of Borj Cedria (CBBC), Hammam-Lif, Tunisia
| | - Rahim Mehrabi
- Department of Agricultural Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Caucasella Diaz-Trujillo
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands.,Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Elham Zamani
- Department of Plant Pathology, Tarbiat Modares University, Tehran, Iran
| | - Henk J Schouten
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Theo A J van der Lee
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Cees Waalwijk
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Maarten A de Waard
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Els C P Verstappen
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - Harold J G Meijer
- Wageningen Plant Research, Wageningen University and Research, Wageningen, the Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
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182
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Luo X, Cao J, Huang J, Wang Z, Guo Z, Chen Y, Ma S, Liu J. Genome sequencing and comparative genomics reveal the potential pathogenic mechanism of Cercospora sojina Hara on soybean. DNA Res 2018; 25:25-37. [PMID: 28985305 PMCID: PMC5824798 DOI: 10.1093/dnares/dsx035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/16/2017] [Indexed: 01/10/2023] Open
Abstract
Frogeye leaf spot, caused by Cercospora sojina Hara, is a common disease of soybean in most soybean-growing countries of the world. In this study, we report a high-quality genome sequence of C. sojina by Single Molecule Real-Time sequencing method. The 40.8-Mb genome encodes 11,655 predicated genes, and 8,474 genes are revealed by RNA sequencing. Cercospora sojina genome contains large numbers of gene clusters that are involved in synthesis of secondary metabolites, including mycotoxins and pigments. However, much less carbohydrate-binding module protein encoding genes are identified in C. sojina genome, when compared with other phytopathogenic fungi. Bioinformatics analysis reveals that C. sojina harbours about 752 secreted proteins, and 233 of them are effectors. During early infection, the genes for metabolite biosynthesis and effectors are significantly enriched, suggesting that they may play essential roles in pathogenicity. We further identify 13 effectors that can inhibit BAX-induced cell death. Taken together, our results provide insights into the infection mechanisms of C. sojina on soybean.
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Affiliation(s)
- Xuming Luo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jidong Cao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junkai Huang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zongyi Wang
- Beijing Key Laboratory of Agricultural Product Detection and Control for Spoilage Organisms and Pesticides, Beijing University of Agriculture, Beijing 102206, China
| | - Zhengyan Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shumei Ma
- Department of Plant Protection, College of Agriculture Resources and Environment, Heilongjiang University, Harbin 150080, China
| | - Jun Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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183
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Krishnan P, Ma X, McDonald BA, Brunner PC. Widespread signatures of selection for secreted peptidases in a fungal plant pathogen. BMC Evol Biol 2018; 18:7. [PMID: 29368587 PMCID: PMC5784588 DOI: 10.1186/s12862-018-1123-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fungal plant pathogens secrete a large arsenal of hydrolytic enzymes during the course of infection, including peptidases. Secreted peptidases have been extensively studied for their role as effectors. In this study, we combined transcriptomics, comparative genomics and evolutionary analyses to investigate all 39 secreted peptidases in the fungal wheat pathogen Zymoseptoria tritici and its close relatives Z. pseudotritici and Z. ardabiliae. RESULTS RNA-seq data revealed that a majority of the secreted peptidases displayed differential transcription during the course of Z. tritici infection, indicative of specialization for different stages in the life cycle. Evolutionary analyses detected widespread evidence of adaptive evolution acting on at least 28 of the peptidases. A few peptidases displayed lineage-specific rates of molecular evolution, suggesting altered selection pressure in Z. tritici following host specialization on domesticated wheat. The peptidases belonging to MEROPS families A1 and G1 emerged as a particularly interesting group that may play key roles in host-pathogen co-evolution, host adaptation and pathogenicity. Sister genes in the A1 and G1 families showed accelerated substitution rates after gene duplications. CONCLUSIONS These results suggest widespread evolution of secreted peptidases leading to novel gene functions, consistent with predicted models of "escape from adaptive conflict" and "neo-functionalization". Our analyses identified candidate genes worthy of functional analyses that may encode effector functions, for example by suppressing plant defenses during the biotrophic phase of infection.
