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Chaverri P, Romberg MK, Montero-Vargas M, McKemy JM, Rane KK, Balbalian CJ, Castlebury LA. Phylogeographic and Phylogenomic Structure of the Quarantine Plant Pathogen Colletotrichum liriopes, Including New Reports in the United States. PLANT DISEASE 2023; 107:2816-2824. [PMID: 36802295 DOI: 10.1094/pdis-10-22-2324-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: 06/18/2023]
Abstract
Global agricultural trade has accelerated the emergence and re-emergence of new plant pathogens. In the United States, the fungal pathogen Colletotrichum liriopes is still considered a foreign quarantine pathogen that affects ornamental plants (i.e., Liriope spp.). Even though this species has been reported in East Asia on various asparagaceous hosts, its first and only report in the United States was in 2018. However, that study used only ITS nrDNA for identification, and no available culture or voucher specimen was maintained. The main objective of the present study was to determine the geographic and host distribution of specimens identified as C. liriopes. To accomplish this, new and existing isolates, sequences, and genomes obtained from various hosts and geographic locations (i.e., China, Colombia, Mexico, and the United States) were compared with the ex-type of C. liriopes. Multilocus phylogenetic (ITS, Tub2, GAPDH, CHS-1, and HIS3), phylogenomic, and splits tree analyses revealed that all the studied isolates/sequences form a well-supported clade with little intraspecific variation. Morphological characterizations support these findings. The minimum spanning network, low nucleotide diversity, and negative Tajima's D from both multilocus and genomic data suggest that there was a recent movement/invasion of a few East Asian genotypes to other countries where the ornamental plants are produced (e.g., South America) and subsequently to the importing countries, such as the United States. The study reveals that the geographic and host distribution of C. liriopes sensu stricto is expanded to the United States (i.e., at least Maryland, Mississippi, and Tennessee) and on various hosts in addition to Asparagaceae and Orchidaceae. The present study produces fundamental knowledge that can be used in efforts to reduce costs or losses from agricultural trade and to expand our understanding of pathogen movement.
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Affiliation(s)
- Priscila Chaverri
- USDA ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705, U.S.A
- Oak Ridge Institute for Science and Education, USDA ARS Research Participation Program, Oak Ridge, TN 37830, U.S.A
- Department of Natural Sciences, Bowie State University, Bowie, MD 20715, U.S.A
| | | | - Maripaz Montero-Vargas
- Advanced Computing Laboratory, Costa Rica National High Technology Center (CeNAT), San José, Costa Rica
| | | | - Karen K Rane
- Plant Diagnostic Laboratory, University of Maryland, College Park, MD 20742, U.S.A
| | - Clarissa J Balbalian
- Plant Diagnostic Laboratory, Mississippi State University, Mississippi State, MS 39762, U.S.A
| | - Lisa A Castlebury
- USDA ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705, U.S.A
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The use of evolutionary analyses to predict functionally relevant traits in filamentous plant pathogens. Curr Opin Microbiol 2023; 73:102244. [PMID: 36889024 DOI: 10.1016/j.mib.2022.102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 03/08/2023]
Abstract
Identifying traits involved in plant-pathogen interactions is one of the major objectives in molecular plant pathology. Evolutionary analyses may assist in the identification of genes encoding traits that are involved in virulence and local adaptation, including adaptation to agricultural intervention strategies. In the past decades, the number of available genome sequences of fungal plant pathogens has rapidly increased, providing a rich source for the discovery of functionally important genes as well as inference of species histories. Positive selection in the form of diversifying or directional selection leaves particular signatures in genome alignments and can be identified with statistical genetics methods. This review summarises the concepts and approaches used in evolutionary genomics and lists major discoveries related to plant-pathogen adaptative evolution. We underline the significant contribution of evolutionary genomics in discovering virulence-related traits and the study of plant-pathogen ecology and adaptive evolution.
