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Bernasconi Z, Stirnemann U, Heuberger M, Sotiropoulos AG, Graf J, Wicker T, Keller B, Sánchez-Martín J. Mutagenesis of Wheat Powdery Mildew Reveals a Single Gene Controlling Both NLR and Tandem Kinase-Mediated Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:264-276. [PMID: 37934013 DOI: 10.1094/mpmi-09-23-0136-fi] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Blumeria graminis f. sp. tritici (Bgt) is a globally important fungal wheat pathogen. Some wheat genotypes contain powdery mildew resistance (Pm) genes encoding immune receptors that recognize specific fungal-secreted effector proteins, defined as avirulence (Avr) factors. Identifying Avr factors is vital for understanding the mechanisms, functioning, and durability of wheat resistance. Here, we present AvrXpose, an approach to identify Avr genes in Bgt by generating gain-of-virulence mutants on Pm genes. We first identified six Bgt mutants with gain of virulence on Pm3b and Pm3c. They all had point mutations, deletions or insertions of transposable elements within the corresponding AvrPm3b2/c2 gene or its promoter region. We further selected six mutants on Pm3a, aiming to identify the yet unknown AvrPm3a3 recognized by Pm3a, in addition to the previously described AvrPm3a2/f2. Surprisingly, Pm3a virulence in the obtained mutants was always accompanied by an additional gain of virulence on the unrelated tandem kinase resistance gene WTK4. No virulence toward 11 additional R genes tested was observed, indicating that the gain of virulence was specific for Pm3a and WTK4. Several independently obtained Pm3a-WTK4 mutants have mutations in Bgt-646, a gene encoding a putative, nonsecreted ankyrin repeat-containing protein. Gene expression analysis suggests that Bgt-646 regulates a subset of effector genes. We conclude that Bgt-646 is a common factor required for avirulence on both a specific nucleotide-binding leucine-rich repeat and a WTK immune receptor. Our findings suggest that, beyond effectors, another type of pathogen protein can control the race-specific interaction between powdery mildew and wheat. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zoe Bernasconi
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Ursin Stirnemann
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Matthias Heuberger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alexandros G Sotiropoulos
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Centre for Crop Health, University of Southern Queensland, Darling Heights, Queensland, Australia
| | - Johannes Graf
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Department of Microbiology and Genetics, Spanish-Portuguese Agricultural Research Centre (CIALE), University of Salamanca, Salamanca, Spain
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Camenzind M, Koller T, Armbruster C, Jung E, Brunner S, Herren G, Keller B. Breeding for durable resistance against biotrophic fungal pathogens using transgenes from wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:8. [PMID: 38263979 PMCID: PMC10803697 DOI: 10.1007/s11032-024-01451-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/11/2024] [Indexed: 01/25/2024]
Abstract
Breeding for resistant crops is a sustainable way to control disease and relies on the introduction of novel resistance genes. Here, we tested three strategies on how to use transgenes from wheat to achieve durable resistance against fungal pathogens in the field. First, we tested the highly effective, overexpressed single transgene Pm3e in the background of spring wheat cultivar Bobwhite in a long-term field trial over many years. Together with previous results, this revealed that transgenic wheat line Pm3e#2 conferred complete powdery mildew resistance during a total of nine field seasons without a negative impact on yield. Furthermore, overexpressed Pm3e provided resistance to powdery mildew isolates from our worldwide collection when crossed into the elite wheat cultivar Fiorina. Second, we pyramided the four overexpressed transgenes Pm3a, Pm3b, Pm3d, and Pm3f in the background of cultivar Bobwhite and showed that the pyramided line Pm3a,b,d,f was completely resistant to powdery mildew in five field seasons. Third, we performed field trials with three barley lines expressing adult plant resistance gene Lr34 from wheat during three field seasons. Line GLP8 expressed Lr34 under control of the pathogen-inducible Hv-Ger4c promoter and provided partial barley powdery mildew and leaf rust resistance in the field with small, negative effects on yield components which might need compensatory breeding. Overall, our study demonstrates and discusses three successful strategies for achieving fungal disease resistance of wheat and barley in the field using transgenes from wheat. These strategies might confer long-term resistance if applied in a sustainable way. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01451-2.
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Affiliation(s)
- Marcela Camenzind
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Teresa Koller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Cygni Armbruster
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | | | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
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Kunz L, Sotiropoulos AG, Graf J, Razavi M, Keller B, Müller MC. The broad use of the Pm8 resistance gene in wheat resulted in hypermutation of the AvrPm8 gene in the powdery mildew pathogen. BMC Biol 2023; 21:29. [PMID: 36755285 PMCID: PMC9909948 DOI: 10.1186/s12915-023-01513-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Worldwide wheat production is under constant threat by fast-evolving fungal pathogens. In the last decades, wheat breeding for disease resistance heavily relied on the introgression of chromosomal segments from related species as genetic sources of new resistance. The Pm8 resistance gene against the powdery mildew disease has been introgressed from rye into wheat as part of a large 1BL.1RS chromosomal translocation encompassing multiple disease resistance genes and yield components. Due to its high agronomic value, this translocation has seen continuous global use since the 1960s on large growth areas, even after Pm8 resistance was overcome by the powdery mildew pathogen. The long-term use of Pm8 at a global scale provided the unique opportunity to study the consequences of such extensive resistance gene application on pathogen evolution. RESULTS Using genome-wide association studies in a population of wheat mildew isolates, we identified the avirulence effector AvrPm8 specifically recognized by Pm8. Haplovariant mining in a global mildew population covering all major wheat growing areas of the world revealed 17 virulent haplotypes of the AvrPm8 gene that grouped into two functional categories. The first one comprised amino acid polymorphisms at a single position along the AvrPm8 protein, which we confirmed to be crucial for the recognition by Pm8. The second category consisted of numerous destructive mutations to the AvrPm8 open reading frame such as disruptions of the start codon, gene truncations, gene deletions, and interference with mRNA splicing. With the exception of a single, likely ancient, gain-of-virulence mutation found in mildew isolates around the world, all AvrPm8 virulence haplotypes were found in geographically restricted regions, indicating that they occurred recently as a consequence of the frequent Pm8 use. CONCLUSIONS In this study, we show that the broad and prolonged use of the Pm8 gene in wheat production worldwide resulted in a multitude of gain-of-virulence mechanisms affecting the AvrPm8 gene in the wheat powdery mildew pathogen. Based on our findings, we conclude that both standing genetic variation as well as locally occurring new mutations contributed to the global breakdown of the Pm8 resistance gene introgression.
