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Nallathambi P, Umamaheswari C, Reddy B, Aarthy B, Javed M, Ravikumar P, Watpade S, Kashyap PL, Boopalakrishnan G, Kumar S, Sharma A, Kumar A. Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics. J Fungi (Basel) 2024; 10:267. [PMID: 38667938 PMCID: PMC11051031 DOI: 10.3390/jof10040267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb genome size, potentially encoding 8480 genes. Notably, more than 73.80% of the genome, spanning approximately 102.14 Mb, comprises retro-elements, LTR elements, and P elements, influencing evolution and adaptation significantly. The phylogenomic analysis placed B. graminis f. sp. tritici Wtn1 in a distinct monocot-infecting clade. A total of 583 tRNA anticodon sequences were identified from the whole genome of the native virulent strain B. graminis f. sp. tritici, which comprises distinct genome features with high counts of tRNA anticodons for leucine (70), cysteine (61), alanine (58), and arginine (45), with only two stop codons (Opal and Ochre) present and the absence of the Amber stop codon. Comparative InterProScan analysis unveiled "shared and unique" proteins in B. graminis f. sp. tritici Wtn1. Identified were 7707 protein-encoding genes, annotated to different categories such as 805 effectors, 156 CAZymes, 6102 orthologous proteins, and 3180 distinct protein families (PFAMs). Among the effectors, genes like Avra10, Avrk1, Bcg-7, BEC1005, CSEP0105, CSEP0162, BEC1016, BEC1040, and HopI1 closely linked to pathogenesis and virulence were recognized. Transcriptome analysis highlighted abundant proteins associated with RNA processing and modification, post-translational modification, protein turnover, chaperones, and signal transduction. Examining the Environmental Information Processing Pathways in B. graminis f. sp. tritici Wtn1 revealed 393 genes across 33 signal transduction pathways. The key pathways included yeast MAPK signaling (53 genes), mTOR signaling (38 genes), PI3K-Akt signaling (23 genes), and AMPK signaling (21 genes). Additionally, pathways like FoxO, Phosphatidylinositol, the two-component system, and Ras signaling showed significant gene representation, each with 15-16 genes, key SNPs, and Indels in specific chromosomes highlighting their relevance to environmental responses and pathotype evolution. The SNP and InDel analysis resulted in about 3.56 million variants, including 3.45 million SNPs, 5050 insertions, and 5651 deletions within the whole genome of B. graminis f. sp. tritici Wtn1. These comprehensive genome and transcriptome datasets serve as crucial resources for understanding the pathogenicity, virulence effectors, retro-elements, and evolutionary origins of B. graminis f. sp. tritici Wtn1, aiding in developing robust strategies for the effective management of wheat powdery mildew.
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Affiliation(s)
- Perumal Nallathambi
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Chandrasekaran Umamaheswari
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Bhaskar Reddy
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
| | - Balakrishnan Aarthy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Mohammed Javed
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
| | - Priya Ravikumar
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Santosh Watpade
- ICAR-Indian Agricultural Research Institute, Regional Station, Shimla 171004, Himachal Pradesh, India;
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | | | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | - Anju Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | - Aundy Kumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
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Germination Development of Powdery Mildew on Natural and Artificial Wheat Leaf Surfaces: A Study to Investigate Plant Wax Signals. SMALL SCIENCE 2023. [DOI: 10.1002/smsc.202200092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Virulence Structure and Genetic Diversity of Blumeria graminis f. sp. avenae from Different Regions of Europe. PLANTS 2022; 11:plants11101358. [PMID: 35631783 PMCID: PMC9145444 DOI: 10.3390/plants11101358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/14/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022]
Abstract
The structure and dynamics of changes in pathogen populations can be analysed by assessing the level of virulence and genetic diversity. The aim of the present study was to determine the diversity of Blumeria graminis f. sp. avenae populations. Diversity and virulence of B. graminis f. sp. avenae was assessed based on 80 single-spore isolates collected in different European countries such as Poland (40 isolates), Germany (10), Finland (10), Czech Republic (10) and Ireland (10) using ISSR (Inter-Simple Sequence Repeats) and SCoT (Start Codon Targeted) markers. This work demonstrated differences in virulence of B. graminis f. sp. avenae isolates sampled from different countries. Molecular analysis showed that both systems were useful for assessing genetic diversity, but ISSR markers were superior and generated more polymorphic products, as well as higher PIC and RP values. UPMGA and PCoA divided the isolates into groups corresponding with their geographical origin. In conclusion, the low level of genetic differentiation of the analysed isolates has suggested that the evolution of B. graminis f. sp. Avenae population is slow, and thus the evolutionary potential of the pathogen is low. This work paves the way for future studies on B. graminis f. sp. Avenae population structure and dynamics based on genetic variability.
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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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Pogoda M, Liu F, Douchkov D, Djamei A, Reif JC, Schweizer P, Schulthess AW. Identification of novel genetic factors underlying the host-pathogen interaction between barley (Hordeum vulgare L.) and powdery mildew (Blumeria graminis f. sp. hordei). PLoS One 2020; 15:e0235565. [PMID: 32614894 PMCID: PMC7332009 DOI: 10.1371/journal.pone.0235565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022] Open
Abstract
Powdery mildew is an important foliar disease of barley (Hordeum vulgare L.) caused by the biotrophic fungus Blumeria graminis f. sp. hordei (Bgh). The understanding of the resistance mechanism is essential for future resistance breeding. In particular, the identification of race-nonspecific resistance genes is important because of their regarded durability and broad-spectrum activity. We assessed the severity of powdery mildew infection on detached seedling leaves of 267 barley accessions using two poly-virulent isolates and performed a genome-wide association study exploiting 201 of these accessions. Two-hundred and fourteen markers, located on six barley chromosomes are associated with potential race-nonspecific Bgh resistance or susceptibility. Initial steps for the functional validation of four promising candidates were performed based on phenotype and transcription data. Specific candidate alleles were analyzed via transient gene silencing as well as transient overexpression. Microarray data of the four selected candidates indicate differential regulation of the transcription in response to Bgh infection. Based on our results, all four candidate genes seem to be involved in the responses to powdery mildew attack. In particular, the transient overexpression of specific alleles of two candidate genes, a potential arabinogalactan protein and the barley homolog of Arabidopsis thaliana’s Light-Response Bric-a-Brac/-Tramtrack/-Broad Complex/-POxvirus and Zinc finger (AtLRB1) or AtLRB2, were top candidates of novel powdery mildew susceptibility genes.
