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Liu M, Braun U, Takamatsu S, Hambleton S, Shoukouhi P, Bisson KR, Hubbard K. Taxonomic revision of Blumeria based on multi-gene DNA sequences, host preferences and morphology. MYCOSCIENCE 2021; 62:143-165. [PMID: 37091321 PMCID: PMC9157761 DOI: 10.47371/mycosci.2020.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 01/20/2023]
Abstract
A taxonomic revision of the hitherto monotypic genus Blumeria was conducted incorporating multi-gene sequence analyses, host preference data and morphological criteria. The sequenced loci included rDNA ITS, partial chitin synthase gene (CHS1), as well as fragments of two unnamed orthologous genes (Bgt-1929, Bgt-4572). The combined evidence led to a reassessment and a new neotypification of B. graminiss. str. (emend.), and the description of seven additional species, viz. B. americana sp. nov. (mainly on hosts of the Triticeae), B. avenae sp. nov. (on Avena spp.), B. bromi-cathartici sp. nov. (on Bromus catharticus), B. bulbigera comb. nov. (on Bromus spp.), B. dactylidis sp. nov. (on Dactylis glomerata as the main host, but also on various other hosts), B. graminicola sp. nov. (on Poa spp. as principal hosts, but also on various other hosts), and B. hordei sp. nov. (on Hordeum spp.). Synonyms were assessed, some were lectotypified, and questionable names previously associated with powdery mildew on monocots were discussed although their identities remained unresolved. Keys to the described species were developed.
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Affiliation(s)
- Miao Liu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada
- First two authors should be considered as having equal contribution
| | - Uwe Braun
- Martin Luther University, Institute of Biology, Department of Geobotany
- First two authors should be considered as having equal contribution
| | | | - Sarah Hambleton
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada
| | - Parivash Shoukouhi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada
| | | | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada
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Kusch S, Frantzeskakis L, Thieron H, Panstruga R. Small RNAs from cereal powdery mildew pathogens may target host plant genes. Fungal Biol 2018; 122:1050-1063. [PMID: 30342621 DOI: 10.1016/j.funbio.2018.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022]
Abstract
Small RNAs (sRNAs) play a key role in eukaryotic gene regulation, for example by gene silencing via RNA interference (RNAi). The biogenesis of sRNAs depends on proteins that are generally conserved in all eukaryotic lineages, yet some species that lack part or all the components of the mechanism exist. Here we explored the presence of the RNAi machinery and its expression as well as the occurrence of sRNA candidates and their putative endogenous as well as host targets in phytopathogenic powdery mildew fungi. We focused on the species Blumeria graminis, which occurs in various specialized forms (formae speciales) that each have a strictly limited host range. B. graminis f. sp. hordei and B. graminis f. sp. tritici, colonizing barley and wheat, respectively, have genomes that are characterized by extensive gene loss. Nonetheless, we find that the RNAi machinery appears to be largely complete and expressed during infection. sRNA sequencing data enabled the identification of putative sRNAs in both pathogens. While a considerable part of the sRNA candidates have predicted target sites in endogenous genes and transposable elements, a small proportion appears to have targets in planta, suggesting potential cross-kingdom RNA transfer between powdery mildew fungi and their respective plant hosts.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Hannah Thieron
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
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3
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Kallamadi PR, Dandu K, Kirti PB, Rao CM, Thakur SS, Mulpuri S. An Insight into Powdery Mildew-Infected, Susceptible, Resistant, and Immune Sunflower Genotypes. Proteomics 2018; 18:e1700418. [DOI: 10.1002/pmic.201700418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 05/26/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Prathap Reddy Kallamadi
- ICAR- Indian Institute of Oilseeds Research; Rajendranagar 500 030 Hyderabad India
- University of Hyderabad; Prof. C.R. Rao Road 500 046 Hyderabad India
| | - Kamakshi Dandu
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | | | - Chintalagiri Mohan Rao
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | - Suman S Thakur
- CSIR- Centre for Cellular and Molecular Biology; Uppal Road, Habsiguda 500 007 Hyderabad India
| | - Sujatha Mulpuri
- ICAR- Indian Institute of Oilseeds Research; Rajendranagar 500 030 Hyderabad India
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4
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Frantzeskakis L, Kracher B, Kusch S, Yoshikawa-Maekawa M, Bauer S, Pedersen C, Spanu PD, Maekawa T, Schulze-Lefert P, Panstruga R. Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen. BMC Genomics 2018; 19:381. [PMID: 29788921 PMCID: PMC5964911 DOI: 10.1186/s12864-018-4750-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