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Affiliation(s)
- Parvathy Krishnan
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Xin Ma
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland
| | - Patrick C Brunner
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, -8092, Zurich, CH, Switzerland.
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184
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Plissonneau C, Hartmann FE, Croll D. Pangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome. BMC Biol 2018; 16:5. [PMID: 29325559 PMCID: PMC5765654 DOI: 10.1186/s12915-017-0457-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/16/2017] [Indexed: 01/01/2023] Open
Abstract
Background Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence. Results We constructed and analyzed the pangenome of Zymoseptoria tritici, a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes. Conclusions The pangenome construction of a highly polymorphic eukaryotic pathogen showed that a single reference genome significantly underestimates the gene space of a species. The substantial accessory genome provides a cradle for adaptive evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0457-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.,UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Avenue Lucien Bretignières, BP 01, Thiverval-Grignon, F-78850, France
| | - Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400, Orsay, France
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
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185
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Chen J, Liu C, Gui Y, Si K, Zhang D, Wang J, Short DPG, Huang J, Li N, Liang Y, Zhang W, Yang L, Ma X, Li T, Zhou L, Wang B, Bao Y, Subbarao KV, Zhang G, Dai X. Comparative genomics reveals cotton-specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium. THE NEW PHYTOLOGIST 2018; 217:756-770. [PMID: 29084346 PMCID: PMC5765495 DOI: 10.1111/nph.14861] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/21/2017] [Indexed: 05/20/2023]
Abstract
Verticillium dahliae isolates are most virulent on the host from which they were originally isolated. Mechanisms underlying these dominant host adaptations are currently unknown. We sequenced the genome of V. dahliae Vd991, which is highly virulent on its original host, cotton, and performed comparisons with the reference genomes of JR2 (from tomato) and VdLs.17 (from lettuce). Pathogenicity-related factor prediction, orthology and multigene family classification, transcriptome analyses, phylogenetic analyses, and pathogenicity experiments were performed. The Vd991 genome harbored several exclusive, lineage-specific (LS) genes within LS regions (LSRs). Deletion mutants of the seven genes within one LSR (G-LSR2) in Vd991 were less virulent only on cotton. Integration of G-LSR2 genes individually into JR2 and VdLs.17 resulted in significantly enhanced virulence on cotton but did not affect virulence on tomato or lettuce. Transcription levels of the seven LS genes in Vd991 were higher during the early stages of cotton infection, as compared with other hosts. Phylogenetic analyses suggested that G-LSR2 was acquired from Fusarium oxysporum f. sp. vasinfectum through horizontal gene transfer. Our results provide evidence that horizontal gene transfer from Fusarium to Vd991 contributed significantly to its adaptation to cotton and may represent a significant mechanism in the evolution of an asexual plant pathogen.
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Affiliation(s)
- Jie‐Yin Chen
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Chun Liu
- BGI‐ShenzhenShenzhenGuangdong518083China
| | - Yue‐Jing Gui
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Kai‐Wei Si
- BGI‐ShenzhenShenzhenGuangdong518083China
| | - Dan‐Dan Zhang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Jie Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Dylan P. G. Short
- Department of Plant PathologyUniversity of CaliforniaDavisCA95616USA
| | | | - Nan‐Yang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Yong Liang
- BGI‐ShenzhenShenzhenGuangdong518083China
| | - Wen‐Qi Zhang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Lin Yang
- BGI‐ShenzhenShenzhenGuangdong518083China
| | - Xue‐Feng Ma
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Ting‐Gang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Lei Zhou
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Bao‐Li Wang
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Yu‐Ming Bao
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | | | | | - Xiao‐Feng Dai
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
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186
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Gardiner DM, Benfield AH, Stiller J, Stephen S, Aitken K, Liu C, Kazan K. A high-resolution genetic map of the cereal crown rot pathogen Fusarium pseudograminearum provides a near-complete genome assembly. MOLECULAR PLANT PATHOLOGY 2018; 19:217-226. [PMID: 27888554 PMCID: PMC6638115 DOI: 10.1111/mpp.12519] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/21/2016] [Accepted: 11/22/2016] [Indexed: 05/18/2023]
Abstract
Fusarium pseudograminearum is an important pathogen of wheat and barley, particularly in semi-arid environments. Previous genome assemblies for this organism were based entirely on short read data and are highly fragmented. In this work, a genetic map of F. pseudograminearum has been constructed for the first time based on a mapping population of 178 individuals. The genetic map, together with long read scaffolding of a short read-based genome assembly, was used to give a near-complete assembly of the four F. pseudograminearum chromosomes. Large regions of synteny between F. pseudograminearum and F. graminearum, the related pathogen that is the primary causal agent of cereal head blight disease, were previously proposed in the core conserved genome, but the construction of a genetic map to order and orient contigs is critical to the validation of synteny and the placing of species-specific regions. Indeed, our comparative analyses of the genomes of these two related pathogens suggest that rearrangements in the F. pseudograminearum genome have occurred in the chromosome ends. One of these rearrangements includes the transposition of an entire gene cluster involved in the detoxification of the benzoxazolinone (BOA) class of plant phytoalexins. This work provides an important genomic and genetic resource for F. pseudograminearum, which is less well characterized than F. graminearum. In addition, this study provides new insights into a better understanding of the sexual reproduction process in F. pseudograminearum, which informs us of the potential of this pathogen to evolve.