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Affiliation(s)
- Lukas Kunz
- grid.7400.30000 0004 1937 0650Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Alexandros G. Sotiropoulos
- grid.7400.30000 0004 1937 0650Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Johannes Graf
- grid.7400.30000 0004 1937 0650Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Mohammad Razavi
- grid.419414.d0000 0000 9770 1268Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
| | - Marion C. Müller
- grid.7400.30000 0004 1937 0650Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland ,grid.6936.a0000000123222966Chair of Phytopathology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Schaefer LK, Parlange F, Buchmann G, Jung E, Wehrli A, Herren G, Müller MC, Stehlin J, Schmid R, Wicker T, Keller B, Bourras S. Cross-Kingdom RNAi of Pathogen Effectors Leads to Quantitative Adult Plant Resistance in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:253. [PMID: 32211008 PMCID: PMC7076181 DOI: 10.3389/fpls.2020.00253] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/18/2020] [Indexed: 05/30/2023]
Abstract
Cross-kingdom RNA interference (RNAi) is a biological process allowing plants to transfer small regulatory RNAs to invading pathogens to trigger the silencing of target virulence genes. Transient assays in cereal powdery mildews suggest that silencing of one or two effectors could lead to near loss of virulence, but evidence from stable RNAi lines is lacking. We established transient host-induced gene silencing (HIGS) in wheat, and demonstrate that targeting an essential housekeeping gene in the wheat powdery mildew pathogen (Blumeria graminis f. sp. tritici) results in significant reduction of virulence at an early stage of infection. We generated stable transgenic RNAi wheat lines encoding a HIGS construct simultaneously silencing three B.g. tritici effectors including SvrPm3 a1/f1 , a virulence factor involved in the suppression of the Pm3 powdery mildew resistance gene. We show that all targeted effectors are effectively downregulated by HIGS, resulting in reduced fungal virulence on adult wheat plants. Our findings demonstrate that stable HIGS of effector genes can lead to quantitative gain of resistance without major pleiotropic effects in wheat.
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Affiliation(s)
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriele Buchmann
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Andreas Wehrli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Jonas Stehlin
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Roman Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Bourras S, Kunz L, Xue M, Praz CR, Müller MC, Kälin C, Schläfli M, Ackermann P, Flückiger S, Parlange F, Menardo F, Schaefer LK, Ben-David R, Roffler S, Oberhaensli S, Widrig V, Lindner S, Isaksson J, Wicker T, Yu D, Keller B. The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nat Commun 2019; 10:2292. [PMID: 31123263 PMCID: PMC6533294 DOI: 10.1038/s41467-019-10274-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/03/2019] [Indexed: 12/25/2022] Open
Abstract
The wheat Pm3 resistance gene against the powdery mildew pathogen occurs as an allelic series encoding functionally different immune receptors which induce resistance upon recognition of isolate-specific avirulence (AVR) effectors from the pathogen. Here, we describe the identification of five effector proteins from the mildew pathogens of wheat, rye, and the wild grass Dactylis glomerata, specifically recognized by the PM3B, PM3C and PM3D receptors. Together with the earlier identified AVRPM3A2/F2, the recognized AVRs of PM3B/C, (AVRPM3B2/C2), and PM3D (AVRPM3D3) belong to a large group of proteins with low sequence homology but predicted structural similarities. AvrPm3b2/c2 and AvrPm3d3 are conserved in all tested isolates of wheat and rye mildew, and non-host infection assays demonstrate that Pm3b, Pm3c, and Pm3d are also restricting the growth of rye mildew on wheat. Furthermore, divergent AVR homologues from non-adapted rye and Dactylis mildews are recognized by PM3B, PM3C, or PM3D, demonstrating their involvement in host specificity.
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Affiliation(s)
- Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.
| | - Lukas Kunz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Coraline Rosalie Praz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Carol Kälin
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Michael Schläfli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Patrick Ackermann
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | | | - Roi Ben-David
- Institute of Plant Science, ARO-Volcani Center, 50250, Bet Dagan, Israel
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Victoria Widrig
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Stefan Lindner
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Jonatan Isaksson
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China.
- College of Life Science, Wuhan University, Wuhan, 430072, China.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
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Amselem J, Cornut G, Choisne N, Alaux M, Alfama-Depauw F, Jamilloux V, Maumus F, Letellier T, Luyten I, Pommier C, Adam-Blondon AF, Quesneville H. RepetDB: a unified resource for transposable element references. Mob DNA 2019; 10:6. [PMID: 30719103 PMCID: PMC6350395 DOI: 10.1186/s13100-019-0150-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/24/2019] [Indexed: 11/11/2022] Open
Abstract
Background Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation are considered essential in any genome sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements in high-throughput sequencing technologies. A fully automated de novo annotation process for TEs is therefore required to cope with the deluge of sequence data. However, all automated procedures are error-prone, and an automated procedure for TE identification and classification would be no exception. It is therefore crucial to provide not only the TE reference sequences, but also evidence justifying their classification, at the scale of the whole genome. A few TE databases already exist, but none provides evidence to justify TE classification. Moreover, biological information about the sequences remains globally poor. Results We present here the RepetDB database developed in the framework of GnpIS, a genetic and genomic information system. RepetDB is designed to store and retrieve detected, classified and annotated TEs in a standardized manner. RepetDB is an implementation with extensions of InterMine, an open-source data warehouse framework used here to store, search, browse, analyze and compare all the data recorded for each TE reference sequence. InterMine can display diverse information for each sequence and allows simple to very complex queries. Finally, TE data are displayed via a worldwide data discovery portal. RepetDB is accessible at urgi.versailles.inra.fr/repetdb. Conclusions RepetDB is designed to be a TE knowledge base populated with full de novo TE annotations of complete (or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates the exploration of specific TE families, superfamilies or orders across a large range of species. It also makes possible cross-species searches and comparisons of TE family content between genomes.
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Affiliation(s)
- Joëlle Amselem
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | | | - Michael Alaux
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | | | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | | | - Isabelle Luyten
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
| | - Cyril Pommier
- URGI, INRA, Université Paris-Saclay, 78026 Versailles, France
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Keller B, Wicker T, Krattinger SG. Advances in Wheat and Pathogen Genomics: Implications for Disease Control. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:67-87. [PMID: 30149791 DOI: 10.1146/annurev-phyto-080516-035419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The gene pool of wheat and its wild and domesticated relatives contains a plethora of resistance genes that can be exploited to make wheat more resilient to pathogens. Only a few of these genes have been isolated and studied at the molecular level. In recent years, we have seen a shift from classical breeding to genomics-assisted breeding, which makes use of the enormous advancements in DNA sequencing and high-throughput molecular marker technologies for wheat improvement. These genomic advancements have the potential to transform wheat breeding in the near future and to significantly increase the speed and precision at which new cultivars can be bred. This review highlights the genomic improvements that have been made in wheat and its pathogens over the past years and discusses their implications for disease-resistance breeding.
