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Masaki HI, de Villiers S, Qi P, Prado KA, Kaimenyi DK, Tesfaye K, Alemu T, Takan J, Dida M, Ringo J, Mbinda W, Khang CH, Devos KM. Host Specificity Controlled by PWL1 and PWL2 Effector Genes in the Finger Millet Blast Pathogen Magnaporthe oryzae in Eastern Africa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:584-591. [PMID: 37245238 DOI: 10.1094/mpmi-01-23-0012-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Magnaporthe oryzae, a devastating pathogen of finger millet (Eleusine coracana), secretes effector molecules during infection to manipulate host immunity. This study determined the presence of avirulence effector genes PWL1 and PWL2 in 221 Eleusine blast isolates from eastern Africa. Most Ethiopian isolates carried both PWL1 and PWL2. Kenyan and Ugandan isolates largely lacked both genes, and Tanzanian isolates carried either PWL1 or lacked both. The roles of PWL1 and PWL2 towards pathogenicity on alternative chloridoid hosts, including weeping lovegrass (Eragrostis curvula), were also investigated. PWL1 and PWL2 were cloned from Ethiopian isolate E22 and were transformed separately into Ugandan isolate U34, which lacked both genes. Resulting transformants harboring either gene gained varying degrees of avirulence on Eragrostis curvula but remained virulent on finger millet. Strains carrying one or both PWL1 and PWL2 infected the chloridoid species Sporobolus phyllotrichus and Eleusine tristachya, indicating the absence of cognate resistance (R) genes for PWL1 and PWL2 in these species. Other chloridoid grasses, however, were fully resistant, regardless of the presence of one or both PWL1 and PWL2, suggesting the presence of effective R genes against PWL and other effectors. Partial resistance in some Eragrostis curvula accessions to some blast isolates lacking PWL1 and PWL2 also indicated the presence of other interactions between fungal avirulence (AVR) genes and host resistance (R) genes. Related chloridoid species thus harbor resistance genes that could be useful to improve finger millet for blast resistance. Conversely, loss of AVR genes in the fungus could expand its host range, as demonstrated by the susceptibility of Eragrostis curvula to finger millet blast isolates that had lost PWL1 and PWL2. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Hosea Isanda Masaki
- Pwani University, Department of Biochemistry and Biotechnology, Kilifi, Kenya
| | - Santie de Villiers
- Pwani University, Department of Biochemistry and Biotechnology, Kilifi, Kenya
- Pwani University Biosciences Research Centre (PUBReC), Kilifi, Kenya
| | - Peng Qi
- University of Georgia, Department of Plant Biology, Athens, GA 30602, U.S.A
- Institute of Plant Breeding, Genetics and Genomics Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, U.S.A
| | - Kathryn A Prado
- University of Georgia, Department of Plant Biology, Athens, GA 30602, U.S.A
| | - Davies Kiambi Kaimenyi
- Pwani University, Department of Biochemistry and Biotechnology, Kilifi, Kenya
- Pwani University Biosciences Research Centre (PUBReC), Kilifi, Kenya
| | - Kassahun Tesfaye
- Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | | | - John Takan
- National Semi-Arid Resources Research Institute Serere, Soroti, Uganda
| | | | - Justin Ringo
- Tanzania Agricultural Research Institute, Illonga, Tanzania
| | - Wilton Mbinda
- Pwani University, Department of Biochemistry and Biotechnology, Kilifi, Kenya
| | - Chang Hyun Khang
- University of Georgia, Department of Plant Biology, Athens, GA 30602, U.S.A
| | - Katrien M Devos
- University of Georgia, Department of Plant Biology, Athens, GA 30602, U.S.A
- Institute of Plant Breeding, Genetics and Genomics Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, U.S.A
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Approaches to Reduce Rice Blast Disease Using Knowledge from Host Resistance and Pathogen Pathogenicity. Int J Mol Sci 2023; 24:ijms24054985. [PMID: 36902415 PMCID: PMC10003181 DOI: 10.3390/ijms24054985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/23/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Rice is one of the staple foods for the majority of the global population that depends directly or indirectly on it. The yield of this important crop is constantly challenged by various biotic stresses. Rice blast, caused by Magnaporthe oryzae (M. oryzae), is a devastating rice disease causing severe yield losses annually and threatening rice production globally. The development of a resistant variety is one of the most effective and economical approaches to control rice blast. Researchers in the past few decades have witnessed the characterization of several qualitative resistance (R) and quantitative resistance (qR) genes to blast disease as well as several avirulence (Avr) genes from the pathogen. These provide great help for either breeders to develop a resistant variety or pathologists to monitor the dynamics of pathogenic isolates, and ultimately to control the disease. Here, we summarize the current status of the isolation of R, qR and Avr genes in the rice-M. oryzae interaction system, and review the progresses and problems of these genes utilized in practice for reducing rice blast disease. Research perspectives towards better managing blast disease by developing a broad-spectrum and durable blast resistance variety and new fungicides are also discussed.