Background Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). Results The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. Conclusions The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a “one-speed” genome that differs in its architecture and (co-)evolutionary pattern from the “two-speed” genomes reported for several other filamentous phytopathogens. Electronic supplementary material The online version of this article (10.1186/s12864-018-4750-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lamprinos Frantzeskakis
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Barbara Kracher
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Stefan Kusch
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Makoto Yoshikawa-Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Saskia Bauer
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Pietro D Spanu
- Imperial College, Department of Life Sciences, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Takaki Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
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Qian C, Cui C, Wang X, Zhou C, Hu P, Li M, Li R, Xiao J, Wang X, Chen P, Xing L, Cao A. Molecular characterisation of the broad-spectrum resistance to powdery mildew conferred by the Stpk-V gene from the wild species Haynaldia villosa. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:875-885. [PMID: 28881082 DOI: 10.1111/plb.12625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
A key member of the Pm21 resistance gene locus, Stpk-V, derived from Haynaldia villosa, was shown to confer broad-spectrum resistance to wheat powdery mildew. The present study was planned to investigate the resistance mechanism mediated by Stpk-V. Transcriptome analysis was performed in Stpk-V transgenic plants and recipient Yangmai158 upon Bgt infection, and detailed histochemical observations were conducted. Chromosome location of Stpk-V orthologous genes in Triticeae species was conducted for evolutionary study and over-expression of Stpk-V both in barley and Arabidopsis was performed for functional study. The transcriptome results indicate, at the early infection stage, the ROS pathway, JA pathway and some PR proteins associated with the SA pathway were activated in both the resistant Stpk-V transgenic plants and susceptible Yangmai158. However, at the later infection stage, the genes up-regulated at the early stage were continuously held only in the transgenic plants, and a large number of new genes were also activated in the transgenic plants but not in Yangmai158. Results indicate that sustained activation of the early response genes combined with later-activated genes mediated by Stpk-V is critical for resistance in Stpk-V transgenic plants. Stpk-V orthologous genes in the representative grass species are all located on homologous group six chromosomes, indicating that Stpk-V is an ancient gene in the grasses. Over-expression of Stpk-V enhanced host resistance to powdery mildew in barley but not in Arabidopsis. Our results enable a better understanding of the resistance mechanism mediated by Stpk-V, and establish a solid foundation for its use in cereal breeding as a gene resource.
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Affiliation(s)
- C Qian
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
- Laboratory of Forage Breeding, Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - C Cui
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - X Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - C Zhou
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - P Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - M Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - R Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - J Xiao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - X Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - P Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - L Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
| | - A Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, China
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6
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Menardo F, Praz CR, Wicker T, Keller B. Rapid turnover of effectors in grass powdery mildew (Blumeria graminis). BMC Evol Biol 2017; 17:223. [PMID: 29089018 PMCID: PMC5664452 DOI: 10.1186/s12862-017-1064-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/02/2017] [Indexed: 11/21/2022] Open
Abstract
Background Grass powdery mildew (Blumeria graminis, Ascomycota) is a major pathogen of cereal crops and has become a model organism for obligate biotrophic fungal pathogens of plants. The sequenced genomes of two formae speciales (ff.spp.), B.g. hordei and B.g. tritici (pathogens of barley and wheat), were found to be enriched in candidate effector genes (CEGs). Similar to other filamentous pathogens, CEGs in B. graminis are under positive selection. Additionally, effectors are more likely to have presence-absence polymorphisms than other genes among different strains. Results Here we identified effectors in the genomes of three additional host-specific lineages of B. graminis (B.g. poae, B.g. avenae and B.g. infecting Lolium) which diverged between 24 and 5 million years ago (Mya). We found that most CEGs in B. graminis are clustered in families and that most families are present in both reference genomes (B.g. hordei and B.g. tritici) and in the genomes of all three newly annotated lineages. We identified conserved protein domains including a novel lipid binding domain. The phylogenetic analysis showed that frequent gene duplications and losses shaped the diversity of the effector repertoires of the different lineages through their evolutionary history. We observed several lineage-specific expansions where large clades of CEGs originated