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Yang LN, Ouyang H, Nkurikiyimfura O, Fang H, Waheed A, Li W, Wang YP, Zhan J. Genetic variation along an altitudinal gradient in the Phytophthora infestans effector gene Pi02860. Front Microbiol 2022; 13:972928. [PMID: 36160230 PMCID: PMC9492930 DOI: 10.3389/fmicb.2022.972928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Effector genes, together with climatic and other environmental factors, play multifaceted roles in the development of plant diseases. Understanding the role of environmental factors, particularly climate conditions affecting the evolution of effector genes, is important for predicting the long-term value of the genes in controlling agricultural diseases. Here, we collected Phytophthora infestans populations from five locations along a mountainous hill in China and sequenced the effector gene Pi02860 from >300 isolates. To minimize the influence of other ecological factors, isolates were sampled from the same potato cultivar on the same day. We also expressed the gene to visualise its cellular location, assayed its pathogenicity and evaluated its response to experimental temperatures. We found that Pi02860 exhibited moderate genetic variation at the nucleotide level which was mainly generated by point mutation. The mutations did not change the cellular location of the effector gene but significantly modified the fitness of P. infestans. Genetic variation and pathogenicity of the effector gene were positively associated with the altitude of sample sites, possibly due to increased mutation rate induced by the vertical distribution of environmental factors such as UV radiation and temperature. We further found that Pi02860 expression was regulated by experimental temperature with reduced expression as experimental temperature increased. Together, these results indicate that UV radiation and temperature are important environmental factors regulating the evolution of effector genes and provide us with considerable insight as to their future sustainable action under climate and other environmental change.
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Affiliation(s)
- Li-Na Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, China
- *Correspondence: Li-Na Yang,
| | - Haibing Ouyang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Oswald Nkurikiyimfura
- Institute of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hanmei Fang
- Institute of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Abdul Waheed
- Institute of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenyang Li
- Institute of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Jiasui Zhan,
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Molecular diversity, haplotype distribution and genetic variation flow of Bipolaris sorokiniana fungus causing spot blotch disease in different wheat-growing zones. J Appl Genet 2022; 63:793-803. [PMID: 35931929 DOI: 10.1007/s13353-022-00716-w] [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: 07/02/2021] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 10/16/2022]
Abstract
Bipolaris sorokiniana (BS) is an economically important fungal pathogen causing spot blotch of wheat (Trtiticum aestivum) and found in all wheat-growing zones of India. Very scanty and fragmentary information is available on its genetic diversity. The current research is the first detailed report on the geographic distribution and evolution of BS population in five geographically distinct wheat-growing zones (North Western Plain Zone (NWPZ), North Eastern Plain zone (NEPZ), North Hill Zone (NHZ), Southern Hill Zone (SHZ) and Peninsular Zone (PZ)) of India, studied by performing nucleotide sequence comparison of internal transcribed spacer region of 528 isolates. A moderate to low levels of haplotypic diversity was noticed in different wheat-growing zones. Phylogenetic analysis suggests that B. sorokiniana exist in two distinct lineages as all isolates under study were grouped in two different clades and found analogous to the findings of haplotypic and TCS network analysis. The genetic parameters revealed the existence of 40 haplotypes with three major haplotypes (H-1, H-2 and H-3) which showed star-like structure network surrounded by several single haplotypes, revealing high frequency of the mutations (Eta = 2 - 158) in total analyzed population. H-1 was observed as a predominant haplotype and prevalent in all the five zones. Moderate level of genetic differentiation was found between NHZ and other zones like NWPZ (Fst = 0.332) and SHZ (Fst = 0.382) and PZ (Fst = 0.299), whereas it was low between NEPZ and PZ (Fst = 0.034). Higher transfer rate of genetic variation was noticed between NEPZ and PZ (Nm = 7.06), while it was found minimum between NHZ and SHZ (Nm = 0.40). Moreover, negative score of neutrality statistics (Tajima's D and Fu's FS test) for NWPZ population suggested recent population expansion. However, positive score for both the neutrality tests observed in NEPZ indicated the dominance of balancing selection in structuring their population. Recombination events were observed in the NWPZ and NHZ population, while it was absent in SHZ, NEPZ and PZ population. Thus, the lack of any specific genetic population structure in all the zones indicates for the expansion history only from one common source population, i.e. NWPZ, a mega zone of wheat production in India. Overall, it seems that the predominance of individual haplotypes with a moderate level of genetic variation and human-mediated movement of contaminated seed and dispersal of inoculum, mutations and recombination as prime evolutionary processes play essential role in defining the genetic structure of BS population.