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Affiliation(s)
- Maria Pogoda
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Fang Liu
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Dimitar Douchkov
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Armin Djamei
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Jochen C. Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Patrick Schweizer
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Albert W. Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- * E-mail:
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Liu N, Lei Y, Zhang M, Zheng W, Shi Y, Qi X, Chen H, Zhou Y, Gong G. Latent Infection of Powdery Mildew on Volunteer Wheat in Sichuan Province, China. PLANT DISEASE 2019; 103:1084-1091. [PMID: 31009363 DOI: 10.1094/pdis-06-18-1003-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wheat powdery mildew, caused by the fungal pathogen Blumeria graminis f. sp. tritici, is one of the most destructive wheat diseases in China, especially in Sichuan Province. Successfully oversummered B. graminis f. sp. tritici can become a primary infection source for wheat seedlings in the fall. Determining the latent infection level of B. graminis f. sp. tritici in volunteer wheat and the oversummering areas of B. graminis f. sp. tritici is important for estimating potential B. graminis f. sp. tritici epidemics. In this study, we clarified the critical role of volunteer wheat in the B. graminis f. sp. tritici oversummering cycle and determined whether latent B. graminis f. sp. tritici infection was present in volunteer wheat by using real-time polymerase chain reaction (real-time PCR). The results indicated that volunteer wheat was mostly found in the northeast and middle regions of Sichuan, where lower temperatures and higher precipitation are common. A total of 13.2% of samples showed symptoms of B. graminis f. sp. tritici (spores) in the field, and 36.8% of samples were found to carry the B. graminis f. sp. tritici pathogen, even though no symptoms were observed. Volunteer wheat with B. graminis f. sp. tritici infection symptoms was found at an altitude of 536 m but volunteer wheat latently infected by B. graminis f. sp. tritici was identified at the lowest altitude of 323 m. Crop shade (e.g., corn and lima bean) provided suitable conditions for the survival of volunteer wheat in the summer. In addition, volunteer wheat played a key role in the B. graminis f. sp. tritici oversummering cycle. Moreover, B. graminis f. sp. tritici could oversummer by infecting generations of volunteer wheat in the summer, thereby becoming the primary infection source for autumn-sown wheat. The results showed that the latent infection of wheat diseases could be rapidly quantified by real-time PCR. Here, the primary disease center of autumn-sown wheat in Ya'an and Wenjiang were detected accurately based on this method. This study provides solid evidence for identifying the disease center, which offers guidance for wheat disease control and management.
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Affiliation(s)
- Na Liu
- 1 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- 2 College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China; and
| | - Yu Lei
- 1 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- 3 College of Biological Engineering, Sichuan University of Science & Engineering, Zigong 643000, China
| | - Min Zhang
- 1 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenming Zheng
- 2 College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China; and
| | - Yongchun Shi
- 2 College of Life Sciences, Henan Agricultural University, Zhengzhou, Henan, 450002, China; and
| | - Xiaobo Qi
- 1 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Huabao Chen
- 1 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - You Zhou
- 1 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoshu Gong
- 1 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
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Saur IML, Bauer S, Kracher B, Lu X, Franzeskakis L, Müller MC, Sabelleck B, Kümmel F, Panstruga R, Maekawa T, Schulze-Lefert P. Multiple pairs of allelic MLA immune receptor-powdery mildew AVR A effectors argue for a direct recognition mechanism. eLife 2019; 8:e44471. [PMID: 30777147 PMCID: PMC6414202 DOI: 10.7554/elife.44471] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 01/03/2023] Open
Abstract
Nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins in plants and animals mediate intracellular pathogen sensing. Plant NLRs typically detect strain-specific pathogen effectors and trigger immune responses often linked to localized host cell death. The barley Mla disease resistance locus has undergone extensive functional diversification in the host population and encodes numerous allelic NLRs each detecting a matching isolate-specific avirulence effector (AVRA) of the fungal pathogen Blumeria graminis f. sp. hordei (Bgh). We report here the isolation of Bgh AVRa7, AVRa9, AVRa10, and AVRa22, which encode small secreted proteins recognized by allelic MLA7, MLA9, MLA10, and MLA22 receptors, respectively. These effectors are sequence-unrelated, except for allelic AVRa10 and AVRa22 that are co-maintained in pathogen populations in the form of a balanced polymorphism. Contrary to numerous examples of indirect recognition of bacterial effectors by plant NLRs, co-expression experiments with matching Mla-AVRa pairs indicate direct detection of the sequence-unrelated fungal effectors by MLA receptors.
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Affiliation(s)
- Isabel ML Saur
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Saskia Bauer
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Barbara Kracher
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Xunli Lu
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Lamprinos Franzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Marion C Müller
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Björn Sabelleck
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Takaki Maekawa
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Paul Schulze-Lefert
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant SciencesDüsseldorfGermany
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Bourgeois Y, Stritt C, Walser JC, Gordon SP, Vogel JP, Roulin AC. Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:438-451. [PMID: 30044522 DOI: 10.1111/tpj.14042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/20/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide selection scans (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species, and affects different genomic regions across the two populations. Gene ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in B. distachyon. We eventually cross-validated our results with quantitative trait locus data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near base-perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.
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Affiliation(s)
- Yann Bourgeois
- New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Christoph Stritt
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Jean-Claude Walser
- Genetic Diversity Centre, ETH Zürich, Universitätstrasse 16, Zurich, Switzerland
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anne C Roulin
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
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Wu Y, Ma X, Pan Z, Kale SD, Song Y, King H, Zhang Q, Presley C, Deng X, Wei CI, Xiao S. Comparative genome analyses reveal sequence features reflecting distinct modes of host-adaptation between dicot and monocot powdery mildew. BMC Genomics 2018; 19:705. [PMID: 30253736 PMCID: PMC6156980 DOI: 10.1186/s12864-018-5069-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/11/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Powdery mildew (PM) is one of the most important and widespread plant diseases caused by biotrophic fungi. Notably, while monocot (grass) PM fungi exhibit high-level of host-specialization, many dicot PM fungi display a broad host range. To understand such distinct modes of host-adaptation, we sequenced the genomes of four dicot PM biotypes belonging to Golovinomyces cichoracearum or Oidium neolycopersici. RESULTS We compared genomes of the four dicot PM together with those of Blumeria graminis f.sp. hordei (both DH14 and RACE1 isolates), B. graminis f.sp. tritici, and Erysiphe necator infectious on barley, wheat and grapevine, respectively. We found that despite having a similar gene number (6620-6961), the PM genomes vary from 120 to 222 Mb in size. This high-level of genome size variation is indicative of highly differential transposon activities in the PM genomes. While the total number of genes in any given PM genome is only about half of that in the genomes of closely related ascomycete fungi, most (~ 93%) of the ascomycete core genes (ACGs) can be found in the PM genomes. Yet, 186 ACGs were found absent in at least two of the eight PM genomes, of which 35 are missing in some dicot PM biotypes, but present in the three monocot PM genomes, indicating remarkable, independent and perhaps ongoing gene loss in different PM lineages. Consistent with this, we found that only 4192 (3819 singleton) genes are shared by all the eight PM genomes, the remaining genes are lineage- or biotype-specific. Strikingly, whereas the three monocot PM genomes possess up to 661 genes encoding candidate secreted effector proteins (CSEPs) with families containing up to 38 members, all the five dicot PM fungi have only 116-175 genes encoding CSEPs with limited gene amplification. CONCLUSIONS Compared to monocot (grass) PM fungi, dicot PM fungi have a much smaller effectorome. This is consistent with their contrasting modes of host-adaption: while the monocot PM fungi show a high-level of host specialization, which may reflect an advanced host-pathogen arms race, the dicot PM fungi tend to practice polyphagy, which might have lessened selective pressure for escalating an with a particular host.
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Affiliation(s)
- Ying Wu
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xianfeng Ma
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Changsha, 410128 China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shiv D. Kale
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Yi Song
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Harlan King
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Qiong Zhang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Christian Presley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cheng-I Wei
- College of Agriculture & Natural Resources, University of Maryland, College Park, MD 20742 USA
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
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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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11
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Comparative Methods for Molecular Determination of Host-Specificity Factors in Plant-Pathogenic Fungi. Int J Mol Sci 2018; 19:ijms19030863. [PMID: 29543717 PMCID: PMC5877724 DOI: 10.3390/ijms19030863] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/12/2018] [Accepted: 03/14/2018] [Indexed: 12/11/2022] Open
Abstract
Many plant-pathogenic fungi are highly host-specific. In most cases, host-specific interactions evolved at the time of speciation of the respective host plants. However, host jumps have occurred quite frequently, and still today the greatest threat for the emergence of new fungal diseases is the acquisition of infection capability of a new host by an existing plant pathogen. Understanding the mechanisms underlying host-switching events requires knowledge of the factors determining host-specificity. In this review, we highlight molecular methods that use a comparative approach for the identification of host-specificity factors. These cover a wide range of experimental set-ups, such as characterization of the pathosystem, genotyping of host-specific strains, comparative genomics, transcriptomics and proteomics, as well as gene prediction and functional gene validation. The methods are described and evaluated in view of their success in the identification of host-specificity factors and the understanding of their functional mechanisms. In addition, potential methods for the future identification of host-specificity factors are discussed.