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Affiliation(s)
- Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
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Hu Y, Liang Y, Zhang M, Tan F, Zhong S, Li X, Gong G, Chang X, Shang J, Tang S, Li T, Luo P. Comparative transcriptome profiling of Blumeria graminis f. sp. tritici during compatible and incompatible interactions with sister wheat lines carrying and lacking Pm40. PLoS One 2018; 13:e0198891. [PMID: 29975700 PMCID: PMC6033381 DOI: 10.1371/journal.pone.0198891] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/25/2018] [Indexed: 11/18/2022] Open
Abstract
Blumeria graminis f. sp. tritici (Bgt) is an obligate biotrophic fungus that causes wheat powdery mildew, which is a devastating disease in wheat. However, little is known about the pathogenesis of this fungus, and differences in the pathogenesis of the same pathogen at various resistance levels in hosts have not been determined. In the present study, leaf tissues of both Pm40-expressing hexaploid wheat line L658 and its Pm40-deficient sister line L958 were harvested at 0 (without inoculation), 6, 12, 24, 48 and 72 hours post-inoculation (hpi) with Bgt race 15 and then subjected to RNA sequencing (RNA-seq). In addition, we also observed changes in fungal growth morphology at the aforementioned time points. There was a high correlation between percentage of reads mapped to the Bgt reference genome and biomass of the fungus within the leaf tissue during the growth process. The percentage of mapped reads of Bgt in compatible interactions was significantly higher (at the p<0.05 level) than that of reads in incompatible interactions from 24 to 72 hpi. Further functional annotations indicated that expression levels of genes encoding H+-transporting ATPase, putative secreted effector proteins (PSEPs) and heat shock proteins (HSPs) were significantly up-regulated in compatible interactions compared with these levels in incompatible interactions, particularly at 72 hpi. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that genes involved in the endocytosis pathway were also enriched in compatible interactions. Overall, genes encoding H+-transporting ATPase, PSEPs and HSPs possibly played crucial roles in successfully establishing the pathogenesis of compatible interactions during late stages of inoculation. The study results also indicated that endocytosis is likely to play a potential role in Bgt in establishing compatible interactions.
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Affiliation(s)
- Yuting Hu
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yinping Liang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min Zhang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Feiquan Tan
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengfu Zhong
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xin Li
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoshu Gong
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Chang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jing Shang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shengwen Tang
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tao Li
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peigao Luo
- Provincial Key Laboratory of Plant Breeding and Genetics, College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
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Nottensteiner M, Zechmann B, McCollum C, Hückelhoven R. A barley powdery mildew fungus non-autonomous retrotransposon encodes a peptide that supports penetration success on barley. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3745-3758. [PMID: 29757394 PMCID: PMC6022598 DOI: 10.1093/jxb/ery174] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/09/2018] [Indexed: 05/22/2023]
Abstract
Pathogens overcome plant immunity by means of secreted effectors. Host effector targets often act in pathogen defense, but might also support fungal accommodation or nutrition. The barley ROP GTPase HvRACB is involved in accommodation of fungal haustoria of the powdery mildew fungus Blumeria graminis f.sp. hordei (Bgh) in barley epidermal cells. We found that HvRACB interacts with the ROP-interactive peptide 1 (ROPIP1) that is encoded on the active non-long terminal repeat retroelement Eg-R1 of Bgh. Overexpression of ROPIP1 in barley epidermal cells and host-induced post-transcriptional gene silencing (HIGS) of ROPIP1 suggested that ROPIP1 is involved in virulence of Bgh. Bimolecular fluorescence complementation and co-localization supported that ROPIP1 can interact with activated HvRACB in planta. We show that ROPIP1 is expressed by Bgh on barley and translocated into the cytoplasm of infected barley cells. ROPIP1 is recruited to microtubules upon co-expression of MICROTUBULE ASSOCIATED ROP GTPase ACTIVATING PROTEIN (HvMAGAP1) and can destabilize cortical microtubules. The data suggest that Bgh ROPIP targets HvRACB and manipulates host cell microtubule organization for facilitated host cell entry. This points to a possible neo-functionalization of retroelement-derived transcripts for the evolution of a pathogen virulence effector.
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Affiliation(s)
- Mathias Nottensteiner
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Bernd Zechmann
- Center for Microscopy and Imaging, Baylor University, Waco, TX, USA
| | - Christopher McCollum
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Ralph Hückelhoven
- Chair of Phytopathology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Correspondence:
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McNally KE, Menardo F, Lüthi L, Praz CR, Müller MC, Kunz L, Ben‐David R, Chandrasekhar K, Dinoor A, Cowger C, Meyers E, Xue M, Zeng F, Gong S, Yu D, Bourras S, Keller B. Distinct domains of the AVRPM3 A2/F2 avirulence protein from wheat powdery mildew are involved in immune receptor recognition and putative effector function. THE NEW PHYTOLOGIST 2018; 218:681-695. [PMID: 29453934 PMCID: PMC6175116 DOI: 10.1111/nph.15026] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/05/2018] [Indexed: 05/22/2023]
Abstract
Recognition of the AVRPM3A2/F2 avirulence protein from powdery mildew by the wheat PM3A/F immune receptor induces a hypersensitive response after co-expression in Nicotiana benthamiana. The molecular determinants of this interaction and how they shape natural AvrPm3a2/f2 allelic diversity are unknown. We sequenced the AvrPm3a2/f2 gene in a worldwide collection of 272 mildew isolates. Using the natural polymorphisms of AvrPm3a2/f2 as well as sequence information from related gene family members, we tested 85 single-residue-altered AVRPM3A2/F2 variants with PM3A, PM3F and PM3FL456P/Y458H (modified for improved signaling) in Nicotiana benthamiana for effects on recognition. An intact AvrPm3a2/f2 gene was found in all analyzed isolates and the protein variant recognized by PM3A/F occurred globally at high frequencies. Single-residue alterations in AVRPM3A2/F2 mostly disrupted, but occasionally enhanced, the recognition response by PM3A, PM3F and PM3FL456P/Y458H . Residues enhancing hypersensitive responses constituted a protein domain separate from both naturally occurring polymorphisms and positively selected residues of the gene family. These results demonstrate the utility of using gene family sequence diversity to screen residues for their role in recognition. This approach identified a putative interaction surface in AVRPM3A2/F2 not polymorphic in natural alleles. We conclude that molecular mechanisms besides recognition drive AvrPm3a2/f2 diversification.