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Affiliation(s)
- Donald M. Gardiner
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Aurelie H. Benfield
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Jiri Stiller
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Stuart Stephen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Karen Aitken
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Chunji Liu
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
| | - Kemal Kazan
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, 306 Carmody Road, St LuciaBrisbaneQldAustralia
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187
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Stewart EL, Croll D, Lendenmann MH, Sanchez‐Vallet A, Hartmann FE, Palma‐Guerrero J, Ma X, McDonald BA. Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici. MOLECULAR PLANT PATHOLOGY 2018; 19:201-216. [PMID: 27868326 PMCID: PMC6638037 DOI: 10.1111/mpp.12515] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.
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Affiliation(s)
- Ethan l. Stewart
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2Zürich8092Switzerland
| | - Daniel Croll
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2Zürich8092Switzerland
| | - Mark H. Lendenmann
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2Zürich8092Switzerland
| | | | - Fanny E. Hartmann
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2Zürich8092Switzerland
| | | | - Xin Ma
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2Zürich8092Switzerland
| | - Bruce A. McDonald
- Plant Pathology Group, ETH Zürich, Universitätstrasse 2Zürich8092Switzerland
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Thynne E, McDonald MC, Solomon PS. Transition from heterothallism to homothallism is hypothesised to have facilitated speciation among emerging Botryosphaeriaceae wheat-pathogens. Fungal Genet Biol 2017; 109:36-45. [DOI: 10.1016/j.fgb.2017.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 10/14/2017] [Accepted: 10/16/2017] [Indexed: 02/05/2023]
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189
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Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K. Cut-and-Paste Transposons in Fungi with Diverse Lifestyles. Genome Biol Evol 2017; 9:3463-3477. [PMID: 29228286 PMCID: PMC5751038 DOI: 10.1093/gbe/evx261] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 02/06/2023] Open
Abstract
Transposable elements (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighborhoods, and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a "cut-and-paste" fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches. DNA TEs have been identified across the whole data set and display uneven distribution from both DNA TE classification and fungal taxonomy perspectives. DNA TE content correlates with genome size, which confirms that many transposon families proliferate simultaneously. In contrast, it is independent from intron density, average gene distance and GC content. TE count is associated with species' lifestyle and tends to be elevated in plant symbionts and decreased in animal parasites. Lastly, we found that fungi with both RIP and RNAi systems have more total DNA TE sequences but less elements retaining a functional transposase, what reflects stringent control over transposition.