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12
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Ben-David R, Dinoor A, Peleg Z, Fahima T. Reciprocal Hosts' Responses to Powdery Mildew Isolates Originating from Domesticated Wheats and Their Wild Progenitor. FRONTIERS IN PLANT SCIENCE 2018; 9:75. [PMID: 29527213 PMCID: PMC5829517 DOI: 10.3389/fpls.2018.00075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/15/2018] [Indexed: 03/14/2024]
Abstract
The biotroph wheat powdery mildew, Blumeria graminis (DC.) E.O. Speer, f. sp. tritici Em. Marchal (Bgt), has undergone long and dynamic co-evolution with its hosts. In the last 10,000 years, processes involved in plant evolution under domestication, altered host-population structure. Recently both virulence and genomic profiling separated Bgt into two groups based on their origin from domestic host and from wild emmer wheat. While most studies focused on the Bgt pathogen, there is significant knowledge gaps in the role of wheat host diversity in this specification. This study aimed to fill this gap by exploring qualitatively and also quantitatively the disease response of diverse host panel to powdery mildew [105 domesticated wheat genotypes (Triticum turgidum ssp. dicoccum, T. turgidum ssp. durum, and T. aestivum) and 241 accessions of its direct progenitor, wild emmer wheat (T. turgidum ssp. dicoccoides)]. A set of eight Bgt isolates, originally collected from domesticated and wild wheat was used for screening this wheat collection. The isolates from domesticated wheat elicited susceptible to moderate plant responses on domesticated wheat lines and high resistance on wild genotypes (51.7% of the tested lines were resistant). Isolates from wild emmer elicited reciprocal disease responses: high resistance of domesticated germplasm and high susceptibility of the wild material (their original host). Analysis of variance of the quantitative phenotypic responses showed a significant Isolates × Host species interaction [P(F) < 0.0001] and further supported these findings. Furthermore, analysis of the range of disease severity values showed that when the group of host genotypes was inoculated with Bgt isolate from the reciprocal host, coefficient of variation was significantly higher than when inoculated with its own isolates. This trend was attributed to the role of major resistance genes in the latter scenario (high proportion of complete resistance). By testing the association between disease severity and geographical distance from the source of inoculum, we have found higher susceptibility in wild emmer close to the source. Both qualitative and quantitative assays showed a reciprocal resistance pattern in the wheat host and are well aligned with the recent findings of significant differentiation into wild-emmer and domesticated-wheat populations in the pathogen.
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Affiliation(s)
- Roi Ben-David
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization-Volcani Center, Rishon LeZion, Israel
| | - Amos Dinoor
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Zvi Peleg
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of Evolution, University of Haifa, Haifa, Israel
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13
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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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14
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Gouveia MMC, Ribeiro A, Várzea VM, Rodrigues CJ. Genetic diversity inHemileia vastatrixbased on RAPD markers. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832815] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- M. Manuela C. Gouveia
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto de Investigação Científica Tropical, Quinta do Marquês, 2784-505 Oeiras, Portugal, and Departamento de Biologia, Centro de Estudos da Macaronésia, Universidade da Madeira, 9000-390 Funchal, Portugal
| | | | | | - Carlos J. Rodrigues
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto de Investigação Científica Tropical, Quinta do Marquês, 2784-505 Oeiras, Portugal
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15
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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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16
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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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17
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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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18
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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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19
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Gao YR, Han YT, Zhao FL, Li YJ, Cheng Y, Ding Q, Wang YJ, Wen YQ. Identification and utilization of a new Erysiphe necator isolate NAFU1 to quickly evaluate powdery mildew resistance in wild Chinese grapevine species using detached leaves. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 98:12-24. [PMID: 26590705 DOI: 10.1016/j.plaphy.2015.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/03/2015] [Accepted: 11/03/2015] [Indexed: 05/01/2023]
Abstract
The most economically important disease of cultivated grapevines worldwide is powdery mildew caused by the biotrophic fungal pathogen Erysiphe necator. To integrate effective genetic resistance into cultivated grapevines, numerous disease resistance screens of diverse Vitis germplasm, including wild species, have been conducted to identify powdery mildew resistance, but the results have been inconsistent. Here, a new powdery mildew isolate that is infectious on grapevines, designated Erysiphe necator NAFU1 (En. NAFU1), was identified and characterized by phylogeny inferred from the internal transcribed spacer (ITS) of pathogen ribosomal DNA sequences. Three classical methods were compared for the maintenance of En. NAFU1, and the most convenient method was maintenance on detached leaves and propagation by contact with infected leaves. Furthermore, controlled inoculations of En. NAFU1 were performed using detached leaves from 57 wild Chinese grapevine accessions to quickly evaluate powdery mildew resistance based on trypan blue staining of leaf sections. The results were compared with previous natural epidemics in the field. Among the screened accessions inoculated with En. NAFU1, 22.8% were resistant, 33.3% were moderately resistant, and 43.9% were susceptible. None of the accessions assessed herein were immune from infection. These results support previous findings documenting the presence of race-specific resistance to E. necator in wild Chinese grapevine. The resistance of wild Chinese grapevine to En. NAFU1 could be due to programmed cell death. The present results suggest that En. NAFU1 isolate could be used for future large-scale screens of resistance to powdery mildew in diverse Vitis germplasms and investigations of the interaction between grapevines and pathogens.
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Affiliation(s)
- Yu-Rong Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Yong-Tao Han
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Feng-Li Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Ya-Juan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Yuan Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Qin Ding
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Yue-Jin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China
| | - Ying-Qiang Wen
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China.
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Xia C, Zhang X, Christensen MJ, Nan Z, Li C. Epichloë endophyte affects the ability of powdery mildew (Blumeria graminis) to colonise drunken horse grass (Achnatherum inebrians). FUNGAL ECOL 2015. [DOI: 10.1016/j.funeco.2015.02.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cheng Y, Yao J, Zhang H, Huang L, Kang Z. Cytological and molecular analysis of nonhost resistance in rice to wheat powdery mildew and leaf rust pathogens. PROTOPLASMA 2015; 252:1167-1179. [PMID: 25547964 DOI: 10.1007/s00709-014-0750-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/15/2014] [Indexed: 06/04/2023]
Abstract
Cereal powdery mildews caused by Blumeria graminis and cereal rusts caused by Puccinia spp. are constant disease threats that limit the production of almost all important cereal crops. Rice is an intensively grown agricultural cereal that is atypical because of its immunity to all powdery mildew and rust fungi. We analyzed the nonhost interactions between rice and the wheat powdery mildew fungus B. graminis f. sp. tritici (Bgt) and the wheat leaf rust fungus Puccinia triticina (Ptr) to identify the basis of nonhost resistance (NHR) in rice against cereal powdery mildew and rust fungi at cytological and molecular levels. No visible symptoms were observed on rice leaves inoculated with Bgt or Ptr. Microscopic observations showed that both pathogens exhibited aberrant differentiation and significantly reduced penetration frequencies on rice compared to wheat. The development of Bgt and Ptr was also completely arrested at early infection stages in cases of successful penetration into rice leaves. Attempted infection of rice by Bgt and Ptr induced similar defense responses, including callose deposition, accumulation of reactive oxygen species, and hypersensitive response in rice epidermal and mesophyll cells, respectively. Furthermore, a set of defense-related genes were upregulated in rice against Bgt and Ptr infection. Rice is an excellent monocot model for genetic and molecular studies. Therefore, our results demonstrate that rice is a useful model to study the mechanisms of NHR to cereal powdery mildew and rust fungi, which provides useful information for the development of novel and durable strategies to control these important pathogens.