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Affiliation(s)
- Kaitlin Elyse McNally
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Linda Lüthi
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Coraline Rosalie Praz
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Lukas Kunz
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Roi Ben‐David
- Institute of Plant ScienceARO‐Volcani Center50250Bet DaganIsrael
| | - Kottakota Chandrasekhar
- Department of Plant Pathology and MicrobiologyThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Amos Dinoor
- Department of Plant Pathology and MicrobiologyThe Robert H. Smith Faculty of Agriculture, Food and EnvironmentThe Hebrew University of JerusalemRehovot76100Israel
| | - Christina Cowger
- United States Department of Agriculture‐Agricultural Research Service (USDA‐ARS)North Carolina State UniversityRaleighNC27695USA
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695USA
| | - Emily Meyers
- Department of Plant PathologyNorth Carolina State UniversityRaleighNC27695USA
| | - Mingfeng Xue
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
| | - Fangsong Zeng
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
| | - Shuangjun Gong
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
- College of Life ScienceWuhan University430072WuhanChina
| | - Dazhao Yu
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural Sciences430064WuhanChina
- Ministry of AgricultureKey Laboratory of Integrated Pest Management in Crops in Central China430064WuhanChina
- College of Life ScienceWuhan University430072WuhanChina
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZürichZollikerstrasse 1078008ZürichSwitzerland
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11
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Analysis of Transposable Elements in Coccidioides Species. J Fungi (Basel) 2018; 4:jof4010013. [PMID: 29371508 PMCID: PMC5872316 DOI: 10.3390/jof4010013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 12/24/2022] Open
Abstract
Coccidioides immitis and C. posadasii are primary pathogenic fungi that cause disease in immunologically-normal animals and people. The organism is found exclusively in arid regions of the Southwestern United States, Mexico, and South America, but not in other parts of the world. This study is a detailed analysis of the transposable elements (TE) in Coccidioides spp. As is common in most fungi, Class I and Class II transposons were identified and the LTR Gypsy superfamily is the most common. The minority of Coccidioides Gypsy transposons contained regions highly homologous to polyprotein domains. Phylogenetic analysis of the integrase and reverse transcriptase sequences revealed that many, but not all, of the Gypsy reverse transcriptase and integrase domains clustered by species suggesting extensive transposition after speciation of the two Coccidiodies spp. The TEs were clustered and the distribution is enriched for the ends on contigs. Analysis of gene expression data from C. immitis found that protein-coding genes within 1 kB of hAT or Gypsy TEs were poorly expressed. The expression of C. posadasii genes within 1 kB of Gypsy TEs was also significantly lower compared to all genes but the difference in expression was smaller than C. immitis. C. posadasii orthologs of C. immitis Gyspsy-associated genes were also likely to be TE-associated. In both C. immitis and C. posadasii the TEs were preferentially associated with genes annotated with protein kinase gene ontology terms. These observations suggest that TE may play a role in influencing gene expression in Coccidioides spp. Our hope is that these bioinformatic studies of the potential TE influence on expression and evolution of Coccidioides will prompt the development of testable hypotheses to better understand the role of TEs in the biology and gene regulation of Coccidioides spp.
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12
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Praz CR, Menardo F, Robinson MD, Müller MC, Wicker T, Bourras S, Keller B. Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen. FRONTIERS IN PLANT SCIENCE 2018; 9:49. [PMID: 29441081 PMCID: PMC5797619 DOI: 10.3389/fpls.2018.00049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/10/2018] [Indexed: 05/20/2023]
Abstract
Powdery mildew is an important disease of cereals. It is caused by one species, Blumeria graminis, which is divided into formae speciales each of which is highly specialized to one host. Recently, a new form capable of growing on triticale (B.g. triticale) has emerged through hybridization between wheat and rye mildews (B.g. tritici and B.g. secalis, respectively). In this work, we used RNA sequencing to study the molecular basis of host adaptation in B.g. triticale. We analyzed gene expression in three B.g. tritici isolates, two B.g. secalis isolates and two B.g. triticale isolates and identified a core set of putative effector genes that are highly expressed in all formae speciales. We also found that the genes differentially expressed between isolates of the same form as well as between different formae speciales were enriched in putative effectors. Their coding genes belong to several families including some which contain known members of mildew avirulence (Avr) and suppressor (Svr) genes. Based on these findings we propose that effectors play an important role in host adaptation that is mechanistically based on Avr-Resistance gene-Svr interactions. We also found that gene expression in the B.g. triticale hybrid is mostly conserved with the parent-of-origin, but some genes inherited from B.g. tritici showed a B.g. secalis-like expression. Finally, we identified 11 unambiguous cases of putative effector genes with hybrid-specific, non-parent of origin gene expression, and we propose that they are possible determinants of host specialization in triticale mildew. These data suggest that altered expression of multiple effector genes, in particular Avr and Svr related factors, might play a role in mildew host adaptation based on hybridization.
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Affiliation(s)
- Coraline R. Praz
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Mark D. Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Marion C. Müller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- *Correspondence: Salim Bourras
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- Beat Keller
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13
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Gao B, Wang S, Wang Y, Shen D, Xue S, Chen C, Cui H, Song C. Low diversity, activity, and density of transposable elements in five avian genomes. Funct Integr Genomics 2017; 17:427-439. [PMID: 28190211 PMCID: PMC5486457 DOI: 10.1007/s10142-017-0545-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 12/16/2016] [Accepted: 01/30/2017] [Indexed: 11/29/2022]
Abstract
In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds.
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Affiliation(s)
- Bo Gao
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Saisai Wang
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Yali Wang
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Dan Shen
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Songlei Xue
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Cai Chen
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Hengmi Cui
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China
| | - Chengyi Song
- Joint International Research Laboratory of Agriculture and Agri-product Safety, College of Animal Science and Technology, Yangzhou University, 48 Wenhui East Road, Yangzhou, Jiangsu, 225009, China.
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14
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Feehan JM, Scheibel KE, Bourras S, Underwood W, Keller B, Somerville SC. Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing. J Vis Exp 2017. [PMID: 28448006 DOI: 10.3791/55463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.
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Affiliation(s)
- Joanna M Feehan
- Department of Plant and Microbial Biology, University of California Berkeley; John Innes Centre, Norwich Research Park
| | | | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich
| | | | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich
| | - Shauna C Somerville
- Department of Plant and Microbial Biology, University of California Berkeley;
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15
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Praz CR, Bourras S, Zeng F, Sánchez‐Martín J, Menardo F, Xue M, Yang L, Roffler S, Böni R, Herren G, McNally KE, Ben‐David R, Parlange F, Oberhaensli S, Flückiger S, Schäfer LK, Wicker T, Yu D, Keller B. AvrPm2 encodes an RNase-like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus. THE NEW PHYTOLOGIST 2017; 213:1301-1314. [PMID: 27935041 PMCID: PMC5347869 DOI: 10.1111/nph.14372] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/02/2016] [Indexed: 05/20/2023]
Abstract
There is a large diversity of genetically defined resistance genes in bread wheat against the powdery mildew pathogen Blumeria graminis (B. g.) f. sp. tritici. Many confer race-specific resistance to this pathogen, but until now only the mildew avirulence gene AvrPm3a2/f2 that is recognized by Pm3a/f was known molecularly. We performed map-based cloning and genome-wide association studies to isolate a candidate for the mildew avirulence gene AvrPm2. We then used transient expression assays in Nicotiana benthamiana to demonstrate specific and strong recognition of AvrPm2 by Pm2. The virulent AvrPm2 allele arose from a conserved 12 kb deletion, while there is no protein sequence diversity in the gene pool of avirulent B. g. tritici isolates. We found one polymorphic AvrPm2 allele in B. g. triticale and one orthologue in B. g. secalis and both are recognized by Pm2. AvrPm2 belongs to a small gene family encoding structurally conserved RNase-like effectors, including Avra13 from B. g. hordei, the cognate Avr of the barley resistance gene Mla13. These results demonstrate the conservation of functional avirulence genes in two cereal powdery mildews specialized on different hosts, thus providing a possible explanation for successful introgression of resistance genes from rye or other grass relatives to wheat.