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Affiliation(s)
- Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Steczkiewicz
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Poland
| | | | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, CeNT, University of Warsaw, Poland
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190
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Forward Genetics Approach Reveals Host Genotype-Dependent Importance of Accessory Chromosomes in the Fungal Wheat Pathogen Zymoseptoria tritici. mBio 2017; 8:mBio.01919-17. [PMID: 29184021 PMCID: PMC5705923 DOI: 10.1128/mbio.01919-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The fungal wheat pathogen Zymoseptoria tritici possesses a large complement of accessory chromosomes showing presence/absence polymorphism among isolates. These chromosomes encode hundreds of genes; however, their functional role and why the chromosomes have been maintained over long evolutionary times are so far not known. In this study, we addressed the functional relevance of eight accessory chromosomes in reference isolate IPO323. We induced chromosome losses by inhibiting the β-tubulin assembly during mitosis using carbendazim and generated several independent isogenic strains, each lacking one of the accessory chromosomes. We confirmed chromosome losses by electrophoretic karyotyping and whole-genome sequencing. To assess the importance of the individual chromosomes during host infection, we performed in planta assays comparing disease development results in wild-type and chromosome mutant strains. Loss of the accessory chromosomes 14, 16, 18, 19, and 21 resulted in increased virulence on wheat cultivar Runal but not on cultivars Obelisk, Titlis, and Riband. Moreover, some accessory chromosomes affected the switch from biotrophy to necrotrophy as strains lacking accessory chromosomes 14, 18, 19, and 21 showed a significantly earlier onset of necrosis than the wild type on the Runal cultivar. In general, we observed that the timing of the lifestyle switch affects the fitness of Z. tritici. Taking the results together, this study was the first to use a forward-genetics approach to demonstrate a cultivar-dependent functional relevance of the accessory chromosomes of Z. tritici during host infection. Zymoseptoria tritici is a prominent fungal pathogen of wheat of worldwide distribution. This fungus shows a remarkable genome organization, with a large number of chromosomes that are present in only some isolates and therefore considered to be “accessory” chromosomes. To date, the function of these accessory chromosomes in Z. tritici has been unknown, although their maintenance in the species over evolutionary times suggests a functional relevance. Here we deleted whole accessory chromosomes to test the effect of these chromosomes on host specificity and virulence of the fungus. We show for the first time that some accessory chromosomes of Z. tritici affect the fitness of the fungus during host infection in a cultivar-dependent manner. These results show that the accessory chromosomes encode host-specific virulence determinants having a negative effect on fitness. Understanding the population dynamic of the accessory chromosomes and the molecular interaction of pathogen and plant traits is crucial to improve wheat-breeding strategies.
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191
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Plasticity of the MFS1 Promoter Leads to Multidrug Resistance in the Wheat Pathogen Zymoseptoria tritici. mSphere 2017; 2:mSphere00393-17. [PMID: 29085913 PMCID: PMC5656749 DOI: 10.1128/msphere.00393-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 11/20/2022] Open
Abstract
The ascomycete Zymoseptoria tritici is the causal agent of Septoria leaf blotch on wheat. Disease control relies mainly on resistant wheat cultivars and on fungicide applications. The fungus displays a high potential to circumvent both methods. Resistance against all unisite fungicides has been observed over decades. A different type of resistance has emerged among wild populations with multidrug-resistant (MDR) strains. Active fungicide efflux through overexpression of the major facilitator gene MFS1 explains this emerging resistance mechanism. Applying a bulk-progeny sequencing approach, we identified in this study a 519-bp long terminal repeat (LTR) insert in the MFS1 promoter, a relic of a retrotransposon cosegregating with the MDR phenotype. Through gene replacement, we show the insert as a mutation responsible for MFS1 overexpression and the MDR phenotype. Besides this type I insert, we found two different types of promoter inserts in more recent MDR strains. Type I and type II inserts harbor potential transcription factor binding sites, but not the type III insert. Interestingly, all three inserts correspond to repeated elements present at different genomic locations in either IPO323 or other Z. tritici strains. These results underline the plasticity of repeated elements leading to fungicide resistance in Z. tritici and which contribute to its adaptive potential. IMPORTANCE Disease control through fungicides remains an important means to protect crops from fungal diseases and to secure the harvest. Plant-pathogenic fungi, especially Zymoseptoria tritici, have developed resistance against most currently used active ingredients, reducing or abolishing their efficacy. While target site modification is the most common resistance mechanism against single modes of action, active efflux of multiple drugs is an emerging phenomenon in fungal populations reducing additionally fungicides' efficacy in multidrug-resistant strains. We have investigated the mutations responsible for increased drug efflux in Z. tritici field strains. Our study reveals that three different insertions of repeated elements in the same promoter lead to multidrug resistance in Z. tritici. The target gene encodes the membrane transporter MFS1 responsible for drug efflux, with the promoter inserts inducing its overexpression. These results underline the plasticity of repeated elements leading to fungicide resistance in Z. tritici.