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Shen LL, Waheed A, Wang YP, Nkurikiyimfura O, Wang ZH, Yang LN, Zhan J. Mitochondrial Genome Contributes to the Thermal Adaptation of the Oomycete Phytophthora infestans. Front Microbiol 2022; 13:928464. [PMID: 35836411 PMCID: PMC9273971 DOI: 10.3389/fmicb.2022.928464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
As a vital element of climate change, elevated temperatures resulting from global warming present new challenges to natural and agricultural sustainability, such as ecological disease management. Mitochondria regulate the energy production of cells in responding to environmental fluctuation, but studying their contribution to the thermal adaptation of species is limited. This knowledge is needed to predict future disease epidemiology for ecology conservation and food security. Spatial distributions of the mitochondrial genome (mtDNA) in 405 Phytophthora infestans isolates originating from 15 locations were characterized. The contribution of MtDNA to thermal adaptation was evaluated by comparative analysis of mtDNA frequency and intrinsic growth rate, relative population differentiation in nuclear and mtDNA, and associations of mtDNA distribution with local geography climate conditions. Significant variation in frequency, intrinsic growth rate, and spatial distribution was detected in mtDNA. Population differentiation in mtDNA was significantly higher than that in the nuclear genome, and spatial distribution of mtDNA was strongly associated with local climatic conditions and geographic parameters, particularly air temperature, suggesting natural selection caused by a local temperature is the main driver of the adaptation. Dominant mtDNA grew faster than the less frequent mtDNA. Our results provide useful insights into the evolution of pathogens under global warming. Given its important role in biological functions and adaptation to local air temperature, mtDNA intervention has become an increasing necessity for future disease management. To secure ecological integrity and food production under global warming, a synergistic study on the interactive effect of changing temperature on various components of biological and ecological functions of mitochondria in an evolutionary frame is urgently needed.
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Affiliation(s)
- Lin-Lin Shen
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Abdul Waheed
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Yan-Ping Wang
- Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, China
| | - Oswald Nkurikiyimfura
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zong-Hua Wang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Li-Na Yang
- Institute of Oceanography, Minjiang University, Fuzhou, China
- *Correspondence: Li-Na Yang
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Brugman E, Wibowo A, Widiastuti A. Phytophthora palmivora from Sulawesi and Java Islands, Indonesia, reveals high genotypic diversity and lack of population structure. Fungal Biol 2022; 126:267-276. [DOI: 10.1016/j.funbio.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 11/26/2022]
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Chepsergon J, Motaung TE, Moleleki LN. "Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants? Virulence 2021; 12:1921-1935. [PMID: 34304703 PMCID: PMC8516161 DOI: 10.1080/21505594.2021.1948277] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/11/2021] [Accepted: 06/18/2021] [Indexed: 12/30/2022] Open
Abstract
Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.