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Affiliation(s)
- Coraline R. Praz
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Fansong Zeng
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | | | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Lijun Yang
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Stefan Roffler
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Rainer Böni
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Gerard Herren
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Kaitlin E. McNally
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Roi Ben‐David
- Institute of Plant ScienceARO‐Volcani CenterBet Dagan50250Israel
| | - Francis Parlange
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Luisa K. Schäfer
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
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16
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Braga RM, Santana MF, Costa RVD, Brommonschenkel SH, de Araújo EF, de Queiroz MV. Transposable elements belonging to the Tc1-Mariner superfamily are heavily mutated in Colletotrichum graminicola. Mycologia 2017; 106:629-41. [DOI: 10.3852/13-262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Raíssa Mesquita Braga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, Avenida Professor Lineu Prestes 1374, Cidade Universitária, São Paulo, Brasil. CEP: 05508-900
| | - Mateus Ferreira Santana
- Departamento de Microbiologia, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs s/n, Campus Universitário, Viçosa, Brasil. CEP: 36570-000
| | - Rodrigo Veras da Costa
- Embrapa Milho e Sorgo, Rod MG 424 Km 65, Sete Lagoas, Minas Gerais, Brasil. CEP: 35701-970
| | - Sergio Herminio Brommonschenkel
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs s/n, Campus Universitário, Viçosa, Brasil. CEP: 36570-000
| | - Elza Fernandes de Araújo
- Fundação de Amparo à Pesquisa do Estado de Minas Gerais, Rua Raul Pompeia 101, São Pedro, Belo Horizonte, Brasil. CEP: 30330-080
| | - Marisa Vieira de Queiroz
- Departamento de Microbiologia, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs s/n, Campus Universitário, Viçosa, Brasil. CEP: 36570-000
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17
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Ben-David R, Parks R, Dinoor A, Kosman E, Wicker T, Keller B, Cowger C. Differentiation Among Blumeria graminis f. sp. tritici Isolates Originating from Wild Versus Domesticated Triticum Species in Israel. PHYTOPATHOLOGY 2016; 106:861-870. [PMID: 27019062 DOI: 10.1094/phyto-07-15-0177-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Israel and its vicinity constitute a center of diversity of domesticated wheat species (Triticum aestivum and T. durum) and their sympatrically growing wild relatives, including wild emmer wheat (T. dicoccoides). We investigated differentiation within the forma specialis of their obligate powdery mildew pathogen, Blumeria graminis f. sp. tritici. A total of 61 B. graminis f. sp. tritici isolates were collected from the three host species in four geographic regions of Israel. Genetic relatedness of the isolates was characterized using both virulence patterns on 38 wheat lines (including 21 resistance gene differentials) and presumptively neutral molecular markers (simple-sequence repeats and single-nucleotide polymorphisms). All isolates were virulent on at least some genotypes of all three wheat species tested. All assays divided the B. graminis f. sp. tritici collection into two distinct groups, those from domesticated hosts and those from wild emmer wheat. One-way migration was detected from the domestic wheat B. graminis f. sp. tritici population to the wild emmer B. graminis f. sp. tritici population at a rate of five to six migrants per generation. This gene flow may help explain the overlap between the distinct domestic and wild B. graminis f. sp. tritici groups. Overall, B. graminis f. sp. tritici is significantly differentiated into wild-emmer and domesticated-wheat populations, although the results do not support the existence of a separate f. sp. dicocci.
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Affiliation(s)
- Roi Ben-David
- First author: Department of Vegetables and Field Crops, Institute of Plant Sciences, ARO-Volcani Center, Bet Dagan 5025000, Israel; second and seventh authors: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; fourth author: Institute for Cereal Crops Improvement (ICCI), The George S. Wise Faculty for Life Sciences Tel Aviv University, Tel Aviv 69978, Israel; and fifth and sixth authors: Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Ryan Parks
- First author: Department of Vegetables and Field Crops, Institute of Plant Sciences, ARO-Volcani Center, Bet Dagan 5025000, Israel; second and seventh authors: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; fourth author: Institute for Cereal Crops Improvement (ICCI), The George S. Wise Faculty for Life Sciences Tel Aviv University, Tel Aviv 69978, Israel; and fifth and sixth authors: Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Amos Dinoor
- First author: Department of Vegetables and Field Crops, Institute of Plant Sciences, ARO-Volcani Center, Bet Dagan 5025000, Israel; second and seventh authors: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; fourth author: Institute for Cereal Crops Improvement (ICCI), The George S. Wise Faculty for Life Sciences Tel Aviv University, Tel Aviv 69978, Israel; and fifth and sixth authors: Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Evsey Kosman
- First author: Department of Vegetables and Field Crops, Institute of Plant Sciences, ARO-Volcani Center, Bet Dagan 5025000, Israel; second and seventh authors: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; fourth author: Institute for Cereal Crops Improvement (ICCI), The George S. Wise Faculty for Life Sciences Tel Aviv University, Tel Aviv 69978, Israel; and fifth and sixth authors: Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Thomas Wicker
- First author: Department of Vegetables and Field Crops, Institute of Plant Sciences, ARO-Volcani Center, Bet Dagan 5025000, Israel; second and seventh authors: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; fourth author: Institute for Cereal Crops Improvement (ICCI), The George S. Wise Faculty for Life Sciences Tel Aviv University, Tel Aviv 69978, Israel; and fifth and sixth authors: Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Beat Keller
- First author: Department of Vegetables and Field Crops, Institute of Plant Sciences, ARO-Volcani Center, Bet Dagan 5025000, Israel; second and seventh authors: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; fourth author: Institute for Cereal Crops Improvement (ICCI), The George S. Wise Faculty for Life Sciences Tel Aviv University, Tel Aviv 69978, Israel; and fifth and sixth authors: Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
| | - Christina Cowger
- First author: Department of Vegetables and Field Crops, Institute of Plant Sciences, ARO-Volcani Center, Bet Dagan 5025000, Israel; second and seventh authors: United States Department of Agriculture-Agricultural Research Service, Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: The Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; fourth author: Institute for Cereal Crops Improvement (ICCI), The George S. Wise Faculty for Life Sciences Tel Aviv University, Tel Aviv 69978, Israel; and fifth and sixth authors: Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland
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Goldfarb M, Santana MF, Salomão TMF, Queiroz MVD, Barros EGD. Evidence of ectopic recombination and a repeat-induced point (RIP) mutation in the genome of Sclerotinia sclerotiorum, the agent responsible for white mold. Genet Mol Biol 2016; 39:426-30. [PMID: 27560652 PMCID: PMC5004834 DOI: 10.1590/1678-4685-gmb-2015-0241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/20/2015] [Indexed: 12/24/2022] Open
Abstract
Two retrotransposons from the superfamilies Copia and
Gypsy named as Copia-LTR_SS and
Gypsy-LTR_SS, respectively, were identified in
the genomic bank of Sclerotinia sclerotiorum. These transposable
elements (TEs) contained direct and preserved long terminal repeats (LTR). Domains
related to codified regions for gag protein, integrase, reverse transcriptase and
RNAse H were identified in Copia-LTR_SS, whereas in
Gypsy-LTR_SS only domains for gag, reverse
transcriptase and RNAse H were found. The abundance of identified LTR-Solo suggested
possible genetic recombination events in the S. sclerotiorum genome.