in only one lineage from a single gene through repeated gene duplications. When we applied a birth-death model we found that the turnover rate (the rate at which genes are deleted and duplicated) of CEG families is much higher than for non-CEG families. The analysis of genomic context revealed that the immediate surroundings of CEGs are enriched in transposable elements (TE) which could play a role in the duplication and deletion of CEGs. Conclusions The CEG repertoires of related pathogens diverged dramatically in short evolutionary times because of rapid turnover and of positive selection fixing non-synonymous mutations. While signatures of positive selection on effector sequences are the expected outcome of the evolutionary “arms race” between pathogen and plant immune system, it is more difficult to infer the mechanisms and evolutionary forces that maintained an extreme turnover rate in CEG families of B. graminis for several millions of years. Electronic supplementary material The online version of this article (10.1186/s12862-017-1064-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Coraline R Praz
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
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Li J, Yang X, Liu X, Yu H, Du C, Li M, He D. Proteomic analysis of the compatible interaction of wheat and powdery mildew (Blumeria graminis f. sp. tritici). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 111:234-243. [PMID: 27951493 DOI: 10.1016/j.plaphy.2016.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 05/20/2023]
Abstract
Proteome characteristics of wheat leaves with the powdery mildew pathogen Blumeria graminis f. sp. tritici (Bgt) infection were investigated by two-dimensional electrophoresis and tandem MALDI-TOF/TOF-MS. We identified 46 unique proteins which were differentially expressed at 24, 48, and 72 h post-inoculation. The functional classification of these proteins showed that most of them were involved in photosynthesis, carbohydrate and nitrogen metabolism, defense responses, and signal transduction. Upregulated proteins included primary metabolism pathways and defense responses, while proteins related to photosynthesis and signal transduction were mostly downregulated. As expected, more antioxidative proteins were activated at the later infection stage than the earlier stage, suggesting that the antioxidative system of host plays a role in maintaining the compatible interaction between wheat and powdery mildew. A high accumulation of 6-phosphogluconate dehydrogenase and isocitrate dehydrogenase in infected leaves indicated the regulation of the TCA cycle and pentose phosphate pathway in parallel to the activation of host defenses. The downregulation of MAPK5 could be facilitated for the compatible interaction of wheat plants and Bgt. qRT-PCR analysis supported the data of protein expression profiles. Our results reveal the relevance of primary plant metabolism and defense responses during compatible interaction, and provide new insights into the biology of susceptible wheat in response to Bgt infection.
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Affiliation(s)
- Jie Li
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xiwen Yang
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Xinhao Liu
- Lab of Plant Protection, Kaifeng Agriculture and Forestry Science Institute, Kaifeng, Henan 475004, China
| | - Haibo Yu
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Congyang Du
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Mengda Li
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Dexian He
- Key Laboratory of Regulating and Controlling Crop Growth and Development (Henan Agriculture University) Ministry of Education; Collaborative Innovation Center of Henan Grain Crops; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan 450002, China.
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Komínková E, Dreiseitl A, Malečková E, Doležel J, Valárik M. Genetic Diversity of Blumeria graminis f. sp. hordei in Central Europe and Its Comparison with Australian Population. PLoS One 2016; 11:e0167099. [PMID: 27875588 PMCID: PMC5119828 DOI: 10.1371/journal.pone.0167099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Population surveys of Blumeria graminis f. sp. hordei (Bgh), a causal agent of more than 50% of barley fungal infections in the Czech Republic, have been traditionally based on virulence tests, at times supplemented with non-specific Restriction fragment length polymorphism or Random amplified polymorphic DNA markers. A genomic sequence of Bgh, which has become available recently, enables identification of potential markers suitable for population genetics studies. Two major strategies relying on transposable elements and microsatellites were employed in this work to develop a set of Repeat junction markers, Single sequence repeat and Single nucleotide polymorphism markers. A resolution power of the new panel of markers comprising 33 polymorphisms was demonstrated by a phylogenetic analysis of 158 Bgh isolates. A core set of 97 Czech isolates was compared to a set 50 Australian isolates on the background of 11 diverse isolates collected throughout the world. 73.2% of Czech isolates were found to be genetically unique. An extreme diversity of this collection was in strong contrast with the uniformity of the Australian one. This work paves the way for studies of population structure and dynamics based on genetic variability among different Bgh isolates originating from geographically limited regions.