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Affiliation(s)
- Jane Chepsergon
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Thabiso E. Motaung
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Lucy Novungayo Moleleki
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, Gauteng, South Africa
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Shen LL, Waheed A, Wang YP, Nkurikiyimfura O, Wang ZH, Yang LN, Zhan J. Multiple Mechanisms Drive the Evolutionary Adaptation of Phytophthora infestans Effector Avr1 to Host Resistance. J Fungi (Basel) 2021; 7:jof7100789. [PMID: 34682211 PMCID: PMC8538934 DOI: 10.3390/jof7100789] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
Effectors, a group of small proteins secreted by pathogens, play a central role in antagonistic interactions between plant hosts and pathogens. The evolution of effector genes threatens plant disease management and sustainable food production, but population genetic analyses to understand evolutionary mechanisms of effector genes are limited compared to molecular and functional studies. Here we investigated the evolution of the Avr1 effector gene from 111 Phytophthora infestans isolates collected from six areas covering three potato cropping regions in China using a population genetic approach. High genetic variation of the effector gene resulted from diverse mechanisms including base substitution, pre-termination, intragenic recombination and diversifying selection. Nearly 80% of the 111 sequences had a point mutation in the 512th nucleotide (T512G), which generated a pre-termination stop codon truncating 38 amino acids in the C-terminal, suggesting that the C-terminal may not be essential to ecological and biological functions of P. infestans. A significant correlation between the frequency of Avr1 sequences with the pre-termination and annual mean temperature in the collection sites suggests that thermal heterogeneity might be one of contributors to the diversifying selection, although biological and biochemical mechanisms of the likely thermal adaptation are not known currently. Our results highlight the risk of rapid adaptation of P. infestans and possibly other pathogens as well to host resistance, and the application of eco-evolutionary principles is necessary for sustainable disease management in agricultural ecosystems.
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Affiliation(s)
- Lin-Lin Shen
- Key Lab for Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou 350002, China; (L.-L.S.); (A.W.); (O.N.)
| | - Abdul Waheed
- Key Lab for Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou 350002, China; (L.-L.S.); (A.W.); (O.N.)
| | - Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu 611130, China;
| | - Oswald Nkurikiyimfura
- Key Lab for Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou 350002, China; (L.-L.S.); (A.W.); (O.N.)
| | - Zong-Hua Wang
- Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Li-Na Yang
- Key Lab for Biopesticide and Chemical Biology, Fujian Agriculture and Forestry University, Ministry of Education, Fuzhou 350002, China; (L.-L.S.); (A.W.); (O.N.)
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
- Correspondence: (L.-N.Y.); (J.Z.); Tel.: +86-177-2080-5328 (L.-N.Y.); +46-18-673-639 (J.Z.)
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Correspondence: (L.-N.Y.); (J.Z.); Tel.: +86-177-2080-5328 (L.-N.Y.); +46-18-673-639 (J.Z.)
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Sacristán S, Goss EM, Eves-van den Akker S. How Do Pathogens Evolve Novel Virulence Activities? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:576-586. [PMID: 33522842 DOI: 10.1094/mpmi-09-20-0258-ia] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.We consider the state of knowledge on pathogen evolution of novel virulence activities, broadly defined as anything that increases pathogen fitness with the consequence of causing disease in either the qualitative or quantitative senses, including adaptation of pathogens to host immunity and physiology, host species, genotypes, or tissues, or the environment. The evolution of novel virulence activities as an adaptive trait is based on the selection exerted by hosts on variants that have been generated de novo or arrived from elsewhere. In addition, the biotic and abiotic environment a pathogen experiences beyond the host may influence pathogen virulence activities. We consider host-pathogen evolution, host range expansion, and external factors that can mediate pathogen evolution. We then discuss the mechanisms by which pathogens generate and recombine the genetic variation that leads to novel virulence activities, including DNA point mutation, transposable element activity, gene duplication and neofunctionalization, and genetic exchange. In summary, if there is an (epi)genetic mechanism that can create variation in the genome, it will be used by pathogens to evolve virulence factors. Our knowledge of virulence evolution has been biased by pathogen evolution in response to major gene resistance, leaving other virulence activities underexplored. Understanding the key driving forces that give rise to novel virulence activities and the integration of evolutionary concepts and methods with mechanistic research on plant-microbe interactions can help inform crop protection.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040-Madrid, Spain
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, U.S.A
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Waheed A, Wang YP, Nkurikiyimfura O, Li WY, Liu ST, Lurwanu Y, Lu GD, Wang ZH, Yang LN, Zhan J. Effector Avr4 in Phytophthora infestans Escapes Host Immunity Mainly Through Early Termination. Front Microbiol 2021; 12:646062. [PMID: 34122360 PMCID: PMC8192973 DOI: 10.3389/fmicb.2021.646062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Abstract
Effector genes play critical roles in the antagonistic interactions between plants and pathogens. However, knowledge of mutation mechanisms and evolutionary processes in effector genes and the contribution of climatic factors to the evolution of effector genes are fragmented but important in sustainable management of plant diseases and securing food supply under changing climates. Here, we used a population genetic approach to explore the evolution of the Avr4 gene in Phytophthora infestans, the causal agent of potato blight. We found that the Avr4 gene exhibited a high genetic diversity generated by point mutation and sequence deletion. Frameshifts caused by a single base-pair deletion at the 194th nucleotide position generate two stop codons, truncating almost the entire C-terminal, which is important for effector function and R4 recognition in all sequences. The effector is under natural selection for adaptation supported by comparative analyses of population differentiation (FST ) and isolation-by-distance between Avr4 sequences and simple sequence repeat marker loci. Furthermore, we found that local air temperature was positively associated with pairwise FST in the Avr4 sequences. These results suggest that the evolution of the effector gene is influenced by local air temperature, and the C-terminal truncation is one of the main mutation mechanisms in the P. infestans effector gene to circumvent the immune response of potato plants. The implication of these results to agricultural and natural sustainability in future climate conditions is discussed.