Furthermore, alignment of the sequences for LTR elements from each superfamily
suggested the presence of a RIP (repeat-induced point mutation) silencing mechanism
that may directly affect the evolution of this species.
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Affiliation(s)
- Míriam Goldfarb
- Laboratório de Biologia Molecular de Plantas, Instituto de Biotecnologia Aplicada (BIOAGRO), Universidade Federal de Viçosa (UFV), 36570-000, Viçosa, MG, Brazil
| | - Mateus Ferreira Santana
- Laboratório de Genética Molecular e de Microrganismo, Instituto de Biotecnologia Aplicada (BIOAGRO), Universidade Federal de Viçosa (UFV), 36570-000, Viçosa, MG, Brazil
| | - Tânia Maria Fernandes Salomão
- Laboratório de Biologia Molecular de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), 36570-000, Viçosa, MG, Brazil
| | - Marisa Vieira de Queiroz
- Laboratório de Genética Molecular e de Microrganismo, Instituto de Biotecnologia Aplicada (BIOAGRO), Universidade Federal de Viçosa (UFV), 36570-000, Viçosa, MG, Brazil
| | - Everaldo Gonçalves de Barros
- Laboratório de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160, Brasília, DF, Brazil
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Cowger C, Parks R, Kosman E. Structure and Migration in U.S. Blumeria graminis f. sp. tritici Populations. PHYTOPATHOLOGY 2016; 106:295-304. [PMID: 26623997 DOI: 10.1094/phyto-03-15-0066-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
While wheat powdery mildew occurs throughout the south-central and eastern United States, epidemics are especially damaging in the Mid-Atlantic states. The structure of the U.S. Blumeria graminis f. sp. tritici population was assessed based on a sample of 238 single-spored isolates. The isolates were collected from 16 locations in 12 states (18 site-years) as chasmothecial samples in 2003 or 2005, or as conidial samples in 2007 or 2010. DNA was evaluated using nine single nucleotide polymorphism (SNP) markers in four housekeeping genes, and 10 simple sequence repeat (SSR) markers. The SSR markers were variably polymorphic, with allele numbers ranging from 3 to 39 per locus. Genotypic diversity was high (210 haplotypes) and in eight of the site-years, every isolate had a different SSR genotype. SNP haplotypic diversity was lower; although 15 haplotypes were identified, the majority of isolates possessed one of two haplotypes. The chasmothecial samples showed no evidence of linkage disequilibrium (P = 0.36), while the conidial samples did (P = 0.001), but the two groups had nearly identical mean levels of genetic diversity, which was moderate. There was a weakly positive relationship between genetic distance and geographic distance (R(2) = 0.25, P = 0.001), indicating modest isolation by distance. Most locations in the Mid-Atlantic and Great Lakes regions clustered together genetically, while Southeast locations formed a distinct but adjacent cluster; all of these were genetically separated from Southern Plains locations and an intermediate location in Kentucky. One-way migration was detected at a rate of approximately five individuals per generation from populations west of the Appalachian Mountains to those to the east, despite the fact that the Atlantic states experience more frequent and damaging wheat mildew epidemics. Overall, the evidence argues for a large-scale mosaic of overlapping populations that re-establish themselves from local sources, rather than continental-scale extinction and re-establishment, and a low rate of long-distance dispersal roughly from west to east, consistent with prevailing wind directions.
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Affiliation(s)
- Christina Cowger
- First and second author: U.S. Department of Agriculture-Agricultural Research Service, CB7616, Department of Plant Pathology, North Carolina State University, Raleigh 27695; and third author: Faculty of Life Sciences, Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ryan Parks
- First and second author: U.S. Department of Agriculture-Agricultural Research Service, CB7616, Department of Plant Pathology, North Carolina State University, Raleigh 27695; and third author: Faculty of Life Sciences, Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - Evsey Kosman
- First and second author: U.S. Department of Agriculture-Agricultural Research Service, CB7616, Department of Plant Pathology, North Carolina State University, Raleigh 27695; and third author: Faculty of Life Sciences, Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
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Menardo F, Praz CR, Wyder S, Ben-David R, Bourras S, Matsumae H, McNally KE, Parlange F, Riba A, Roffler S, Schaefer LK, Shimizu KK, Valenti L, Zbinden H, Wicker T, Keller B. Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species. Nat Genet 2016; 48:201-5. [PMID: 26752267 DOI: 10.1038/ng.3485] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/11/2015] [Indexed: 11/09/2022]
Abstract
Throughout the history of agriculture, many new crop species (polyploids or artificial hybrids) have been introduced to diversify products or to increase yield. However, little is known about how these new crops influence the evolution of new pathogens and diseases. Triticale is an artificial hybrid of wheat and rye, and it was resistant to the fungal pathogen powdery mildew (Blumeria graminis) until 2001 (refs. 1,2,3). We sequenced and compared the genomes of 46 powdery mildew isolates covering several formae speciales. We found that B. graminis f. sp. triticale, which grows on triticale and wheat, is a hybrid between wheat powdery mildew (B. graminis f. sp. tritici) and mildew specialized on rye (B. graminis f. sp. secalis). Our data show that the hybrid of the two mildews specialized on two different hosts can infect the hybrid plant species originating from those two hosts. We conclude that hybridization between mildews specialized on different species is a mechanism of adaptation to new crops introduced by agriculture.
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Affiliation(s)
- Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Coraline R Praz
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Stefan Wyder
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Roi Ben-David
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Hiromi Matsumae
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zurich, Switzerland
| | - Kaitlin E McNally
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Andrea Riba
- Biozentrum, University of Basel, Basel, Switzerland
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Luisa K Schaefer
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Kentaro K Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zurich, Switzerland
| | - Luca Valenti
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Helen Zbinden
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
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Bourras S, McNally KE, Müller MC, Wicker T, Keller B. Avirulence Genes in Cereal Powdery Mildews: The Gene-for-Gene Hypothesis 2.0. FRONTIERS IN PLANT SCIENCE 2016; 7:241. [PMID: 26973683 PMCID: PMC4771761 DOI: 10.3389/fpls.2016.00241] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 02/12/2016] [Indexed: 05/22/2023]
Abstract
The gene-for-gene hypothesis states that for each gene controlling resistance in the host, there is a corresponding, specific gene controlling avirulence in the pathogen. Allelic series of the cereal mildew resistance genes Pm3 and Mla provide an excellent system for genetic and molecular analysis of resistance specificity. Despite this opportunity for molecular research, avirulence genes in mildews remain underexplored. Earlier work in barley powdery mildew (B.g. hordei) has shown that the reaction to some Mla resistance alleles is controlled by multiple genes. Similarly, several genes are involved in the specific interaction of wheat mildew (B.g. tritici) with the Pm3 allelic series. We found that two mildew genes control avirulence on Pm3f: one gene is involved in recognition by the resistance protein as demonstrated by functional studies in wheat and the heterologous host Nicotiana benthamiana. A second gene is a suppressor, and resistance is only observed in mildew genotypes combining the inactive suppressor and the recognized Avr. We propose that such suppressor/avirulence gene combinations provide the basis of specificity in mildews. Depending on the particular gene combinations in a mildew race, different genes will be genetically identified as the "avirulence" gene. Additionally, the observation of two LINE retrotransposon-encoded avirulence genes in B.g. hordei further suggests that the control of avirulence in mildew is more complex than a canonical gene-for-gene interaction. To fully understand the mildew-cereal interactions, more knowledge on avirulence determinants is needed and we propose ways how this can be achieved based on recent advances in the field.