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Affiliation(s)
- Eva Komínková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Antonín Dreiseitl
- Department of Integrated Plant Protection, Agrotest Fyto Ltd., Kroměříž, Czech Republic
| | - Eva Malečková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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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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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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11
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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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12
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Removing PCR for the elimination of undesired DNA fragments cycle by cycle. Sci Rep 2014; 3:2303. [PMID: 23892515 PMCID: PMC3725479 DOI: 10.1038/srep02303] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/11/2013] [Indexed: 01/21/2023] Open
Abstract
A novel removing polymerase chain reaction (R-PCR) technique was developed, which can eliminate undesired genes, cycle by cycle, with efficiencies of 60.9% (cDNAs), 73.6% (genomic DNAs), and ~ 100% (four DNA fragments were tested). Major components of the R-PCR include drivers, a thermostable restriction enzyme - ApeKI, and a poly(dA) adapter with mismatched restriction enzyme recognition sites. Drivers were generated from the undesired genes. In each cycle of R-PCR, drivers anneal to complementary sequences and allow extension by Taq DNA polymerase. Thus, ApeKI restriction sites in the undesired genes are recovered, and adapters of these undesired DNA fragments are removed. Using R-PCR, we isolated maize upregulated defense-responsive genes and Blumeria graminis specialized genes, including key pathogenesis-related effectors. Our results show that after the R-PCR reaction, most undesired genes, including very abundant genes, became undetectable. The R-PCR is an easy and cost-efficient method to eliminate undesired genes and clone desired genes.
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Hurni S, Brunner S, Buchmann G, Herren G, Jordan T, Krukowski P, Wicker T, Yahiaoui N, Mago R, Keller B. Rye Pm8 and wheat Pm3 are orthologous genes and show evolutionary conservation of resistance function against powdery mildew. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:957-69. [PMID: 24124925 DOI: 10.1111/tpj.12345] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/25/2013] [Accepted: 10/04/2013] [Indexed: 05/18/2023]
Abstract
The improvement of wheat through breeding has relied strongly on the use of genetic material from related wild and domesticated grass species. The 1RS chromosome arm from rye was introgressed into wheat and crossed into many wheat lines, as it improves yield and fungal disease resistance. Pm8 is a powdery mildew resistance gene on 1RS which, after widespread agricultural cultivation, is now widely overcome by adapted mildew races. Here we show by homology-based cloning and subsequent physical and genetic mapping that Pm8 is the rye orthologue of the Pm3 allelic series of mildew resistance genes in wheat. The cloned gene was functionally validated as Pm8 by transient, single-cell expression analysis and stable transformation. Sequence analysis revealed a complex mosaic of ancient haplotypes among Pm3- and Pm8-like genes from different members of the Triticeae. These results show that the two genes have evolved independently after the divergence of the species 7.5 million years ago and kept their function in mildew resistance. During this long time span the co-evolving pathogens have not overcome these genes, which is in strong contrast to the breakdown of Pm8 resistance since its introduction into commercial wheat 70 years ago. Sequence comparison revealed that evolutionary pressure acted on the same subdomains and sequence features of the two orthologous genes. This suggests that they recognize directly or indirectly the same pathogen effectors that have been conserved in the powdery mildews of wheat and rye.
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Affiliation(s)
- Severine Hurni
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008, Zürich, Switzerland
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14
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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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Hacquard S, Kracher B, Maekawa T, Vernaldi S, Schulze-Lefert P, Ver Loren van Themaat E. Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts. Proc Natl Acad Sci U S A 2013; 110:E2219-28. [PMID: 23696672 PMCID: PMC3683789 DOI: 10.1073/pnas.1306807110] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Barley powdery mildew, Blumeria graminis f. sp. hordei (Bgh), is an obligate biotrophic ascomycete fungal pathogen that can grow and reproduce only on living cells of wild or domesticated barley (Hordeum sp.). Domestication and deployment of resistant barley cultivars by humans selected for amplification of Bgh isolates with different virulence combinations. We sequenced the genomes of two European Bgh isolates, A6 and K1, for comparative analysis with the reference genome of isolate DH14. This revealed a mosaic genome structure consisting of large isolate-specific DNA blocks with either high or low SNP densities. Some of the highly polymorphic blocks likely accumulated SNPs for over 10,000 years, well before the domestication of barley. These isolate-specific blocks of alternating monomorphic and polymorphic regions imply an exceptionally large standing genetic variation in the Bgh population and might be generated and maintained by rare outbreeding and frequent clonal reproduction. RNA-sequencing experiments with isolates A6 and K1 during four early stages of compatible and incompatible interactions on leaves of partially immunocompromised Arabidopsis mutants revealed a conserved Bgh transcriptional program during pathogenesis compared with the natural host barley despite ~200 million years of reproductive isolation of these hosts. Transcripts encoding candidate-secreted effector proteins are massively induced in successive waves. A specific decrease in candidate-secreted effector protein transcript abundance in the incompatible interaction follows extensive transcriptional reprogramming of the host transcriptome and coincides with the onset of localized host cell death, suggesting a host-inducible defense mechanism that targets fungal effector secretion or production.