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CRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae. Nat Commun 2022; 13:7168. [PMID: 36418866 PMCID: PMC9684475 DOI: 10.1038/s41467-022-34736-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
CRISPR-Cas mediated genome engineering has revolutionized functional genomics. However, understanding of DNA repair following Cas-mediated DNA cleavage remains incomplete. Using Cas12a ribonucleoprotein genome editing in the fungal pathogen, Magnaporthe oryzae, we detail non-canonical DNA repair outcomes from hundreds of transformants. Sanger and nanopore sequencing analysis reveals significant variation in DNA repair profiles, ranging from small INDELs to kilobase size deletions and insertions. Furthermore, we find the frequency of DNA repair outcomes varies between loci. The results are not specific to the Cas-nuclease or selection procedure. Through Ku80 deletion analysis, a key protein required for canonical non-homologous end joining, we demonstrate activity of an alternative end joining mechanism that creates larger DNA deletions, and uses longer microhomology compared to C-NHEJ. Together, our results suggest preferential DNA repair pathway activity in the genome that can create different mutation profiles following repair, which could create biased genome variation and impact genome engineering and genome evolution.
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:6638986. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Corresponding author: 1712 Claflin Road, 4004 Throckmorton Hall, Manhattan, KS 66502, United States. E-mail:
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Ngou BPM, Ding P, Jones JDG. Thirty years of resistance: Zig-zag through the plant immune system. THE PLANT CELL 2022; 34:1447-1478. [PMID: 35167697 PMCID: PMC9048904 DOI: 10.1093/plcell/koac041] [Citation(s) in RCA: 255] [Impact Index Per Article: 127.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/02/2022] [Indexed: 05/05/2023]
Abstract
Understanding the plant immune system is crucial for using genetics to protect crops from diseases. Plants resist pathogens via a two-tiered innate immune detection-and-response system. The first plant Resistance (R) gene was cloned in 1992 . Since then, many cell-surface pattern recognition receptors (PRRs) have been identified, and R genes that encode intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) have been cloned. Here, we provide a list of characterized PRRs and NLRs. In addition to immune receptors, many components of immune signaling networks were discovered over the last 30 years. We review the signaling pathways, physiological responses, and molecular regulation of both PRR- and NLR-mediated immunity. Recent studies have reinforced the importance of interactions between the two immune systems. We provide an overview of interactions between PRR- and NLR-mediated immunity, highlighting challenges and perspectives for future research.
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Affiliation(s)
| | - Pingtao Ding
- Author for correspondence: (B.P.M.N.); (P.D.); (J.J.)