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22
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Amselem J, Vigouroux M, Oberhaensli S, Brown JKM, Bindschedler LV, Skamnioti P, Wicker T, Spanu PD, Quesneville H, Sacristán S. Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. BMC Genomics 2015; 16:917. [PMID: 26556056 PMCID: PMC4641428 DOI: 10.1186/s12864-015-2185-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/03/2015] [Indexed: 12/31/2022] Open
Abstract
Background The Avrk1 and Avra10 avirulence (AVR) genes encode effectors that increase the pathogenicity of the fungus Blumeria graminis f.sp. hordei (Bgh), the powdery mildew pathogen, in susceptible barley plants. In resistant barley, MLK1 and MLA10 resistance proteins recognize the presence of AVRK1 and AVRA10, eliciting the hypersensitive response typical of gene for gene interactions. Avrk1 and Avra10 have more than 1350 homologues in Bgh genome, forming the EKA (Effectors homologous to Avrk1 and Avra10) gene family. Results We tested the hypothesis that the EKA family originated from degenerate copies of Class I LINE retrotransposons by analysing the EKA family in the genome of Bgh isolate DH14 with bioinformatic tools specially developed for the analysis of Transposable Elements (TE) in genomes. The Class I LINE retrotransposon copies homologous to Avrk1 and Avra10 represent 6.5 % of the Bgh annotated genome and, among them, we identified 293 AVR/effector candidate genes. We also experimentally identified peptides that indicated the translation of several predicted proteins from EKA family members, which had higher relative abundance in haustoria than in hyphae. Conclusions Our analyses indicate that Avrk1 and Avra10 have evolved from part of the ORF1 gene of Class I LINE retrotransposons. The co-option of Avra10 and Avrk1 as effectors from truncated copies of retrotransposons explains the huge number of homologues in Bgh genome that could act as dynamic reservoirs from which new effector genes may evolve. These data provide further evidence for recruitment of retrotransposons in the evolution of new biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2185-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joelle Amselem
- INRA, UR1164 URGI Unité de Recherche Génomique-Info, Institut National de la Recherche Agronomique de Versailles-Grignon, Versailles, 78026, France. .,INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, 78850, Thiverval-Grignon, France.
| | | | - Simone Oberhaensli
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - James K M Brown
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | | | - Pari Skamnioti
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, Iera Odos 75, TK 11855, Athens, Greece.
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, UK.
| | - Hadi Quesneville
- INRA, UR1164 URGI Unité de Recherche Génomique-Info, Institut National de la Recherche Agronomique de Versailles-Grignon, Versailles, 78026, France.
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain.
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23
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Genetic and molecular characterization of a locus involved in avirulence of Blumeria graminis f. sp. tritici on wheat Pm3 resistance alleles. Fungal Genet Biol 2015; 82:181-92. [DOI: 10.1016/j.fgb.2015.06.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/10/2015] [Accepted: 06/09/2015] [Indexed: 01/26/2023]
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24
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MpSaci is a widespread gypsy-Ty3 retrotransposon highly represented by non-autonomous copies in the Moniliophthora perniciosa genome. Curr Genet 2015; 61:185-202. [DOI: 10.1007/s00294-014-0469-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 11/21/2014] [Accepted: 12/22/2014] [Indexed: 11/25/2022]
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Zhou K, Kuo A, Grigoriev IV. Reverse transcriptase and intron number evolution. Stem Cell Investig 2014; 1:17. [PMID: 27358863 DOI: 10.3978/j.issn.2306-9759.2014.08.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/04/2014] [Indexed: 11/14/2022]
Abstract
BACKGROUND Introns are universal in eukaryotic genomes and play important roles in transcriptional regulation, mRNA export to the cytoplasm, nonsense-mediated decay as both a regulatory and a splicing quality control mechanism, R-loop avoidance, alternative splicing, chromatin structure, and evolution by exon-shuffling. METHODS Sixteen complete fungal genomes were used 13 of which were sequenced and annotated by JGI. Ustilago maydis, Cryptococcus neoformans, and Coprinus cinereus (also named Coprinopsis cinerea) were from the Broad Institute. Gene models from JGI-annotated genomes were taken from the GeneCatalog track that contained the best representative gene models. Varying fractions of the GeneCatalog were manually curated by external users. For clarity, we used the JGI unique database identifier. RESULTS The last common ancestor of eukaryotes (LECA) has an estimated 6.4 coding exons per gene (EPG) and evolved into the diverse eukaryotic life forms, which is recapitulated by the development of a stem cell. We found a parallel between the simulated reverse transcriptase (RT)-mediated intron loss and the comparative analysis of 16 fungal genomes that spanned a wide range of intron density. Although footprints of RT (RTF) were dynamic, relative intron location (RIL) to the 5'-end of mRNA faithfully traced RT-mediated intron loss and revealed 7.7 EPG for LECA. The mode of exon length distribution was conserved in simulated intron loss, which was exemplified by the shared mode of 75 nt between fungal and Chlamydomonas genomes. The dominant ancient exon length was corroborated by the average exon length of the most intron-rich genes in fungal genomes and consistent with ancient protein modules being ~25 aa. Combined with the conservation of a protein length of 400 aa, the earliest ancestor of eukaryotes could have 16 EPG. During earlier evolution, Ascomycota's ancestor had significantly more 3'-biased RT-mediated intron loss that was followed by dramatic RTF loss. There was a down trend of EPG from more conserved to less conserved genes. Moreover, species-specific genes have higher exon-densities, shorter exons, and longer introns when compared to genes conserved at the phylum level. However, intron length in species-specific genes became shorter than that of genes conserved in all species after genomes experiencing drastic intron loss. The estimated EPG from the most frequent exon length is more than double that from the RIL method. CONCLUSIONS This implies significant intron loss during the very early period of eukaryotic evolution. De novo gene-birth contributes to shorter exons, longer introns, and higher exon-density in species-specific genes relative to conserved genes.