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Affiliation(s)
- Yulin Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
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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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Affiliation(s)
- Ralph Panstruga
- Unit of Plant Cell Biology, RWTH Aachen University, Worringerweg, 1, 52074, Aachen, Germany
| | - Pietro D Spanu
- Department of Life Sciences, Imperial College London, Imperial College Road, London, SW7 2AZ, UK
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Vela-Corcía D, Bellón-Gómez D, López-Ruiz F, Torés JA, Pérez-García A. The Podosphaera fusca TUB2 gene, a molecular “Swiss Army knife” with multiple applications in powdery mildew research. Fungal Biol 2014; 118:228-41. [DOI: 10.1016/j.funbio.2013.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/28/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
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Quecine MC, Bini AP, Romagnoli ER, Andreote FD, Moon DH, Labate CA. Genetic Variability in Puccinia psidii Populations as Revealed by PCR-DGGE and T-RFLP Markers. PLANT DISEASE 2014; 98:16-23. [PMID: 30708618 DOI: 10.1094/pdis-03-13-0332-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Eucalyptus rust caused by Puccinia psidii is responsible for losses of approximately 20% of young Eucalyptus plants, depending on the environmental conditions and the geographic location. Despite its economic importance, there are few studies describing the genetic variability in P. psidii populations that infect different host plants. In the present study, we evaluated the ribosomal DNA internal transcribed spacer region (rDNA-ITS) using polymerase chain reaction denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism to assess the genetic variability in P. psidii populations infecting different Eucalyptus spp. and hybrids, as well as guava, jabuticaba, and syzygium. These culture-independent methods were efficient in differentiating populations based on the host species from which they were collected. In general, the results from both techniques showed that the populations collected from guava, jabuticaba, and syzygium were different from and had a greater level of diversity than the Eucalyptus rust populations. The sequencing of cloned rDNA-ITS fragments confirmed that the vast majority of the profiles generated were from P. psidii. This analysis also revealed interesting single-nucleotide polymorphisms. Therefore, these culture-independent methods are suitable for the rapid assessment of genetic variability within and between populations of this biotrophic fungus on a variety of host species and could be a tool to study the evolution of this pathogen and its interactions with host plants.
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Affiliation(s)
| | | | | | | | - David Henry Moon
- Laboratory "Max Feffer" of Genetic of Plants, Department of Genetics, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, 13418-900, Piracicaba-SP, Brazil
| | - Carlos Alberto Labate
- Laboratory "Max Feffer" of Genetic of Plants, Department of Genetics, Escola Superior de Agricultura "Luiz de Queiroz", University of São Paulo, 13418-900, Piracicaba-SP, Brazil
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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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Dean R, Van Kan JAL, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD. The Top 10 fungal pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2012. [PMID: 22471698 DOI: 10.1111/j.1364-3703.2012.2011.00783.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.
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Affiliation(s)
- Ralph Dean
- Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27695, USA
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Dean R, Van Kan JAL, Pretorius ZA, Hammond-Kosack KE, Di Pietro A, Spanu PD, Rudd JJ, Dickman M, Kahmann R, Ellis J, Foster GD. The Top 10 fungal pathogens in molecular plant pathology. MOLECULAR PLANT PATHOLOGY 2012; 13:414-30. [PMID: 22471698 PMCID: PMC6638784 DOI: 10.1111/j.1364-3703.2011.00783.x] [Citation(s) in RCA: 2067] [Impact Index Per Article: 172.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.
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Affiliation(s)
- Ralph Dean
- Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27695, USA
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Abstract
Biotrophy is a pervasive trait that evolved independently in plant pathogenic fungi and oomycetes. Comparative genomics of the first sequenced biotrophic pathogens highlight remarkable convergences, including gene losses in the metabolism of inorganic nitrogen, inorganic sulfur, and thiamine, and genes encoding carbohydrate active enzymes and secondary metabolism enzymes. Some biotrophs, but not all, display marked increases in overall genome size because of a proliferation of retrotransposons. I argue here that the release of constraints on transposon activity is driven by the advantages conferred by the genetic variability that results from transposition, in particular by the creation and diversification of broad palettes of effector genes. Increases in genome size and gene losses are the consequences of this trade-off. Genes that are not necessary for growth on a plant disappeared, but we still do not know what lost functions make some of these pathogens obligate.
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Affiliation(s)
- Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom.
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30
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Oberhaensli S, Parlange F, Buchmann JP, Jenny FH, Abbott JC, Burgis TA, Spanu PD, Keller B, Wicker T. Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host-pathogen co-evolution. Fungal Genet Biol 2011; 48:327-34. [DOI: 10.1016/j.fgb.2010.10.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 09/29/2010] [Accepted: 10/06/2010] [Indexed: 12/24/2022]
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31
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Wen Y, Wang W, Feng J, Luo MC, Tsuda K, Katagiri F, Bauchan G, Xiao S. Identification and utilization of a sow thistle powdery mildew as a poorly adapted pathogen to dissect post-invasion non-host resistance mechanisms in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:2117-29. [PMID: 21193574 PMCID: PMC3060691 DOI: 10.1093/jxb/erq406] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 11/16/2010] [Accepted: 11/18/2010] [Indexed: 05/19/2023]
Abstract
To better dissect non-host resistance against haustorium-forming powdery mildew pathogens, a sow thistle powdery mildew isolate designated Golovinomyces cichoracearum UMSG1 that has largely overcome penetration resistance but is invariably stopped by post-invasion non-host resistance of Arabidopsis thaliana was identified. The post-invasion non-host resistance is mainly manifested as the formation of a callosic encasement of the haustorial complex (EHC) and hypersensitive response (HR), which appears to be controlled by both salicylic acid (SA)-dependent and SA-independent defence pathways, as supported by the susceptibility of the pad4/sid2 double mutant to the pathogen. While the broad-spectrum resistance protein RPW8.2 enhances post-penetration resistance against G. cichoracearum UCSC1, a well-adapted powdery mildew pathogen, RPW8.2, is dispensable for post-penetration resistance against G. cichoracearum UMSG1, and its specific targeting to the extrahaustorial membrane is physically blocked by the EHC, resulting in HR cell death. Taken together, the present work suggests an evolutionary scenario for the Arabidopsis-powdery mildew interaction: EHC formation is a conserved subcellular defence evolved in plants against haustorial invasion; well-adapted powdery mildew has evolved the ability to suppress EHC formation for parasitic growth and reproduction; RPW8.2 has evolved to enhance EHC formation, thereby conferring haustorium-targeted, broad-spectrum resistance at the post-invasion stage.