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Hu ZJ, Huang YY, Lin XY, Feng H, Zhou SX, Xie Y, Liu XX, Liu C, Zhao RM, Zhao WS, Feng CH, Pu M, Ji YP, Hu XH, Li GB, Zhao JH, Zhao ZX, Wang H, Zhang JW, Fan J, Li Y, Peng YL, He M, Li DQ, Huang F, Peng YL, Wang WM. Loss and Natural Variations of Blast Fungal Avirulence Genes Breakdown Rice Resistance Genes in the Sichuan Basin of China. FRONTIERS IN PLANT SCIENCE 2022; 13:788876. [PMID: 35498644 PMCID: PMC9040519 DOI: 10.3389/fpls.2022.788876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 03/10/2022] [Indexed: 05/11/2023]
Abstract
Magnaporthe oryzae is the causative agent of rice blast, a devastating disease in rice worldwide. Based on the gene-for-gene paradigm, resistance (R) proteins can recognize their cognate avirulence (AVR) effectors to activate effector-triggered immunity. AVR genes have been demonstrated to evolve rapidly, leading to breakdown of the cognate resistance genes. Therefore, understanding the variation of AVR genes is essential to the deployment of resistant cultivars harboring the cognate R genes. In this study, we analyzed the nucleotide sequence polymorphisms of eight known AVR genes, namely, AVR-Pita1, AVR-Pii, AVR-Pia, AVR-Pik, AVR-Pizt, AVR-Pi9, AVR-Pib, and AVR-Pi54 in a total of 383 isolates from 13 prefectures in the Sichuan Basin. We detected the presence of AVR-Pik, AVR-Pi54, AVR-Pizt, AVR-Pi9, and AVR-Pib in the isolates of all the prefectures, but not AVR-Pita1, AVR-Pii, and AVR-Pia in at least seven prefectures, indicating loss of the three AVRs. We also detected insertions of Pot3, Mg-SINE, and indels in AVR-Pib, solo-LTR of Inago2 in AVR-Pizt, and gene duplications in AVR-Pik. Consistently, the isolates that did not harboring AVR-Pia were virulent to IRBLa-A, the monogenic line containing Pia, and the isolates with variants of AVR-Pib and AVR-Pizt were virulent to IRBLb-B and IRBLzt-t, the monogenic lines harboring Pib and Piz-t, respectively, indicating breakdown of resistance by the loss and variations of the avirulence genes. Therefore, the use of blast resistance genes should be alarmed by the loss and nature variations of avirulence genes in the blast fungal population in the Sichuan Basin.
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Affiliation(s)
- Zi-Jin Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yan-Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Yan-Yan Huang
| | - Xiao-Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Hui Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Shi-Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ying Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xin-Xian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Chen Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ru-Meng Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Wen-Sheng Zhao
- State Key Laboratory of Agrobiotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Chuan-Hong Feng
- Plant Protection Station, Department of Agriculture Sichuan Province, Chengdu, China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yun-Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Hong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Guo-Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jing-Hao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhi-Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ji-Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yun-Liang Peng
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - De-Qiang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Fu Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - You-Liang Peng
- State Key Laboratory of Agrobiotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Wen-Ming Wang
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7
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Thwin PH, Funabiki M, Tomita Y, Yamazaki T, Abe A, Sone T. Characterization and proposed spontaneous deletion mechanism of AVR-Pik locus in Pyricularia oryzae. Biosci Biotechnol Biochem 2021; 85:2217-2220. [PMID: 34387309 DOI: 10.1093/bbb/zbab145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/21/2021] [Indexed: 11/13/2022]
Abstract
In phytopathogenic fungi, a mutation in the avirulence gene can lead to the breakdown of resistance in the host plant. The nucleotide sequences of the AVR-Pik locus in the strain Ina168 and its spontaneous mutant Ina168m95-5 of Pyricularia oryzae were determined. An AVR-Pik spontaneous deletion mechanism of Ina168m95-5, including multiple homologous recombination events involving repetitive transposable elements, is proposed.
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Affiliation(s)
| | | | | | | | - Ayumi Abe
- Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo 060-8689, Japan
| | - Teruo Sone
- Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo 060-8689, Japan
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8
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Amoghavarsha C, Pramesh D, Naik GR, Naik MK, Yadav MK, Ngangkham U, Chidanandappa E, Raghunandana A, Sharanabasav H, E Manjunatha S. Morpho-molecular diversity and avirulence genes distribution among the diverse isolates of Magnaporthe oryzae from Southern India. J Appl Microbiol 2021; 132:1275-1290. [PMID: 34327783 DOI: 10.1111/jam.15243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 11/26/2022]
Abstract
AIMS To investigate the diversity of eco-distinct isolates of Magnaporthe oryzae for their morphological, virulence and molecular diversity and relative distribution of five Avr genes. METHODS AND RESULTS Fifty-two M. oryzae isolates were collected from different rice ecosystems of southern India. A majority of them (n = 28) formed a circular colony on culture media. Based on the disease reaction on susceptible cultivar (cv. HR-12), all 52 isolates were classified in to highly virulent (n = 28), moderately virulent (n = 11) and less-virulent (13) types. Among the 52 isolates, 38 were selected for deducing internal transcribed spacer (ITS) sequence diversity. For deducing phylogeny, another set of 36 isolates from other parts of the world was included, which yielded two distinct phylogenetic clusters. We identified eight haplotype groups and 91 variable sites within the ITS sequences, and haplotype-group-2 (Hap_2) was predominant (n = 24). The Tajima's and Fu's Fs neutrality tests exhibited many rare alleles. Furthermore, PCR analysis for detecting the presence of five Avr genes in the different M. oryzae isolates using Avr gene-specific primers in PCR revealed that Avr-Piz-t, Avr-Pik, Avr-Pia and Avr-Pita were present in 73.68%, 73.68%, 63.16% and 47.37% of the isolates studied, respectively; whereas, Avr-Pii was identified only in 13.16% of the isolates. CONCLUSIONS Morpho-molecular and virulence studies revealed the significant diversity among eco-distinct isolates. PCR detection of Avr genes among the M. oryzae population revealed the presence of five Avr genes. Among them, Avr-Piz-t, Avr-Pik and Avr-Pia were more predominant. SIGNIFICANCE AND IMPACT OF THE STUDY The study documented the morphological and genetic variability of eco-distinct M. oryzae isolates. This is the first study demonstrating the distribution of the Avr genes among the eco-distinct population of M. oryzae from southern India. The information generated will help plant breeders to select appropriate resistant gene/s combinations to develop blast disease-resistant rice cultivars.