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Affiliation(s)
- Kemin Zhou
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Alan Kuo
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Igor V Grigoriev
- 1 Computational Genomics, Bristol-Myers Squibb, 311 Pennington Rocky Hill Road, Pennington, NJ 08534, USA ; 2 US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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26
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Santana MF, Silva JCF, Mizubuti ESG, Araújo EF, Condon BJ, Turgeon BG, Queiroz MV. Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophus. BMC Genomics 2014; 15:536. [PMID: 24973942 PMCID: PMC4112212 DOI: 10.1186/1471-2164-15-536] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/17/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Cochliobolus heterostrophus is a dothideomycete that causes Southern Corn Leaf Blight disease. There are two races, race O and race T that differ by the absence (race O) and presence (race T) of ~ 1.2-Mb of DNA encoding genes responsible for the production of T-toxin, which makes race T much more virulent than race O. The presence of repetitive elements in fungal genomes is considered to be an important source of genetic variability between different species. RESULTS A detailed analysis of class I and II TEs identified in the near complete genome sequence of race O was performed. In total in race O, 12 new families of transposons were identified. In silico evidence of recent activity was found for many of the transposons and analyses of expressed sequence tags (ESTs) demonstrated that these elements were actively transcribed. Various potentially active TEs were found near coding regions and may modify the expression and structure of these genes by acting as ectopic recombination sites. Transposons were found on scaffolds carrying polyketide synthase encoding genes, responsible for production of T-toxin in race T. Strong evidence of ectopic recombination was found, demonstrating that TEs can play an important role in the modulation of genome architecture of this species. The Repeat Induced Point mutation (RIP) silencing mechanism was shown to have high specificity in C. heterostrophus, acting only on transposons near coding regions. CONCLUSIONS New families of transposons were identified. In C. heterostrophus, the RIP silencing mechanism is efficient and selective. The co-localization of effector genes and TEs, therefore, exposes those genes to high rates of point mutations. This may accelerate the rate of evolution of these genes, providing a potential advantage for the host. Additionally, it was shown that ectopic recombination promoted by TEs appears to be the major event in the genome reorganization of this species and that a large number of elements are still potentially active. So, this study provides information about the potential impact of TEs on the evolution of C. heterostrophus.
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Affiliation(s)
- Mateus F Santana
- />Laboratório de Genética Molecular e de Micro-organismo, Universidade Federal de Viçosa, Viçosa, Brazil
| | - José CF Silva
- />Instituto Nacional de Ciência e Tecnologia em Interações Planta-Praga, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Eduardo SG Mizubuti
- />Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elza F Araújo
- />Laboratório de Genética Molecular e de Micro-organismo, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Bradford J Condon
- />Department of Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, USA
| | - B Gillian Turgeon
- />Department of Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, USA
| | - Marisa V Queiroz
- />Laboratório de Genética Molecular e de Micro-organismo, Universidade Federal de Viçosa, Viçosa, Brazil
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Troch V, Audenaert K, Wyand RA, Haesaert G, Höfte M, Brown JKM. Formae speciales of cereal powdery mildew: close or distant relatives? MOLECULAR PLANT PATHOLOGY 2014; 15:304-314. [PMID: 24286122 PMCID: PMC6638862 DOI: 10.1111/mpp.12093] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Powdery mildew is an important disease of cereals, affecting both grain yield and end-use quality. The causal agent of powdery mildew on cereals, Blumeria graminis, has been classified into eight formae speciales (ff.spp.), infecting crops and wild grasses. Advances in research on host specificity and resistance, and on pathogen phylogeny and origins, have brought aspects of the subspecific classification system of B. graminis into ff.spp. into question, because it is based on adaptation to certain hosts rather than strict host specialization. Cereals therefore cannot be considered as typical non-hosts to non-adapted ff.spp. We introduce the term 'non-adapted resistance' of cereals to inappropriate ff.spp. of B. graminis, which involves both pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). There is no clear distinction between the mechanisms of resistance to adapted and non-adapted ff.spp. Molecular evolutionary data suggest that the taxonomic grouping of B. graminis into different ff.spp. is not consistent with the phylogeny of the fungus. Imprecise estimates of mutation rates and the lack of genetic variation in introduced populations may explain the uncertainty with regard to divergence times, in the Miocene or Holocene epochs, of ff.spp. of B. graminis which infect cereal crop species. We propose that most evidence favours divergence in the Holocene, during the course of early agriculture. We also propose that the forma specialis concept should be retained for B. graminis pathogenic on cultivated cereals to include clades of the fungus which are strongly specialized to these hosts, i.e. ff.spp. hordei, secalis and tritici, as well as avenae from cultivated A. sativa, and that the forma specialis concept should no longer be applied to B. graminis from most wild grasses.
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Affiliation(s)
- Veronique Troch
- Associated Faculty of Applied Bioscience Engineering, University College Ghent (Ghent University Association), Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium; Department of Crop Protection, Laboratory of Phytopathology, Ghent University, Coupure links 653, BE-9000, Ghent, Belgium
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28
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Cristancho MA, Botero-Rozo DO, Giraldo W, Tabima J, Riaño-Pachón DM, Escobar C, Rozo Y, Rivera LF, Durán A, Restrepo S, Eilam T, Anikster Y, Gaitán AL. Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales. FRONTIERS IN PLANT SCIENCE 2014; 5:594. [PMID: 25400655 PMCID: PMC4215621 DOI: 10.3389/fpls.2014.00594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 10/11/2014] [Indexed: 05/20/2023]
Abstract
Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.
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Affiliation(s)
- Marco A. Cristancho
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- *Correspondence: Marco A. Cristancho, Department of Plant Pathology, National Center for Coffee Research – CENICAFÉ, Km 4 vía a Manizales, Chinchiná 2427, Colombia e-mail:
| | - David Octavio Botero-Rozo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | - William Giraldo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Javier Tabima
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | | | - Carolina Escobar
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Yomara Rozo
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Luis F. Rivera
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Andrés Durán
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
| | - Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de los AndesBogotá, Colombia
| | - Tamar Eilam
- Institute for Cereal Crops Improvement, Tel Aviv UniversityTel Aviv, Israel
| | - Yehoshua Anikster
- Institute for Cereal Crops Improvement, Tel Aviv UniversityTel Aviv, Israel
| | - Alvaro L. Gaitán
- Plant Pathology, National Center for Coffee Research – CENICAFÉChinchiná, Colombia
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The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nat Genet 2013; 45:1092-6. [PMID: 23852167 DOI: 10.1038/ng.2704] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/20/2013] [Indexed: 12/17/2022]
Abstract
Wheat powdery mildew, Blumeria graminis forma specialis tritici, is a devastating fungal pathogen with a poorly understood evolutionary history. Here we report the draft genome sequence of wheat powdery mildew, the resequencing of three additional isolates from different geographic regions and comparative analyses with the barley powdery mildew genome. Our comparative genomic analyses identified 602 candidate effector genes, with many showing evidence of positive selection. We characterize patterns of genetic diversity and suggest that mildew genomes are mosaics of ancient haplogroups that existed before wheat domestication. The patterns of diversity in modern isolates suggest that there was no pronounced loss of genetic diversity upon formation of the new host bread wheat 10,000 years ago. We conclude that the ready adaptation of B. graminis f.sp. tritici to the new host species was based on a diverse haplotype pool that provided great genetic potential for pathogen variation.
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