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Affiliation(s)
- Yingqiang Wen
- College of Horticulture and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- Institute for Bioscience and Biotechnology Research, University of Maryland, Shady Grove, Maryland, USA
| | - Wenming Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Shady Grove, Maryland, USA
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Jiayue Feng
- College of Horticulture and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
- Institute for Bioscience and Biotechnology Research, University of Maryland, Shady Grove, Maryland, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Kenichi Tsuda
- Department of Plant Biology, University of Minnesota, St Paul, Minnesota, USA
| | - Fumiaki Katagiri
- Department of Plant Biology, University of Minnesota, St Paul, Minnesota, USA
| | - Gary Bauchan
- Electron and Confocal Microscopy Unit, USDA-ARS, Beltsville, Maryland, USA
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Shady Grove, Maryland, USA
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, Maryland, USA
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Jordan T, Seeholzer S, Schwizer S, Töller A, Somssich IE, Keller B. The wheat Mla homologue TmMla1 exhibits an evolutionarily conserved function against powdery mildew in both wheat and barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:610-21. [PMID: 21208308 DOI: 10.1111/j.1365-313x.2010.04445.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The race-specific barley powdery mildew (Blumeria graminis f. sp. hordei) resistance gene Mla occurs as an allelic series and encodes CC-NB-LRR type resistance proteins. Inter-generic allele mining resulted in the isolation and characterisation of an Mla homologue from diploid wheat, designated TmMla1, which shares 78% identity with barley HvMLA1 at the protein level. TmMla1 was found to be a functional resistance gene against Blumeria graminis f. sp. tritici in wheat, hereby providing an example of R gene orthologs controlling the same disease in two different species. TmMLA1 exhibits race-specific resistance activity and its N-terminal coiled-coil domain interacts with the barley transcription factor HvWRKY1. Interestingly, TmMLA1 was not functional in barley transient assays. Replacement of the TmMLA1 LRR domain with that of HvMLA1 revealed that this fusion protein conferred resistance against B. graminis f. sp. hordei isolate K1 in barley. Thus, TmMLA1 not only confers resistance in wheat but possibly also in barley against an as yet unknown barley powdery mildew race. The conservation of functional R gene orthologs over at least 12 million years is surprising given the observed rapid breakdown of Mla-based resistance against barley mildew in agricultural ecosystems. This suggests a high stability of Mla resistance in the natural environment before domestication.
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Affiliation(s)
- Tina Jordan
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland.
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Hansjakob A, Bischof S, Bringmann G, Riederer M, Hildebrandt U. Very-long-chain aldehydes promote in vitro prepenetration processes of Blumeria graminis in a dose- and chain length-dependent manner. THE NEW PHYTOLOGIST 2010; 188:1039-54. [PMID: 20731784 DOI: 10.1111/j.1469-8137.2010.03419.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Surface properties of aerial plant organs have been shown to affect the interaction of fungal plant pathogens and their hosts. Conidial germination and differentiation - the so-called prepenetration processes - of the barley powdery mildew fungus (Blumeria graminis f. sp. hordei) are known to be triggered by n-hexacosanal (C(26)-aldehyde), a minor constituent of barley leaf wax. In order to analyze the differentiation-inducing capabilities of typical aldehyde wax constituents on conidia of wheat and barley powdery mildew, synthetic even-numbered very-long-chain aldehydes (C(22)-C(30)) were assayed, applying an in vitro system based on Formvar(®)/n-hexacosane-coated glass slides. n-Hexacosanal was the most effective aldehyde tested. Germination and differentiation rates of powdery mildew conidia increased with increasing concentrations of very-long-chain aldehydes. Relative to n-hexacosanal, the other aldehyde compounds showed a gradual decrease in germination- and differentiation-inducing capabilities with both decreasing and increasing chain length. In addition to n-hexacosanal, several other ubiquitous very-long-chain aldehyde wax constituents were capable of effectively stimulating B. graminis prepenetration processes in a dose- and chain length-dependent manner. Other wax constituents, such as n-alkanes, primary alcohols (with the exception of n-hexacosanol), fatty acids and alkyl esters, did not affect fungal prepenetration.
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Affiliation(s)
- Anton Hansjakob
- Universität Würzburg, Julius-von-Sachs-Institut für Biowissenschaften, Lehrstuhl für Botanik II, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany
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Brewer MT, Milgroom MG. Phylogeography and population structure of the grape powdery mildew fungus, Erysiphe necator, from diverse Vitis species. BMC Evol Biol 2010; 10:268. [PMID: 20809968 PMCID: PMC2941690 DOI: 10.1186/1471-2148-10-268] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 09/01/2010] [Indexed: 11/26/2022] Open
Abstract
Background The grape powdery mildew fungus, Erysiphe necator, was introduced into Europe more than 160 years ago and is now distributed everywhere that grapes are grown. To understand the invasion history of this pathogen we investigated the evolutionary relationships between introduced populations of Europe, Australia and the western United States (US) and populations in the eastern US, where E. necator is thought to be native. Additionally, we tested the hypothesis that populations of E. necator in the eastern US are structured based on geography and Vitis host species. Results We sequenced three nuclear gene regions covering 1803 nucleotides from 146 isolates of E. necator collected from the eastern US, Europe, Australia, and the western US. Phylogeographic analyses show that the two genetic groups in Europe represent two separate introductions and that the genetic groups may be derived from eastern US ancestors. Populations from the western US and Europe share haplotypes, suggesting that the western US population was introduced from Europe. Populations in Australia are derived from European populations. Haplotype richness and nucleotide diversity were significantly greater in the eastern US populations than in the introduced populations. Populations within the eastern US are geographically differentiated; however, no structure was detected with respect to host habitat (i.e., wild or cultivated). Populations from muscadine grapes, V. rotundifolia, are genetically distinct from populations from other Vitis host species, yet no differentiation was detected among populations from other Vitis species. Conclusions Multilocus sequencing analysis of the grape powdery mildew fungus is consistent with the hypothesis that populations in Europe, Australia and the western US are derived from two separate introductions and their ancestors were likely from native populations in the eastern US. The invasion history of E. necator follows a pattern consistent with plant-mediated dispersal, however, more exhaustive sampling is required to make more precise conclusions as to origin. E. necator shows no genetic structure across Vitis host species, except with respect to V. rotundifolia.
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Affiliation(s)
- Marin Talbot Brewer
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
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35
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Parks R, Carbone I, Murphy JP, Cowger C. Population genetic analysis of an Eastern U.S. wheat powdery mildew population reveals geographic subdivision and recent common ancestry with U.K. and Israeli populations. PHYTOPATHOLOGY 2009; 99:840-9. [PMID: 19522582 DOI: 10.1094/phyto-99-7-0840] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The structure of the U.S. wheat powdery mildew population (Blumeria graminis f. sp. tritici) has not been previously investigated, and the global evolutionary history of B. graminis f. sp. tritici is largely unknown. After gathering 141 single-ascosporic B. graminis f. sp. tritici isolates from 10 eastern U.S. locations, 34 isolates from the United Kingdom, and 28 isolates from Israel, we analyzed pathogen population structure using presumptively neutral markers. DNA was extracted from conidia, primers for 12 "housekeeping" genes were designed, and amplicons were examined for polymorphism. Four genes were found to contain a total of 12 single-nucleotide polymorphisms in the U.S. population and were also analyzed in the U.K. and Israeli populations. In total, 25 haplotypes were inferred from the four concatenated genes, with 2 haplotypes comprising over 70% of the U.S. population. Using Hudson's tests and analysis of molecular variance, we found the wheat mildew isolates subdivided into four groups corresponding to distinct regions: the mid-Atlantic United States, the southern United States, the United Kingdom, and Israel. Genotypic diversity was greatest in samples from the United Kingdom, Israel, Virginia, and Kingston, NC. Using rarefaction, a procedure that compensates for differing sample sizes when estimating population richness and diversity, we found that cooler locations with greater conduciveness to regular powdery mildew epidemics had the greatest haplotype richness. Our results suggest that the eastern U.S. B. graminis f. sp. tritici population is young, descended recently from Old World populations with isolation and genetic drift, and is currently subdivided into northern and southern subpopulations.