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Affiliation(s)
- Chittaragi Amoghavarsha
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India.,Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Devanna Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Ganesh R Naik
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India
| | - Manjunath K Naik
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India
| | - Manoj K Yadav
- ICAR-National Rice Research Institute, Cuttack, India
| | - Umakanta Ngangkham
- ICAR-Research Complex for North-Eastern Hill Region, Manipur center, Imphal, Manipur, India
| | - Eranna Chidanandappa
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Adke Raghunandana
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Huded Sharanabasav
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, Karnataka, India
| | - Siddepalli E Manjunatha
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, Karnataka, India
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9
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Zhong Z, Lin L, Zheng H, Bao J, Chen M, Zhang L, Tang W, Ebbole DJ, Wang Z. Emergence of a hybrid PKS-NRPS secondary metabolite cluster in a clonal population of the rice blast fungus Magnaporthe oryzae. Environ Microbiol 2020; 22:2709-2723. [PMID: 32216010 DOI: 10.1111/1462-2920.14994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 12/21/2022]
Abstract
Secondary metabolites (SMs) are crucial for fungi and vary in function from beneficial antibiotics to pathogenicity factors. To generate diversified SMs that enable different functions, SM-coding regions rapidly evolve in fungal genomes. However, the driving force and genetic mechanism of fungal SM diversification in the context of host-pathogen interactions remain largely unknown. Previously, we grouped field populations of the rice blast fungus Magnaporthe oryzae (syn: Pyricularia oryzae) into three major globally distributed clades based on population genomic analyses. Here, we characterize a recent duplication of an avirulent gene-containing SM cluster, ACE1, in a clonal M. oryzae population (Clade 2). We demonstrate that the ACE1 cluster is specifically duplicated in Clade 2, a dominant clade in indica rice-growing areas. With long-read sequencing, we obtained chromosome-level genome sequences of four Clade 2 isolates, which displayed differences in genomic organization of the ACE1 duplication process. Comparative genomic analyses suggested that the original ACE1 cluster experienced frequent rearrangement in Clade 2 isolates and revealed that the new ACE1 cluster is located in a newly formed and transposable element-rich region. Taken together, these results highlight the frequent mutation and expansion of an avirulent gene-containing SM cluster through transposable element-mediated whole-cluster duplication in the context of host-pathogen interactions.
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Affiliation(s)
- Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huakun Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiandong Bao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meilian Chen
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Limei Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Tang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Daniel J Ebbole
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
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10
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Lopez ALC, Yli-Matilla T, Cumagun CJR. Geographic Distribution of Avirulence Genes of the Rice Blast Fungus Magnaporthe oryzae in the Philippines. Microorganisms 2019; 7:E23. [PMID: 30669441 PMCID: PMC6352036 DOI: 10.3390/microorganisms7010023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/16/2022] Open
Abstract
A total of 131 contemporary and 33 reference isolates representing a number of multi-locus genotypes of Magnaporthe oryzae were subjected to a PCR test to detect the presence/absence of avirulence (Avr) genes. Results revealed that the more frequently occurring genes were Avr-Pik (81.50%), Avr-Pita (64.16%) and Avr-Pii (47.98%), whereas the less frequently occurring genes were Avr-Pizt (19.08%) and Avr-Pia (5.20%). It was also laid out that the presence of Avr genes in M. oryzae is strongly associated with agroecosystems where the complementary resistant (R) genes exist. No significant association, however, was noted on the functional Avr genes and the major geographic locations. Furthermore, it was identified that the upland varieties locally known as "Milagrosa" and "Waray" contained all the R genes complementary to the Avr genes tested.