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Affiliation(s)
| | | | - Takaki Maekawa
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Saskia Vernaldi
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
| | - Emiel Ver Loren van Themaat
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany
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Fellers JP, Soltani BM, Bruce M, Linning R, Cuomo CA, Szabo LJ, Bakkeren G. Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements. BMC Genomics 2013; 14:60. [PMID: 23356831 PMCID: PMC3579696 DOI: 10.1186/1471-2164-14-60] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/11/2013] [Indexed: 12/26/2022] Open
Abstract
Background Wheat leaf rust (Puccinia triticina Eriks; Pt) and stem rust fungi (P. graminis f.sp. tritici; Pgt) are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. The Pt genome, currently estimated at 135 Mb, is significantly larger than Pgt, at 88 Mb, but the reason for the expansion is unknown. Three genomic loci of Pt conserved proteins were characterized to gain insight into gene content, genome complexity and expansion. Results A bacterial artificial chromosome (BAC) library was made from P. triticina race 1, BBBD and probed with Pt homologs of genes encoding two predicted Pgt secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in Pgt and local conservation of gene order (microsynteny) was observed. Pairwise protein identities ranged from 26 to 99%. One Pt BAC, containing a RAD18 ortholog, shares syntenic regions with two Pgt scaffolds, which could represent both haplotypes of Pgt. Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to Pgt. These regions are further diverged by differing insertion loci of LTR-retrotransposon, Gypsy, Copia, Mutator, and Harbinger mobile elements. Uncharacterized Pt open reading frames were also found; these proteins are high in lysine and similar to multiple proteins in Pgt. Conclusions The three Pt loci are conserved in gene order, with a range of gene sequence divergence. Conservation of predicted haustoria expressed secreted protein genes between Pt and Pgt is extended to the more distant poplar rust, Melampsora larici-populina. The loci also reveal that genome expansion in Pt is in part due to higher occurrence of repeat-elements in this species.
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Affiliation(s)
- John P Fellers
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Department of Plant Pathology, Manhattan, KS 66506, USA.
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Pedersen C, Ver Loren van Themaat E, McGuffin LJ, Abbott JC, Burgis TA, Barton G, Bindschedler LV, Lu X, Maekawa T, Wessling R, Cramer R, Thordal-Christensen H, Panstruga R, Spanu PD. Structure and evolution of barley powdery mildew effector candidates. BMC Genomics 2012; 13:694. [PMID: 23231440 PMCID: PMC3582587 DOI: 10.1186/1471-2164-13-694] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/28/2012] [Indexed: 11/11/2022] Open
Abstract
Background Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to suppress or avoid host immunity if it is to survive and cause disease. Results Here we characterise a superfamily predicted to be the full complement of Candidates for Secreted Effector Proteins (CSEPs) in the fungal barley powdery mildew parasite B. graminis f.sp. hordei. The 491 genes encoding these proteins constitute over 7% of this pathogen’s annotated genes and most were grouped into 72 families of up to 59 members. They were predominantly expressed in the intracellular feeding structures called haustoria, and proteins specifically associated with the haustoria were identified by large-scale mass spectrometry-based proteomics. There are two major types of effector families: one comprises shorter proteins (100–150 amino acids), with a high relative expression level in the haustoria and evidence of extensive diversifying selection between paralogs; the second type consists of longer proteins (300–400 amino acids), with lower levels of differential expression and evidence of purifying selection between paralogs. An analysis of the predicted protein structures underscores their overall similarity to known fungal effectors, but also highlights unexpected structural affinities to ribonucleases throughout the entire effector super-family. Candidate effector genes belonging to the same family are loosely clustered in the genome and are associated with repetitive DNA derived from retro-transposons. Conclusions We employed the full complement of genomic, transcriptomic and proteomic analyses as well as structural prediction methods to identify and characterize the members of the CSEPs superfamily in B. graminis f.sp. hordei. Based on relative intron position and the distribution of CSEPs with a ribonuclease-like domain in the phylogenetic tree we hypothesize that the associated genes originated from an ancestral gene, encoding a secreted ribonuclease, duplicated successively by repetitive DNA-driven processes and diversified during the evolution of the grass and cereal powdery mildew lineage.