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Affiliation(s)
- Ryan Parks
- Department of Plant Pathology, United States Department of Agriculture-Agricultural Research Service, North Carolina State University, Raleigh, NC 27695, USA.
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Gril T, Celar F, Munda A, Javornik B, Jakse J. AFLP Analysis of Intraspecific Variation Between Monilinia laxa Isolates from Different Hosts. PLANT DISEASE 2008; 92:1616-1624. [PMID: 30764293 DOI: 10.1094/pdis-92-12-1616] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We analyzed with an amplified fragment length polymorphism (AFLP) marker system the genetic diversity and relationships among 67 Monilinia laxa isolates obtained from different host plants. From a total of 1,089 amplified bands scored using 20 primer combinations with two selective nucleotides, 354 were polymorphic and further used in genetic diversity analysis. Genetic relationships among isolates were assessed with different phenetic approaches, including unweighted pair group method with arithmetic mean clustering and principal coordinate analysis; the population's differentiation estimate was analyzed by molecular variance; and model-based clustering was employed to infer population structure. All four analyses clearly showed significant differences between isolates from apple trees and isolates from other host plants. No further grouping according to any other host plant was observed. The results indicate host specialization of apple isolates and support the taxonomic grouping of apple isolates.
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Affiliation(s)
- Tjasa Gril
- Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Franci Celar
- Entomology and Phytopathology, Biotechnical Faculty, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Alenka Munda
- Plant Protection Department, Agricultural Institute of Slovenia, Hacquetova 17, 1000 Ljubljana, Slovenia
| | - Branka Javornik
- Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Jernej Jakse
- Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
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Jankovics T, Bai Y, Kovács GM, Bardin M, Nicot PC, Toyoda H, Matsuda Y, Niks RE, Kiss L. Oidium neolycopersici: intraspecific variability inferred from amplified fragment length polymorphism analysis and relationship with closely related powdery mildew fungi infecting various plant species. PHYTOPATHOLOGY 2008; 98:529-540. [PMID: 18943220 DOI: 10.1094/phyto-98-5-0529] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Previous works indicated a considerable variation in the pathogenicity, virulence, and host range of Oidium neolycopersici isolates causing tomato powdery mildew epidemics in many parts of the world. In this study, rDNA internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) patterns were analyzed in 17 O. neolycopersici samples collected in Europe, North America, and Japan, including those which overcame some of the tomato major resistance genes. The ITS sequences were identical in all 10 samples tested and were also identical to ITS sequences of eight previously studied O. neolycopersici specimens. The AFLP analysis revealed a high genetic diversity in O. neolycopersici and indicated that all 17 samples represented different genotypes. This might suggest the existence of either a yet unrevealed sexual reproduction or other genetic mechanisms that maintain a high genetic variability in O. neolycopersici. No clear correlation was found between the virulence and the AFLP patterns of the O. neolycopersici isolates studied. The relationship between O. neolycopersici and powdery mildew anamorphs infecting Aquilegia vulgaris, Chelidonium majus, Passiflora caerulea, and Sedum alboroseum was also investigated. These anamorphs are morphologically indistinguishable from and phylogenetically closely related to O. neolycopersici. The cross-inoculation tests and the analyses of ITS sequences and AFLP patterns jointly indicated that the powdery mildew anamorphs collected from the above mentioned plant species all represent distinct, but closely related species according to the phylogenetic species recognition. All these species were pathogenic only to their original host plant species, except O. neolycopersici which infected S. alboroseum, tobacco, petunia, and Arabidopsis thaliana, in addition to tomato, in cross-inoculation tests. This is the first genome-wide study that investigates the relationships among powdery mildews that are closely related based on ITS sequences and morphology. The results indicate that morphologically indistinguishable powdery mildews that differed in only one to five single nucleotide positions in their ITS region are to be considered as different taxa with distinct host ranges.
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Affiliation(s)
- T Jankovics
- Plant Protection Institute of the Hungarian Academy of Sciences, H-1525 Budapest, P.O. Box 102, Hungary
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Zaffarano PL, McDonald BA, Linde CC. Rapid speciation following recent host shifts in the plant pathogenic fungus Rhynchosporium. Evolution 2008; 62:1418-36. [PMID: 18384659 DOI: 10.1111/j.1558-5646.2008.00390.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Agriculture played a significant role in increasing the number of pathogen species and in expanding their geographic range during the last 10,000 years. We tested the hypothesis that a fungal pathogen of cereals and grasses emerged at the time of domestication of cereals in the Fertile Crescent and subsequently speciated after adaptation to its hosts. Rhynchosporium secalis, originally described from rye, causes an important disease on barley called scald, although it also infects other species of Hordeum and Agropyron. Phylogenetic analyses based on four DNA sequence loci identified three host-associated lineages that were confirmed by cross-pathogenicity tests. Bayesian analyses of divergence time suggested that the three lineages emerged between approximately 1200 to 3600 years before present (B.P.) with a 95% highest posterior density ranging from 100 to 12,000 years B.P. depending on the implemented clock models. The coalescent inference of demographic history revealed a very recent population expansion for all three pathogens. We propose that Rhynchosporium on barley, rye, and Agropyron host species represent three cryptic pathogen species that underwent independent evolution and ecological divergence by host-specialization. We postulate that the recent emergence of these pathogens followed host shifts. The subsequent population expansions followed the expansion of the cultivated host populations and accompanying expansion of the weedy Agropyron spp. found in fields of cultivated cereals. Hence, agriculture played a major role in the emergence of the scald diseases, the adaptation of the pathogens to new hosts and their worldwide dissemination.
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Affiliation(s)
- Pascal L Zaffarano
- Plant Pathology, Institute of Integrative Biology, ETH-Zurich, LFW, CH-8092 Zürich, Switzerland.
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Le Gac M, Giraud T. Existence of a pattern of reproductive character displacement in Homobasidiomycota but not in Ascomycota. J Evol Biol 2008; 21:761-72. [PMID: 18312316 DOI: 10.1111/j.1420-9101.2008.01511.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Generally, stronger reproductive isolation is expected between sympatric than between allopatric sibling species. Such reproductive character displacement should predominantly affect premating reproductive isolation and can be due to several mechanisms, including population extinction, fusion of insufficiently isolated incipient species and reinforcement of reproductive isolation in response to low hybrid fitness. Experimental data on several taxa have confirmed these theoretical expectations on reproductive character displacement, but they are restricted to animals and a few plants. Using results reported in the literature on crossing experiments in fungi, we compared the degree and the nature of reproductive isolation between allopatric and sympatric species pairs. In accordance with theoretical expectations, we found a pattern of enhanced premating isolation among sympatric sibling species in Homobasidiomycota. By contrast, we did not find evidence for reproductive character displacement in Ascomycota at similar genetic distances. Both allopatric and sympatric species of Ascomycota had similarly low levels of reproductive isolation, being mostly post-zygotic. This suggests that some phylogeny-dependent life-history trait may strongly influence the evolution of reproductive isolation between closely related species. A significant correlation was found between degree of reproductive isolation and genetic divergence among allopatric species of Homobasidiomycota, but not among sympatric ones or among Ascomycota species.
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Affiliation(s)
- M Le Gac
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud, UMR 8079, Orsay cedex, France.