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Affiliation(s)
- Ana Liza C Lopez
- Jose Rizal Memorial State University⁻Tampilisan Campus, Znac, 7101 Tampilisan, Zamboanga del Norte, Philippines.
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031 Los Baños, Laguna, Philippines.
| | - Tapani Yli-Matilla
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20520 Turku, Finland.
| | - Christian Joseph R Cumagun
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, 4031 Los Baños, Laguna, Philippines.
- Molecular Phytopathology and Mycotoxin Research, University of Göttingen, 37077 Göttingen, Germany.
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11
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Białas A, Zess EK, De la Concepcion JC, Franceschetti M, Pennington HG, Yoshida K, Upson JL, Chanclud E, Wu CH, Langner T, Maqbool A, Varden FA, Derevnina L, Belhaj K, Fujisaki K, Saitoh H, Terauchi R, Banfield MJ, Kamoun S. Lessons in Effector and NLR Biology of Plant-Microbe Systems. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:34-45. [PMID: 29144205 DOI: 10.1101/171223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A diversity of plant-associated organisms secrete effectors-proteins and metabolites that modulate plant physiology to favor host infection and colonization. However, effectors can also activate plant immune receptors, notably nucleotide-binding domain and leucine-rich repeat region (NLR)-containing proteins, enabling plants to fight off invading organisms. This interplay between effectors, their host targets, and the matching immune receptors is shaped by intricate molecular mechanisms and exceptionally dynamic coevolution. In this article, we focus on three effectors, AVR-Pik, AVR-Pia, and AVR-Pii, from the rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae), and their corresponding rice NLR immune receptors, Pik, Pia, and Pii, to highlight general concepts of plant-microbe interactions. We draw 12 lessons in effector and NLR biology that have emerged from studying these three little effectors and are broadly applicable to other plant-microbe systems.
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Affiliation(s)
- Aleksandra Białas
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Erin K Zess
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | | | - Marina Franceschetti
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Helen G Pennington
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Kentaro Yoshida
- 3 Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Jessica L Upson
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Emilie Chanclud
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Chih-Hang Wu
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Abbas Maqbool
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Freya A Varden
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Lida Derevnina
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Khaoula Belhaj
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Koki Fujisaki
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
| | - Hiromasa Saitoh
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
- 5 Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryohei Terauchi
- 3 Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
| | - Mark J Banfield
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Sophien Kamoun
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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12
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Białas A, Zess EK, De la Concepcion JC, Franceschetti M, Pennington HG, Yoshida K, Upson JL, Chanclud E, Wu CH, Langner T, Maqbool A, Varden FA, Derevnina L, Belhaj K, Fujisaki K, Saitoh H, Terauchi R, Banfield MJ, Kamoun S. Lessons in Effector and NLR Biology of Plant-Microbe Systems. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:34-45. [PMID: 29144205 DOI: 10.1094/mpmi-08-17-0196-fi] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A diversity of plant-associated organisms secrete effectors-proteins and metabolites that modulate plant physiology to favor host infection and colonization. However, effectors can also activate plant immune receptors, notably nucleotide-binding domain and leucine-rich repeat region (NLR)-containing proteins, enabling plants to fight off invading organisms. This interplay between effectors, their host targets, and the matching immune receptors is shaped by intricate molecular mechanisms and exceptionally dynamic coevolution. In this article, we focus on three effectors, AVR-Pik, AVR-Pia, and AVR-Pii, from the rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae), and their corresponding rice NLR immune receptors, Pik, Pia, and Pii, to highlight general concepts of plant-microbe interactions. We draw 12 lessons in effector and NLR biology that have emerged from studying these three little effectors and are broadly applicable to other plant-microbe systems.