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192
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Mohammadi N, Mehrabi R, Mirzadi Gohari A, Mohammadi Goltapeh E, Safaie N, Kema GHJ. The ZtVf1 transcription factor regulates development and virulence in the foliar wheat pathogen Zymoseptoria tritici. Fungal Genet Biol 2017; 109:26-35. [PMID: 29031630 DOI: 10.1016/j.fgb.2017.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/03/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022]
Abstract
The dimorphic fungal pathogen, Zymoseptoria tritici undergoes discrete developmental changes to complete its life cycle on wheat. Molecular mechanisms underlying morphogenesis during infection process of Z. tritici are poorly understood. In this study, we have investigated the role of ZtVf1 gene encoding a transcription factor belonging to C2-H2 subfamily. In planta assays revealed that ZtVf1 is required for virulence. Reduced necrotic lesions and low pycnidia density within the lesions resulted in significantly reduced virulence of ZtVf1 mutants. Cytological analysis showed that the impaired virulence of ZtVf1 mutants attributed to reduced penetration and colonization along with hampered pycnidia differentiation. In vitro phenotyping showed that ZtVf1 deletion affects hyphal branching and biomass production suggesting that the reduced tissue colonization by the ZtVf1 mutant might be due to lower hyphal branching and less fungal biomass production. In addition, the majority of infected substomatal cavities by the ZtVf1 mutant filled with compacted mycelia mat that did not differentiate to mature pycnidia indicating that the impaired melanization negatively affected pycnidia formation and maturation. The ZtVf1 might target multiple genes belonging to different cellular processes whose identification is of eminent interest to increase our understanding of this pathosystem. Overall, the data provided in this study indicates that attenuated pathogenicity of ZtVf1 mutant is due to involvement of this gene in the regulation of both early and late stages of infection.
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Affiliation(s)
- Naser Mohammadi
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran; Dryland Agricultural Research Institute, Agricultural Research, Education & Extension Organization (ARREO), Maragheh, Iran
| | - Rahim Mehrabi
- Seed & Plant Improvement Institute, Agricultural Research, Education & Extension Organization (ARREO), P.O. Box 31585-4119, Karaj, Iran; Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | - Amir Mirzadi Gohari
- Department of Plant Pathology, Faculty of Agricultural Sciences and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Ebrahim Mohammadi Goltapeh
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran
| | - Naser Safaie
- Department of Plant Pathology, Faculty of Agriculture, Tarbiat Modares University, P.O. Box 14115-111, Tehran, Iran
| | - Gert H J Kema
- Laboratory of Phytopathology, Wageningen University and Research, 6700AA Wageningen, The Netherlands; Wageningen University and Research, Wageningen Plant Research, P.O. Box 16, 6700AA Wageningen, The Netherlands
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King R, Urban M, Lauder RP, Hawkins N, Evans M, Plummer A, Halsey K, Lovegrove A, Hammond-Kosack K, Rudd JJ. A conserved fungal glycosyltransferase facilitates pathogenesis of plants by enabling hyphal growth on solid surfaces. PLoS Pathog 2017; 13:e1006672. [PMID: 29020037 PMCID: PMC5653360 DOI: 10.1371/journal.ppat.1006672] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/23/2017] [Accepted: 09/27/2017] [Indexed: 11/18/2022] Open
Abstract
Pathogenic fungi must extend filamentous hyphae across solid surfaces to cause diseases of plants. However, the full inventory of genes which support this is incomplete and many may be currently concealed due to their essentiality for the hyphal growth form. During a random T-DNA mutagenesis screen performed on the pleomorphic wheat (Triticum aestivum) pathogen Zymoseptoria tritici, we acquired a mutant unable to extend hyphae specifically when on solid surfaces. In contrast "yeast-like" growth, and all other growth forms, were unaffected. The inability to extend surface hyphae resulted in a complete loss of virulence on plants. The affected gene encoded a predicted type 2 glycosyltransferase (ZtGT2). Analysis of >800 genomes from taxonomically