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Glawe DA. The powdery mildews: a review of the world's most familiar (yet poorly known) plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2008; 46:27-51. [PMID: 18680422 DOI: 10.1146/annurev.phyto.46.081407.104740] [Citation(s) in RCA: 200] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The past decade has seen fundamental changes in our understanding of powdery mildews (Erysiphales). Research on molecular phylogeny demonstrated that Erysiphales are Leotiomycetes (inoperculate discomycetes) rather than Pyrenomycetes or Plectomycetes. Life cycles are surprisingly variable, including both sexual and asexual states, or only sexual states, or only asexual states. At least one species produces dematiaceous conidia. Analyses of rDNA sequences indicate that major lineages are more closely correlated with anamorphic features such as conidial ontogeny and morphology than with teleomorph features. Development of molecular clock models is enabling researchers to reconstruct patterns of coevolution and host-jumping, as well as ancient migration patterns. Geographic distributions of some species appear to be increasing rapidly but little is known about species diversity in many large areas, including North America. Powdery mildews may already be responding to climate change, suggesting they may be useful models for studying effects of climate change on plant diseases.
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Affiliation(s)
- Dean A Glawe
- Department of Plant Pathology, Washington State University and College of Forest Resources, University of Washington, Seattle 98195, USA.
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Stukenbrock EH, McDonald BA. The origins of plant pathogens in agro-ecosystems. ANNUAL REVIEW OF PHYTOPATHOLOGY 2008; 46:75-100. [PMID: 18680424 DOI: 10.1146/annurev.phyto.010708.154114] [Citation(s) in RCA: 326] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant pathogens can emerge in agricultural ecosystems through several mechanisms, including host-tracking, host jumps, hybridization and horizontal gene transfer. High-throughput DNA sequencing coupled with new analytical approaches make it possible to differentiate among these mechanisms and to infer the time and place where pathogens first emerged. We present several examples to illustrate the different mechanisms and timescales associated with the origins of important plant pathogens. In some cases pathogens were domesticated along with their hosts during the invention of agriculture approximately 10,000 years ago. In other cases pathogens appear to have emerged very recently and almost instantaneously following horizontal gene transfer or hybridization. The predominant unifying feature in these examples is the environmental and genetic uniformity of the agricultural ecosystem in which the pathogens emerged. We conclude that agro-ecosystems will continue to select for new pathogens unless they are re-engineered to make them less conducive to pathogen emergence.
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Affiliation(s)
- Eva H Stukenbrock
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, CH-8092 Zurich, Switzerland.
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Francis SA, Roden BC, Adams MJ, Weiland J, Asher MJC. Comparison of ITS sequences from UK and North American sugar-beet powdery mildews and the designation of Erysiphe betae. ACTA ACUST UNITED AC 2007; 111:204-12. [PMID: 17324758 DOI: 10.1016/j.mycres.2006.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Revised: 08/28/2006] [Accepted: 10/07/2006] [Indexed: 11/24/2022]
Abstract
Powdery mildew of sugar beet, a disease of major economic significance, was first described at the beginning of the 20th century, and since then there has been some confusion over the correct taxonomic identity of the causal agent. In Europe, the fungus was initially classified as the novel species Microsphaera betae, later re-named Erysiphe betae, whilst in America it was identified as E. polygoni, despite sugar-beet isolates from both regions having a host range restricted to Beta species. It is possible that more than one fungus causes the disease, as published descriptions of conidiogenesis have differed. In this study, isolates of the fungus collected from sugar beet in the UK and USA were investigated for polymorphisms in the rDNA ITS region to determine if the same species caused the disease in both countries, whether there was any justification for the retention of the name E. polygoni in the USA, and to search for evidence of a second species infecting sugar beet. From a total of 18 isolates examined, 23 ITS sequences were obtained. Fifteen of these, which included the UK and USA isolates, were identical and the remainder had single-base substitutions, indicating that the fungi were conspecific. Dendrogram analysis of Erysiphales ITS regions revealed that the UK and North American isolates were more closely related to E. heraclei than to E. polygoni. It is proposed that the species name Erysiphe betae be used for the powdery mildew fungus that infects sugar beet. No evidence was found in this study for a second sugar-beet powdery mildew species.
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Affiliation(s)
- Sally A Francis
- Broom's Barn Research Station, Higham, Bury St Edmunds, Suffolk, UK
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Inuma T, Khodaparast SA, Takamatsu S. Multilocus phylogenetic analyses within Blumeria graminis, a powdery mildew fungus of cereals. Mol Phylogenet Evol 2007; 44:741-51. [PMID: 17346991 DOI: 10.1016/j.ympev.2007.01.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 11/14/2006] [Accepted: 01/15/2007] [Indexed: 10/23/2022]
Abstract
Blumeria graminis, a powdery mildew fungus, is an important plant pathogen that causes serious damage to a variety of cereal crops. In spite of the importance of the pathogen, information on phylogenetic structure within B. graminis is scarce. In this study we conducted phylogenetic analyses of B. graminis based on the DNA sequences of four different DNA regions (ITS, 28S rDNA, chitin synthase 1, and beta-tubulin). The analyses revealed that the protein-coding regions have higher amounts of phylogenetic signals than rDNA regions and are useful for phylogenetic analyses of B. graminis. The present phylogenetic analyses revealed nine distinct groups in the B. graminis isolates used in this study, a result which was commonly supported by all trees constructed from the four DNA regions. Isolates from a single host genus belonged to a single group except for isolates from Lolium and Bromus, in which the isolates were split into two and three groups, respectively. Isolates from Agropyron, Secale and Triticum formed a distinct clade (Triticum clade) with identical or similar DNA sequences. The Hordeum clade was a sister of the Triticum clade, and Poa and Avena clades were distantly related to the Triticum and Hordeum clades. This phylogenetic relationship of B. graminis is well concordant with the level of reproductive isolation between formae speciales and also with phylogeny inferred from a cytological study. Shimodaira-Hasegawa and Templeton tests using sequences of four different DNA regions significantly rejected the tree topology of plants. Therefore, possibility of co-speciation between B. graminis and its host plants was obscure in this study.
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Affiliation(s)
- Takashi Inuma
- Faculty of Bioresources, Mie University, 1577 Kurima-Machiya, Tsu 514-8507, Japan
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Sicard D, Pennings PS, Grandclément C, Acosta J, Kaltz O, Shykoff JA. SPECIALIZATION AND LOCAL ADAPTATION OF A FUNGAL PARASITE ON TWO HOST PLANT SPECIES AS REVEALED BY TWO FITNESS TRAITS. Evolution 2007; 61:27-41. [PMID: 17300425 DOI: 10.1111/j.1558-5646.2007.00003.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the geographic pattern of adaptation of a fungal parasite, Colletotrichum lindemuthianum, on two host species, Phaseolus vulgaris and P. coccineus for two parasite fitness traits: infectivity (ability to attack a host individual) and aggressivity (degree of sporulation and leaf surface damage). Using a cross-inoculation experiment, we show specialization of the fungus on its host species of origin for both traits even when fungi, which originated from hosts growing in sympatry, were tested on sympatric host populations. Within the two host species, we compared infectivity and aggressivity on local versus allopatric plant-fungus combinations. We found evidence for local adaptation for the two traits on P. vulgaris but not on P. coccineus. There was no significant correlation between the degrees of local adaptation for infectivity and aggressivity, indicating that the genetic basis and the effect of selection may differ between these two traits. For the two fitness traits, a positive correlation between the degree of specialization and the degree of local adaptation was found, suggesting that specialization can be reinforced by local adaptation.
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Affiliation(s)
- Delphine Sicard
- Univ Paris-Sud, Laboratoire Ecologie Systématique et Evolution, UMR 8079, Orsay cedex, France.