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Affiliation(s)
- Aleksandra Białas
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Erin K Zess
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | | | - Marina Franceschetti
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Helen G Pennington
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Kentaro Yoshida
- 3 Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Jessica L Upson
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Emilie Chanclud
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Chih-Hang Wu
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Abbas Maqbool
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Freya A Varden
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Lida Derevnina
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Khaoula Belhaj
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Koki Fujisaki
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
| | - Hiromasa Saitoh
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
- 5 Department of Molecular Microbiology, Tokyo University of Agriculture, Tokyo, Japan
| | - Ryohei Terauchi
- 3 Graduate School of Agricultural Science, Kobe University, Kobe, Japan
- 4 Iwate Biotechnology Research Center, Kitakami, Iwate, Japan; and
| | - Mark J Banfield
- 2 Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom
| | - Sophien Kamoun
- 1 The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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13
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Zhong Z, Norvienyeku J, Chen M, Bao J, Lin L, Chen L, Lin Y, Wu X, Cai Z, Zhang Q, Lin X, Hong Y, Huang J, Xu L, Zhang H, Chen L, Tang W, Zheng H, Chen X, Wang Y, Lian B, Zhang L, Tang H, Lu G, Ebbole DJ, Wang B, Wang Z. Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species. Sci Rep 2016; 6:25591. [PMID: 27151494 PMCID: PMC4858695 DOI: 10.1038/srep25591] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/20/2016] [Indexed: 02/07/2023] Open
Abstract
One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants.
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Affiliation(s)
- Zhenhui Zhong
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Justice Norvienyeku
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meilian Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiandong Bao
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianyu Lin
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liqiong Chen
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yahong Lin
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoxian Wu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zena Cai
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qi Zhang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoye Lin
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yonghe Hong
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jun Huang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Linghong Xu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Honghong Zhang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Long Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Tang
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huakun Zheng
- Haixia Institute of Science and Technology (HIST), Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaofeng Chen
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanli Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Bi Lian
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liangsheng Zhang
- Haixia Institute of Science and Technology (HIST), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Haibao Tang
- Haixia Institute of Science and Technology (HIST), Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guodong Lu
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Daniel J. Ebbole
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Baohua Wang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian University Key Laboratory for Functional Genomics of Plant Fungal Pathogens, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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14
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Schmidt SM, Lukasiewicz J, Farrer R, van Dam P, Bertoldo C, Rep M. Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon. THE NEW PHYTOLOGIST 2016; 209:307-18. [PMID: 26305378 PMCID: PMC5769816 DOI: 10.1111/nph.13584] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/29/2015] [Indexed: 05/06/2023]
Abstract
Development of resistant crops is the most effective way to control plant diseases to safeguard food and feed production. Disease resistance is commonly based on resistance genes, which generally mediate the recognition of small proteins secreted by invading pathogens. These proteins secreted by pathogens are called 'avirulence' proteins. Their identification is important for being able to assess the usefulness and durability of resistance genes in agricultural settings. We have used genome sequencing of a set of strains of the melon wilt fungus Fusarium oxysporum f. sp. melonis (Fom), bioinformatics-based genome comparison and genetic transformation of the fungus to identify AVRFOM2, the gene that encodes the avirulence protein recognized by the melon Fom-2 gene. Both an unbiased and a candidate gene approach identified a single candidate for the AVRFOM2 gene. Genetic complementation of AVRFOM2 in three different race 2 isolates resulted in resistance of Fom-2-harbouring melon cultivars. AvrFom2 is a small, secreted protein with two cysteine residues and weak similarity to secreted proteins of other fungi. The identification of AVRFOM2 will not only be helpful to select melon cultivars to avoid melon Fusarium wilt, but also to monitor how quickly a Fom population can adapt to deployment of Fom-2-containing cultivars in the field.
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Affiliation(s)
- Sarah Maria Schmidt
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Joanna Lukasiewicz
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Rhys Farrer
- Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter van Dam
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Chiara Bertoldo
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
| | - Martijn Rep
- Molecular Plant Pathology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE, Amsterdam, the Netherlands
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15
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Ose T, Oikawa A, Nakamura Y, Maenaka K, Higuchi Y, Satoh Y, Fujiwara S, Demura M, Sone T, Kamiya M. Solution structure of an avirulence protein, AVR-Pia, from Magnaporthe oryzae. JOURNAL OF BIOMOLECULAR NMR 2015; 63:229-235. [PMID: 26362280 DOI: 10.1007/s10858-015-9979-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/18/2015] [Indexed: 06/05/2023]
Affiliation(s)
- Toyoyuki Ose
- Faculty of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Azusa Oikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Yukiko Nakamura
- Faculty of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Katsumi Maenaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, N12, W6, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Yuya Higuchi
- Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Yuki Satoh
- Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Shiho Fujiwara
- Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Teruo Sone
- Graduate School of Agriculture, Hokkaido University, N9, W9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
| | - Masakatsu Kamiya
- Faculty of Advanced Life Science, Hokkaido University, N10, W8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan.