diverse fungi highlighted a generally widespread, but discontinuous, distribution of ZtGT2 orthologues, and a complete absence of any similar proteins in non-filamentous ascomycete yeasts. Deletion mutants of the ZtGT2 orthologue in the taxonomically un-related fungus Fusarium graminearum were also severely impaired in hyphal growth and non-pathogenic on wheat ears. ZtGT2 expression increased during filamentous growth and electron microscopy on deletion mutants (ΔZtGT2) suggested the protein functions to maintain the outermost surface of the fungal cell wall. Despite this, adhesion to leaf surfaces was unaffected in ΔZtGT2 mutants and global RNAseq-based gene expression profiling highlighted that surface-sensing and protein secretion was also largely unaffected. However, ΔZtGT2 mutants constitutively overexpressed several transmembrane and secreted proteins, including an important LysM-domain chitin-binding virulence effector, Zt3LysM. ZtGT2 likely functions in the synthesis of a currently unknown, potentially minor but widespread, extracellular or outer cell wall polysaccharide which plays a key role in facilitating many interactions between plants and fungi by enabling hyphal growth on solid matrices.
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Affiliation(s)
- Robert King
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Martin Urban
- Wheat Pathogenomics Team, Department of BioInteractions and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Rebecca P. Lauder
- Rothamsted Centre for Bioimaging, Department of Plant Sciences, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Nichola Hawkins
- Fungicide resistance group, Department of BioInteractions and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Matthew Evans
- Cereal cell walls group, Department of Plant Sciences, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Amy Plummer
- Cereal cell walls group, Department of Plant Sciences, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Kirstie Halsey
- Rothamsted Centre for Bioimaging, Department of Plant Sciences, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Alison Lovegrove
- Cereal cell walls group, Department of Plant Sciences, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Kim Hammond-Kosack
- Wheat Pathogenomics Team, Department of BioInteractions and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
| | - Jason J. Rudd
- Wheat Pathogenomics Team, Department of BioInteractions and Crop Protection, Rothamsted Research, Harpenden, Herts, United Kingdom
- * E-mail:
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194
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Rodhouse L, Carbonero F. Overview of craft brewing specificities and potentially associated microbiota. Crit Rev Food Sci Nutr 2017; 59:462-473. [PMID: 28910550 DOI: 10.1080/10408398.2017.1378616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The brewing process differs slightly in craft breweries as compared to industrial breweries, as there are fewer control points. This affects the microbiota of the final product. Beer contains several antimicrobial properties that protect it from pathogens, such as low pH, low oxygen and high carbon dioxide content, and the addition of hops. However, these hurdles have limited power controlling spoilage organisms. Contamination by these organisms can originate in the raw materials, persist in the environment, and be introduced by using flavoring ingredients later in the process. Spoilage is a prominent issue in brewing, and can cause quality degradation resulting in consumer rejection and product waste. For example, lactic acid bacteria are predominately associated with producing a ropy texture and haze, along with producing diacetyl which gives the beer butter flavor notes. Other microorganisms may not affect flavor or aroma, but can retard fermentation by consuming nutrients needed by fermentation yeast. Quality control in craft breweries today relies on culturing methods to detect specific spoilage organisms. Using media can be beneficial for detecting the most common beer spoilers, such as Lactobacillus and Pediococci. However, these methods are time consuming with long incubation periods. Molecular methods such as community profiling or high throughput sequencing are better used for identifying entire populations of beer. These methods allow for detection, differentiation, and identification of taxa.