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Jafary H, Szabo LJ, Niks RE. Innate nonhost immunity in barley to different heterologous rust fungi is controlled by sets of resistance genes with different and overlapping specificities. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2006; 19:1270-9. [PMID: 17073309 DOI: 10.1094/mpmi-19-1270] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We developed an evolutionary relevant model system, barley-Puccinia [corrected] rust fungi, to study the inheritance and specificity of plant factors that determine to what extent innate nonhost immunity can be suppressed. A mapping population was developed from a cross between an experimental barley line (SusPtrit) [corrected] with exceptional susceptibility to several heterologous [corrected] (nonhost) rust fungi and regular, immune, cv. Vada [corrected] Seedlings were inoculated with five heterologous [corrected] and two homologous (host) species of rust fungi. Resistance segregated quantitatively for each of the rust fungi. In total, 18 chromosomal regions were implicated. For each rust species, a different set of genes was effective. Of the 18 chromosomal regions, 11 were significantly effective to only one rust species and 7 were effective to more than one rust species, implying genetic linkage or pleiotropy. One resistance (R) gene for hypersensitive resistance to Puccinia hordei-secalini was mapped, suggesting occasional contribution of R genes to nonhost resistance in barley. Quantitative trait loci (QTLs) with effects to multiple rust fungi did not tend to be particularly effective to rust species that were phylogenetically related, as determined from their internal transcribed spacer sequence. We suggest that the QTLs described here play a role as specific and quantitative recognition factors that are specifically negated by the rust to successfully suppress innate immunity.
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Affiliation(s)
- Hossein Jafary
- Department of Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
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Kiss L, Khosla K, Jankovics T, Niinomi S, Braun U, Takamatsu S. A morphologically ill-founded powdery mildew species, Pleochaeta indica, is recognized as a phylogenetic species based on the analysis of the nuclear ribosomal DNA sequences. ACTA ACUST UNITED AC 2006; 110:1301-8. [PMID: 17070029 DOI: 10.1016/j.mycres.2006.07.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2006] [Accepted: 07/26/2006] [Indexed: 11/24/2022]
Abstract
Morphological characteristics of a powdery mildew fungus found on Celtis australis in the Indian Himalayas coincided with those of Pleochaeta indica, described from this tree species in India, as well with those of P. shiraiana, known to infect C. australis and other plant species in Asia. This suggested that the original description of P. indica based on morphological patterns was not well founded and this taxon could be reduced to synonymy with P. shiraiana. However, phylogenetic analyses of the rDNA 28S and ITS sequences determined in some Indian Pleochaeta specimens from C. australis showed that this fungus is closely related, but not identical to P. shiraiana infecting C. sinensis in Japan which served as the basis of the original description of P. shiraiana. Molecular clock analysis of the ITS region and that of the 28S rDNA indicated that the split between the Japanese P. shiraiana infecting C. sinensis and Pleochaeta sp. infecting C. australis in India may have occurred 2.0-8.5 million years ago in the Pliocene and may have coincided with the formation of the Himalayan mountains and the global cooling of the Earth during the late Tertiary. Thus, P. indica is recognized in this study as a distinct phylogenetic species, although our morphological study showed that its description as a morphological species was not well founded. This is a striking example of a cryptic species which is genetically different from close relatives but cannot be distinguished from them based on morphology.
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Affiliation(s)
- Levente Kiss
- Plant Protection Institute, Hungarian Academy of Sciences, H-1525 Budapest, P.O. Box 102, Hungary.
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Wyand RA, Brown JKM. Sequence variation in the CYP51 gene of Blumeria graminis associated with resistance to sterol demethylase inhibiting fungicides. Fungal Genet Biol 2005; 42:726-35. [PMID: 15916909 DOI: 10.1016/j.fgb.2005.04.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 04/12/2005] [Accepted: 04/12/2005] [Indexed: 10/25/2022]
Abstract
Resistance to sterol 14alpha-demethylase inhibiting fungicides (DMIs) has been correlated with mutations in the CYP51 gene, which encodes the target enzyme eburicol 14alpha-demethylase. To test the hypothesis that variation in the CYP51 gene explains variation for DMI sensitivity in barley and wheat powdery mildew species, this gene was sequenced from isolates of Blumeria graminis f.sp. hordei (Bgh) and f.sp. tritici (Bgt), respectively, which differed in their responses to DMIs in agricultural populations in the UK. Two single-nucleotide mutations in the CYP51 gene, which resulted in the amino acid substitutions Y136F and K147Q, were detected. K147Q is a novel mutation present only in Bgh isolates expressing very high levels of resistance. Sequence analysis of the CYP51 gene from the progeny of a cross between DMI-sensitive and resistant Bgh isolates showed that both mutations segregate with resistance, which is consistent with CYP51 controlling a major portion of DMI resistance. However, genetic analysis of resistance to the DMI triadimenol indicates that mutation of the CYP51 gene is not the only mechanism of resistance operating in B. graminis.
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Affiliation(s)
- R A Wyand
- Department of Disease and Stress Biology, John Innes Centre, Colney Lane, Norwich, Norfolk NR4 7UH, UK.
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Abstract
AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment of fragments, (c) asymmetry in the probability of losing and gaining fragments, and (d) problems in distinguishing heterozygote from homozygote bands. In the present study, AFLP data sets of Lactuca s.l. were examined for the presence of phylogenetic signal. An indication of this signal was provided by carrying out tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA). A measure of the support for internal branches in the optimal parsimony tree (MPT) was made using bootstrap, jackknife, and decay analysis. Finally, the extent of congruence in MPTs for AFLP and internal transcribed spacer (ITS)-1 data sets for the same taxa was made using the partition homogeneity test (PHT) and the Templeton test. These analytical studies suggested the presence of phylogenetic signal in the AFLP data sets, although some incongruence was found between AFLP and ITS MPTs. An extensive literature survey undertaken indicated that authors report a general congruence of AFLP and ITS tree topologies across a wide range of taxonomic groups, suggesting that the present results and conclusions have a general bearing. In these earlier studies and those for Lactuca s.l., AFLP markers have been found to be informative at somewhat lower taxonomic levels than ITS sequences. Tentative estimates are suggested for the levels of ITS sequence divergence over which AFLP profiles are likely to be phylogenetically informative.
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Affiliation(s)
- Wim J M Koopman
- Biosystematics Group, Nationaal Herbarium Nederland-, Wageningen University branch, Wageningen University, Generaal Foulkesweg 37, 6703BL, Wageningen, The Netherlands.
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Cunnington JH, Lawrie AC, Pascoe IG. Genetic variation within Podosphaera tridactyla reveals a paraphyletic species complex with biological specialization towards specific Prunus subgenera. ACTA ACUST UNITED AC 2005; 109:357-62. [PMID: 15912953 DOI: 10.1017/s0953756204002072] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Podosphaera tridactyla (Ascomycota: Erysiphales) is a morphologically variable species occurring on Prunus s. lat. In order to assess the genetic variation within this species, the rDNA ITS region was amplified from 29 specimens from a range of Prunus species collected in Australia, Switzerland, and Korea. RFLP analysis of the PCR products revealed six groups, and a comparison of sequences from representatives of these groups revealed three clades: Clade I contained all specimens from Prunus subgen. Prunus; Clade 2 specimens from a variety of Prunus subgenera, except subgen. Prunus, and Podosphaera longiseta was closely allied to this clade; and Clade 3 contained two specimens, from Japan and Korea. Phylogenetic analysis comparing P. tridactyla with of a range of Podosphaera species suggests that P. tridactyla is paraphyletic.
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Affiliation(s)
- James H Cunnington
- Department of Primary Industries, Knoxfield Centre, Private Bag 15, Ferntree Gully Delivery Centre, Victoria 3156, Australia.
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