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Affiliation(s)
- Abdul Waheed
- Key Lab for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan-Ping Wang
- Key Lab for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Oswald Nkurikiyimfura
- Key Lab for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wen-Yang Li
- Key Lab for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shi-Ting Liu
- Key Lab for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yahuza Lurwanu
- Key Lab for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Crop Protection, Bayero University Kano, Kano, Nigeria
| | - Guo-Dong Lu
- Key Lab for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zong-Hua Wang
- Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Li-Na Yang
- Key Lab for Bio Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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11
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Lurwanu Y, Wang Y, Wu E, He D, Waheed A, Nkurikiyimfura O, Wang Z, Shang L, Yang L, Zhan J. Increasing temperature elevates the variation and spatial differentiation of pesticide tolerance in a plant pathogen. Evol Appl 2021; 14:1274-1285. [PMID: 34025767 PMCID: PMC8127700 DOI: 10.1111/eva.13197] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/18/2022] Open
Abstract
Climate change and pesticide resistance are two of the most imminent challenges human society is facing today. Knowledge of how the evolution of pesticide resistance may be affected by climate change such as increasing air temperature on the planet is important for agricultural production and ecological sustainability in the future but is lack in scientific literatures reported from empirical research. Here, we used the azoxystrobin-Phytophthora infestans interaction in agricultural systems to investigate the contributions of environmental temperature to the evolution of pesticide resistance and infer the impacts of global warming on pesticide efficacy and future agricultural production and ecological sustainability. We achieved this by comparing azoxystrobin sensitivity of 180 P. infestans isolates sampled from nine geographic locations in China under five temperature schemes ranging from 13 to 25°C. We found that local air temperature contributed greatly to the difference of azoxystrobin tolerance among geographic populations of the pathogen. Both among-population and within-population variations in azoxystrobin tolerance increased as experimental temperatures increased. We also found that isolates with higher azoxystrobin tolerance adapted to a broader thermal niche. These results suggest that global warming may enhance the risk of developing pesticide resistance in plant pathogens and highlight the increased challenges of administering pesticides for effective management of plant diseases to support agricultural production and ecological sustainability under future thermal conditions.