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Affiliation(s)
- Lindsey Rodhouse
- a Department of Food Science , University of Arkansas , Fayetteville , AR , USA
| | - Franck Carbonero
- a Department of Food Science , University of Arkansas , Fayetteville , AR , USA
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195
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Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles. Microorganisms 2017; 5:microorganisms5030060. [PMID: 28926970 PMCID: PMC5620651 DOI: 10.3390/microorganisms5030060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/08/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H2O2 and menadione/FeCl3 exposure, respectively. Several proteins were detected with altered abundance in response to H2O2, but not menadione/FeCl3 (i.e., valosin-containing protein), indicating distinct responses to these different forms of oxidative stress. One protein, cobalamin-independent methionine synthase, demonstrated a common response in both conditions, which may be a marker for a more general stress response mechanism. Further changes to the A. mellea proteome were investigated using MS-based proteomics, which identified changes to putative secondary metabolism (SM) enzymes upon growth in agar compared to liquid cultures. Metabolomic analyses revealed distinct profiles, highlighting the effect of growth matrix on SM production. This establishes robust methods by which to utilize comparative proteomics to characterize this important phytopathogen.
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196
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Wang B, Liang X, Gleason ML, Zhang R, Sun G. Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche. BMC Genomics 2017; 18:729. [PMID: 28915794 PMCID: PMC5602860 DOI: 10.1186/s12864-017-4118-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/05/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Ectophytic fungi occupy the waxy plant surface, an extreme environment characterized by prolonged desiccation, nutrient limitation, and exposure to solar radiation. The nature of mechanisms that facilitate adaptation to this environment remains unclear. In this study, we sequenced the complete genome of an ectophytic fungus, Ramichloridium luteum, which colonizes the surface of apple fruit, and carried out comparative genomic and transcriptome analysis. RESULTS The R. luteum genome was 28.18 Mb and encoded 9466 genes containing 1.85% repetitive elements. Compared with cell-penetrating pathogens, genes encoding plant cell wall degrading enzymes (PCWDEs), PTH11-like G protein-coupled receptors (GPCRs) and effectors were drastically reduced. In contrast, genes encoding cutinases and secretory lipases were strikingly expanded, and four of nine secretory lipases were probably acquired by horizontal gene transfer from Basidiomycota. Transcriptomic analysis revealed elevated expression of genes involved in cuticle degradation (cutinase, secretory lipase) and stress responses (melanin biosynthesis, aquaporins, lysozymes and HOG pathway). CONCLUSIONS Taken together, our results highlight genomic features associated with evolution of surface niche adaptation by the ectophytic fungus R. luteum, namely the contraction of PCWDEs, PTH11-like GPCRs and effectors, and the expansion of cuticle degradation and stress tolerance.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Mark L. Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011 USA
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province 712100 China
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197
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Affiliation(s)
- R. Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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198
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Gutiérrez-Alonso O, Hawkins NJ, Cools HJ, Shaw MW, Fraaije BA. Dose-dependent selection drives lineage replacement during the experimental evolution of SDHI fungicide resistance in Zymoseptoria tritici. Evol Appl 2017; 10:1055-1066. [PMID: 29151860 PMCID: PMC5680630 DOI: 10.1111/eva.12511] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/16/2017] [Indexed: 01/22/2023] Open
Abstract
Fungicide resistance is a constant threat to agricultural production worldwide. Molecular mechanisms of fungicide resistance have been studied extensively in the wheat pathogen Zymoseptoria tritici. However, less is known about the evolutionary processes driving resistance development. In vitro evolutionary studies give the opportunity to investigate this. Here, we examine the adaptation of Z. tritici to fluxapyroxad, a succinate dehydrogenase (Sdh) inhibitor. Replicate populations of Z. tritici derived from the sensitive isolate IPO323 were exposed to increasing concentrations of fluxapyroxad with or without UV mutagenesis. After ten increases in fungicide concentration, sensitivity had decreased dramatically, with replicate populations showing similar phenotypic trajectories. Sequencing the Sdh subunit B, C, and D encoding genes identified seven mutations associated with resistance to fluxapyroxad. Mutation frequency over time was measured with a pyrosequencing assay, revealing sequential lineage replacement in the UV‐mutagenized populations but not in the untreated populations. Repeating selection from set time‐points with different fungicide concentrations revealed that haplotype replacement of Sdh variants was driven by dose‐dependent selection as fungicide concentration changed, and was not mutation‐limited. These findings suggest that fungicide field applications may select for highly insensitive Sdh variants with higher resistance factors if the fungicide concentration is increased to achieve a better disease control. However, in the absence or presence of lower fungicide concentrations, the spread of these strains might be restricted if the underlying Sdh mutations carry fitness penalties.