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16
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Arazoe T, Miyoshi K, Yamato T, Ogawa T, Ohsato S, Arie T, Kuwata S. Tailor-made CRISPR/Cas system for highly efficient targeted gene replacement in the rice blast fungus. Biotechnol Bioeng 2015; 112:2543-9. [PMID: 26039904 DOI: 10.1002/bit.25662] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas-derived RNA-guided nucleases (RGNs) that can generate DNA double-strand breaks (DSBs) at a specific sequence are widely used for targeted genome editing by induction of DSB repair in many organisms. The CRISPR/Cas system consists of two components: a single Cas9 nuclease and a single-guide RNA (sgRNA). Therefore, the system for constructing RGNs is simple and efficient, but the utilization of RGNs in filamentous fungi has not been validated. In this study, we established the CRISPR/Cas system in the model filamentous fungus, Pyricularia oryzae, using Cas9 that was codon-optimized for filamentous fungi, and the endogenous RNA polymerase (RNAP) III U6 promoter and a RNAP II fungal promoter for the expression of the sgRNA. We further demonstrated that RGNs could recognize the desired sequences and edit endogenous genes through homologous recombination-mediated targeted gene replacement with high efficiency. Our system will open the way for the development of various CRISPR/Cas-based applications in filamentous fungi.
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Affiliation(s)
- Takayuki Arazoe
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Kennosuke Miyoshi
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Tohru Yamato
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Tetsuo Ogawa
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Shuichi Ohsato
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Tsutomu Arie
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-0509, Japan
| | - Shigeru Kuwata
- Graduate School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan. ,
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17
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Kemen AC, Agler MT, Kemen E. Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism. THE NEW PHYTOLOGIST 2015; 206:1207-28. [PMID: 25622918 DOI: 10.1111/nph.13284] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 12/12/2014] [Indexed: 05/03/2023]
Abstract
Research on obligate biotrophic plant parasites, which reproduce only on living hosts, has revealed a broad diversity of filamentous microbes that have independently acquired complex morphological structures, such as haustoria. Genome studies have also demonstrated a concerted loss of genes for metabolism and lytic enzymes, and gain of diversity of genes coding for effectors involved in host defense suppression. So far, these traits converge in all known obligate biotrophic parasites, but unexpected genome plasticity remains. This plasticity is manifested as transposable element (TE)-driven increases in genome size, observed to be associated with the diversification of virulence genes under selection pressure. Genome expansion could result from the governing of the pathogen response to ecological selection pressures, such as host or nutrient availability, or to microbial interactions, such as competition, hyperparasitism and beneficial cooperations. Expansion is balanced by alternating sexual and asexual cycles, as well as selfing and outcrossing, which operate to control transposon activity in populations. In turn, the prevalence of these balancing mechanisms seems to be correlated with external biotic factors, suggesting a complex, interconnected evolutionary network in host-pathogen-microbe interactions. Therefore, the next phase of obligate biotrophic pathogen research will need to uncover how this network, including multitrophic interactions, shapes the evolution and diversity of pathogens.
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Affiliation(s)
- Ariane C Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany
| | - Matthew T Agler
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany
| | - Eric Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829, Cologne, Germany
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18
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Arazoe T, Ogawa T, Miyoshi K, Yamato T, Ohsato S, Sakuma T, Yamamoto T, Arie T, Kuwata S. Tailor-made TALEN system for highly efficient targeted gene replacement in the rice blast fungus. Biotechnol Bioeng 2015; 112:1335-42. [DOI: 10.1002/bit.25559] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Takayuki Arazoe
- Graduate School of Agriculture; Meiji University; 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571 Japan
| | - Tetsuo Ogawa
- Graduate School of Agriculture; Meiji University; 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571 Japan
| | - Kennosuke Miyoshi
- Graduate School of Agriculture; Meiji University; 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571 Japan
| | - Tohru Yamato
- Graduate School of Agriculture; Meiji University; 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571 Japan
| | - Shuichi Ohsato
- Graduate School of Agriculture; Meiji University; 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571 Japan