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Affiliation(s)
- Carsten Pedersen
- Department of Agriculture & Ecology, Plant and Soil Science, University ofCopenhagen, Copenhagen, Denmark
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Plant-pathogen interactions: disease resistance in modern agriculture. Trends Genet 2012; 29:233-40. [PMID: 23153595 DOI: 10.1016/j.tig.2012.10.011] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/19/2012] [Accepted: 10/08/2012] [Indexed: 11/21/2022]
Abstract
The growing human population will require a significant increase in agricultural production. This challenge is made more difficult by the fact that changes in the climatic and environmental conditions under which crops are grown have resulted in the appearance of new diseases, whereas genetic changes within the pathogen have resulted in the loss of previously effective sources of resistance. To help meet this challenge, advanced genetic and statistical methods of analysis have been used to identify new resistance genes through global screens, and studies of plant-pathogen interactions have been undertaken to uncover the mechanisms by which disease resistance is achieved. The informed deployment of major, race-specific and partial, race-nonspecific resistance, either by conventional breeding or transgenic approaches, will enable the production of crop varieties with effective resistance without impacting on other agronomically important crop traits. Here, we review these recent advances and progress towards the ultimate goal of developing disease-resistant crops.
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20
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Ellwood SR, Syme RA, Moffat CS, Oliver RP. Evolution of three Pyrenophora cereal pathogens: recent divergence, speciation and evolution of non-coding DNA. Fungal Genet Biol 2012; 49:825-9. [PMID: 22850609 DOI: 10.1016/j.fgb.2012.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 06/05/2012] [Accepted: 07/19/2012] [Indexed: 12/22/2022]
Abstract
Three of the most important fungal pathogens of cereals are Pyrenophora tritici-repentis, the cause of tan spot on wheat, and Pyrenophora teres f. teres and Pyrenophora teres f. maculata, the cause of spot form and net form of net blotch on barley, respectively. Orthologous intergenic regions were used to examine the genetic relationships and divergence times between these pathogens. Mean divergence times were calculated at 519 kya (±30) between P. teresf. teres and P. teresf. maculata, while P. tritici-repentis diverged from both Pyrenophora teresforms 8.04 Mya (±138 ky). Individual intergenic regions showed a consistent pattern of co-divergence of the P. teresforms from P. tritici-repentis, with the pattern supported by phylogenetic analysis of conserved genes. Differences in calculated divergence times between individual intergenic regions suggested that they are not entirely under neutral selection, a phenomenon shared with higher Eukaryotes. P. tritici-repentis regions varied in divergence time approximately 5-12 Mya from the P. teres lineage, compared to the separation of wheat and barley some 12 Mya, while the P. teresf. teres and P. teresf. maculata intergenic region divergences correspond to the middle Pleistocene. The data suggest there is no correlation between the divergence of these pathogens the domestication of wheat and barley, and show P. teresf. teres and P. teresf. maculata are closely related but autonomous. The results are discussed in the context of speciation and the evolution of intergenic regions.
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Affiliation(s)
- Simon R Ellwood
- Department of Environment and Agriculture, Curtin University, Bentley, Perth, Western Australia 6102, Australia.