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Affiliation(s)
- Omar Gutiérrez-Alonso
- Biointeractions and Crop Protection Department Rothamsted Research Harpenden Hertfordshir UK
| | - Nichola J Hawkins
- Biointeractions and Crop Protection Department Rothamsted Research Harpenden Hertfordshir UK
| | - Hans J Cools
- Jealott's Hill International Research Centre Syngenta Bracknell Berkshire UK
| | - Michael W Shaw
- School of Agriculture Policy and Development University of Reading Reading Berkshire UK
| | - Bart A Fraaije
- Biointeractions and Crop Protection Department Rothamsted Research Harpenden Hertfordshir UK
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199
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Fones HN, Eyles CJ, Kay W, Cowper J, Gurr SJ. A role for random, humidity-dependent epiphytic growth prior to invasion of wheat by Zymoseptoria tritici. Fungal Genet Biol 2017; 106:51-60. [PMID: 28694096 PMCID: PMC5556705 DOI: 10.1016/j.fgb.2017.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 12/02/2022]
Abstract
Zymoseptoria tritici causes Septoria leaf blotch of wheat. The prevailing paradigm of the Z. tritici-wheat interaction assumes fungal ingress through stomata within 24-48h, followed by days of symptomless infection. This is extrapolated from studies testing the mode of fungal ingress under optimal infection conditions. Here, we explicitly assess the timing of entry, using GFP-tagged Z. tritici. We show that early entry is comparatively rare, and extended epiphytic growth possible. We test the hypotheses that our data diverge from earlier studies due to: i. random ingress of Z. tritici into the leaf, with some early entry events; ii. previous reliance upon fungal stains, combined with poor attachment of Z. tritici to the leaf, leading to increased likelihood of observing internal versus external growth, compared to using GFP; iii. use of exceptionally high humidity to promote entry in previous studies. We combine computer simulation of leaf-surface growth with thousands of in planta observations to demonstrate that while spores germinate rapidly on the leaf, over 95% of fungi remain epiphytic, growing randomly over the leaf for ten days or more. We show that epiphytic fungi are easily detached from leaves by rinsing and that humidity promotes epiphytic growth, increasing infection rates. Together, these results explain why epiphytic growth has been dismissed and early ingress assumed. The prolonged epiphytic phase should inform studies of pathogenicity and virulence mutants, disease control strategies, and interpretation of the observed low in planta growth, metabolic quiescence and evasion of plant defences by Zymoseptoria during symptomless infection.
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Affiliation(s)
- Helen N Fones
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Chris J Eyles
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - William Kay
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Josh Cowper
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Sarah J Gurr
- Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, UK; Rothamsted Research, North Wyke, Okehampton, Devon EX20 2SB, UK; Donder's Hon Chair, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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200
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Dallery JF, Lapalu N, Zampounis A, Pigné S, Luyten I, Amselem J, Wittenberg AHJ, Zhou S, de Queiroz MV, Robin GP, Auger A, Hainaut M, Henrissat B, Kim KT, Lee YH, Lespinet O, Schwartz DC, Thon MR, O’Connell RJ. Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genomics 2017; 18:667. [PMID: 28851275 PMCID: PMC5576322 DOI: 10.1186/s12864-017-4083-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/21/2017] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. RESULTS Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. CONCLUSION The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.
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Affiliation(s)
- Jean-Félix Dallery
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Nicolas Lapalu
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Antonios Zampounis
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
- Present Address: Department of Deciduous Fruit Trees, Institute of Plant Breeding and Plant Genetic Resources, Hellenic Agricultural Organization ‘Demeter’, Naoussa, Greece
| | - Sandrine Pigné
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | | | | | | | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin USA
| | - Marisa V. de Queiroz
- Laboratório de Genética Molecular de Fungos, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Guillaume P. Robin
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Annie Auger
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Matthieu Hainaut
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France
- INRA, USC 1408 AFMB, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
| | - Olivier Lespinet
- Laboratoire de Recherche en Informatique, CNRS, Université Paris-Sud, Orsay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Orsay, France
| | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin USA
| | - Michael R. Thon
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Richard J. O’Connell
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
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