| | - Tetsushi Sakuma
- Graduate School of Science; Hiroshima University; Higashi-Hiroshima Japan
| | - Takashi Yamamoto
- Graduate School of Science; Hiroshima University; Higashi-Hiroshima Japan
| | - Tsutomu Arie
- Faculty of Agriculture; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Shigeru Kuwata
- Graduate School of Agriculture; Meiji University; 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571 Japan
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Mesarich CH, Griffiths SA, van der Burgt A, Okmen B, Beenen HG, Etalo DW, Joosten MHAJ, de Wit PJGM. Transcriptome sequencing uncovers the Avr5 avirulence gene of the tomato leaf mold pathogen Cladosporium fulvum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:846-57. [PMID: 24678832 DOI: 10.1094/mpmi-02-14-0050-r] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The Cf-5 gene of tomato confers resistance to strains of the fungal pathogen Cladosporium fulvum carrying the avirulence gene Avr5. Although Cf-5 has been cloned, Avr5 has remained elusive. We report the cloning of Avr5 using a combined bioinformatic and transcriptome sequencing approach. RNA-Seq was performed on the sequenced race 0 strain (0WU; carrying Avr5), as well as a race 5 strain (IPO 1979; lacking a functional Avr5 gene) during infection of susceptible tomato. Forty-four in planta-induced C. fulvum candidate effector (CfCE) genes of 0WU were identified that putatively encode a secreted, small cysteine-rich protein. An expressed transcript sequence comparison between strains revealed two polymorphic CfCE genes in IPO 1979. One of these conferred avirulence to IPO 1979 on Cf-5 tomato following complementation with the corresponding 0WU allele, confirming identification of Avr5. Complementation also led to increased fungal biomass during infection of susceptible tomato, signifying a role for Avr5 in virulence. Seven of eight race 5 strains investigated escape Cf-5-mediated resistance through deletion of the Avr5 gene. Avr5 is heavily flanked by repetitive elements, suggesting that repeat instability, in combination with Cf-5-mediated selection pressure, has led to the emergence of race 5 strains deleted for the Avr5 gene.
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Huang J, Si W, Deng Q, Li P, Yang S. Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae. BMC Genet 2014; 15:45. [PMID: 24725999 PMCID: PMC4021558 DOI: 10.1186/1471-2156-15-45] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/07/2014] [Indexed: 11/24/2022] Open
Abstract
Background Rice blast fungus Magnaporthe oryzae is one of the most devastating pathogens in rice. Avirulence genes in this fungus share a gene-for-gene relationship with the resistance genes in its host rice. Although numerous studies have shown that rice blast R-genes are extremely diverse and evolve rapidly in their host populations, little is known about the evolutionary patterns of the Avr-genes in the pathogens. Results Here, six well-characterized Avr-genes and seven randomly selected non-Avr control genes were used to investigate the genetic variations in 62 rice blast strains from different parts of China. Frequent presence/absence polymorphisms, high levels of nucleotide variation (~10-fold higher than non-Avr genes), high non-synonymous to synonymous substitution ratios, and frequent shared non-synonymous substitution were observed in the Avr-genes of these diversified blast strains. In addition, most Avr-genes are closely associated with diverse repeated sequences, which may partially explain the frequent presence/absence polymorphisms in Avr-genes. Conclusion The frequent deletion and gain of Avr-genes and rapid non-synonymous variations might be the primary mechanisms underlying rapid adaptive evolution of pathogens toward virulence to their host plants, and these features can be used as the indicators for identifying additional Avr-genes. The high number of nucleotide polymorphisms among Avr-gene alleles could also be used to distinguish genetic groups among different strains.
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Affiliation(s)
| | | | | | - Ping Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China.
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Arazoe T, Younomaru T, Ohsato S, Kimura M, Arie T, Kuwata S. Site-specific DNA double-strand break generated by I-SceI endonuclease enhances ectopic homologous recombination inPyricularia oryzae. FEMS Microbiol Lett 2014; 352:221-9. [DOI: 10.1111/1574-6968.12396] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Takayuki Arazoe
- Graduate School of Agriculture; Meiji University; Kawasaki Kanagawa Japan
| | - Tetsuya Younomaru
- Graduate School of Agriculture; Meiji University; Kawasaki Kanagawa Japan
| | - Shuichi Ohsato
- Graduate School of Agriculture; Meiji University; Kawasaki Kanagawa Japan
| | - Makoto Kimura
- Graduate School of Bioagricultural Sciences; Nagoya University; Nagoya Aichi Japan
| | - Tsutomu Arie
- Graduate School of Agriculture; Tokyo University of Agriculture and Technology; Fuchu Tokyo Japan
| | - Shigeru Kuwata
- Graduate School of Agriculture; Meiji University; Kawasaki Kanagawa Japan
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