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Troch V, Audenaert K, Bekaert B, Höfte M, Haesaert G. Phylogeography and virulence structure of the powdery mildew population on its 'new' host triticale. BMC Evol Biol 2012; 12:76. [PMID: 22658131 PMCID: PMC3457899 DOI: 10.1186/1471-2148-12-76] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 05/10/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Powdery mildew, caused by the obligate biotrophic fungus Blumeria graminis, is a major problem in cereal production as it can reduce quality and yield. B. graminis has evolved eight distinct formae speciales (f.sp.) which display strict host specialization. In the last decade, powdery mildew has emerged on triticale, the artificial intergeneric hybrid between wheat and rye. This emergence is probably triggered by a host range expansion of the wheat powdery mildew B. graminis f.sp. tritici. To gain more precise information about the evolutionary processes that led to this host range expansion, we pursued a combined pathological and genetic approach. RESULTS B. graminis isolates were sampled from triticale, wheat and rye from different breeding regions in Europe. Pathogenicity tests showed that isolates collected from triticale are highly pathogenic on most of the tested triticale cultivars. Moreover, these isolates were also able to infect several wheat cultivars (their previous hosts), although a lower aggressiveness was observed compared to isolates collected from wheat. Phylogenetic analysis of nuclear gene regions identified two statistically significant clades, which to a certain extent correlated with pathogenicity. No differences in virulence profiles were found among the sampled regions, but the distribution of genetic variation demonstrated to be geography dependent. A multilocus haplotype network showed that haplotypes pathogenic on triticale are distributed at different sites in the network, but always clustered at or near the tips of the network. CONCLUSIONS This study reveals a genetic structure in B. graminis with population differentiation according to geography and host specificity. In addition, evidence is brought forward demonstrating that the host range expansion of wheat isolates to the new host triticale occurred recently and multiple times at different locations in Europe.
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Affiliation(s)
- Veronique Troch
- Associated Faculty of Applied Bioscience Engineering, University College Ghent, Valentin Vaerwyckweg 1, B-9000, Ghent, Belgium
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Kris Audenaert
- Associated Faculty of Applied Bioscience Engineering, University College Ghent, Valentin Vaerwyckweg 1, B-9000, Ghent, Belgium
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Boris Bekaert
- Associated Faculty of Applied Bioscience Engineering, University College Ghent, Valentin Vaerwyckweg 1, B-9000, Ghent, Belgium
| | - Monica Höfte
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
| | - Geert Haesaert
- Associated Faculty of Applied Bioscience Engineering, University College Ghent, Valentin Vaerwyckweg 1, B-9000, Ghent, Belgium
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
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Parlange F, Oberhaensli S, Breen J, Platzer M, Taudien S, Simková H, Wicker T, Doležel J, Keller B. A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome. Funct Integr Genomics 2011; 11:671-7. [PMID: 21809124 DOI: 10.1007/s10142-011-0240-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 07/03/2011] [Accepted: 07/17/2011] [Indexed: 10/17/2022]
Abstract
Powdery mildew of wheat (Triticum aestivum L.) is caused by the ascomycete fungus Blumeria graminis f.sp. tritici. Genomic approaches open new ways to study the biology of this obligate biotrophic pathogen. We started the analysis of the Bg tritici genome with the low-pass sequencing of its genome using the 454 technology and the construction of the first genomic bacterial artificial chromosome (BAC) library for this fungus. High-coverage contigs were assembled with the 454 reads. They allowed the characterization of 56 transposable elements and the establishment of the Blumeria repeat database. The BAC library contains 12,288 clones with an average insert size of 115 kb, which represents a maximum of 7.5-fold genome coverage. Sequencing of the BAC ends generated 12.6 Mb of random sequence representative of the genome. Analysis of BAC-end sequences revealed a massive invasion of transposable elements accounting for at least 85% of the genome. This explains the unusually large size of this genome which we estimate to be at least 174 Mb, based on a large-scale physical map constructed through the fingerprinting of the BAC library. Our study represents a crucial step in the perspective of the determination and study of the whole Bg tritici genome sequence.
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Affiliation(s)
- Francis Parlange
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, Zurich, Switzerland
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Bleykasten-Grosshans C, Neuvéglise C. Transposable elements in yeasts. C R Biol 2011; 334:679-86. [PMID: 21819950 DOI: 10.1016/j.crvi.2011.05.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 03/31/2011] [Indexed: 11/19/2022]
Abstract
With the development of new sequencing technologies in the past decade, yeast genomes have been extensively sequenced and their structures investigated. Transposable elements (TEs) are ubiquitous in eukaryotes and constitute a limited part of yeast genomes. However, due to their ability to move in genomes and generate dispersed repeated sequences, they contribute to modeling yeast genomes and thereby induce plasticity. This review assesses the TE contents of yeast genomes investigated so far. Their diversity and abundance at the inter- and intraspecific levels are presented, and their effects on gene expression and genome stability is considered. Recent results concerning TE-host interactions are also analyzed.
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Affiliation(s)
- Claudine Bleykasten-Grosshans
- CNRS UMR 7156, Laboratoire Génétique Moléculaire Génomique Microbiologie, Université de Strasbourg, 28 rue Goethe, 67083 Strasbourg cedex, France.
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