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Affiliation(s)
- Yahuza Lurwanu
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Department of Crop ProtectionFaculty of AgricultureBayero UniversityKanoNigeria
| | - Yan‐Ping Wang
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - E‐Jiao Wu
- Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementInstitute of PomologyJiangsu Academy of Agricultural SciencesNanjingChina
| | - Dun‐Chun He
- School of Economics and TradeFujian Jiangxia UniversityFuzhouChina
| | - Abdul Waheed
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Oswald Nkurikiyimfura
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zhen Wang
- Southern Potato Center of ChinaEnshi Academy of Agricultural SciencesEnshiChina
| | - Li‐Ping Shang
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Li‐Na Yang
- Institute of OceanographyMinjiang UniversityFuzhouChina
| | - Jiasui Zhan
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
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12
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Wang YP, Wu EJ, Lurwanu Y, Ding JP, He DC, Waheed A, Nkurikiyimfura O, Liu ST, Li WY, Wang ZH, Yang L, Zhan J. Evidence for a synergistic effect of post-translational modifications and genomic composition of eEF-1α on the adaptation of Phytophthora infestans. Ecol Evol 2021; 11:5484-5496. [PMID: 34026022 PMCID: PMC8131795 DOI: 10.1002/ece3.7442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 12/18/2022] Open
Abstract
Genetic variation plays a fundamental role in pathogen's adaptation to environmental stresses. Pathogens with low genetic variation tend to survive and proliferate more poorly due to their lack of genotypic/phenotypic polymorphisms in responding to fluctuating environments. Evolutionary theory hypothesizes that the adaptive disadvantage of genes with low genomic variation can be compensated for structural diversity of proteins through post-translation modification (PTM) but this theory is rarely tested experimentally and its implication to sustainable disease management is hardly discussed. In this study, we analyzed nucleotide characteristics of eukaryotic translation elongation factor-1α (eEF-lα) gene from 165 Phytophthora infestans isolates and the physical and chemical properties of its derived proteins. We found a low sequence variation of eEF-lα protein, possibly attributable to purifying selection and a lack of intra-genic recombination rather than reduced mutation. In the only two isoforms detected by the study, the major one accounted for >95% of the pathogen collection and displayed a significantly higher fitness than the minor one. High lysine representation enhances the opportunity of the eEF-1α protein to be methylated and the absence of disulfide bonds is consistent with the structural prediction showing that many disordered regions are existed in the protein. Methylation, structural disordering, and possibly other PTMs ensure the ability of the protein to modify its functions during biological, cellular and biochemical processes, and compensate for its adaptive disadvantage caused by sequence conservation. Our results indicate that PTMs may function synergistically with nucleotide codes to regulate the adaptive landscape of eEF-1α, possibly as well as other housekeeping genes, in P. infestans. Compensatory evolution between pre- and post-translational phase in eEF-1α could enable pathogens quickly adapting to disease management strategies while efficiently maintaining critical roles of the protein playing in biological, cellular, and biochemical activities. Implications of these results to sustainable plant disease management are discussed.
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Affiliation(s)
- Yan-Ping Wang
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - E-Jiao Wu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Yahuza Lurwanu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
- Department of Crop Protection Bayero University Kano Kano Nigeria
| | - Ji-Peng Ding
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Dun-Chun He
- School of Economics and Trade Fujian Jiangxia University Fuzhou China
| | - Abdul Waheed
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Oswald Nkurikiyimfura
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Shi-Ting Liu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Wen-Yang Li
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Zong-Hua Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction College of Life Sciences Fujian Agriculture and Forestry University Fuzhou China
- Institute of Oceanography Minjiang University Fuzhou China
| | - Lina Yang
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
- Institute of Oceanography Minjiang University Fuzhou China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden
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13
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Morales JG, Gaviria AE, Gilchrist E. Allelic Variation and Selection in Effector Genes of Phytophthora infestans (Mont.) de Bary. Pathogens 2020; 9:pathogens9070551. [PMID: 32659973 PMCID: PMC7400436 DOI: 10.3390/pathogens9070551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022] Open
Abstract
Phytophthora infestans is a devastating plant pathogen in several crops such as potato (Solanum tuberosum), tomato (Solanum lycopersicum) and Andean fruits such as tree tomato (Solanum betaceum), lulo (Solanum quitoense), uchuva (Physalis peruviana) and wild species in the genus Solanum sp. Despite intense research performed around the world, P. infestans populations from Colombia, South America, are poorly understood. Of particular importance is knowledge about pathogen effector proteins, which are responsible for virulence. The present work was performed with the objective to analyze gene sequences coding for effector proteins of P. infestans from isolates collected from different hosts and geographical regions. Several genetic parameters, phylogenetic analyses and neutrality tests for non-synonymous and synonymous substitutions were calculated. Non-synonymous substitutions were identified for all genes that exhibited polymorphisms at the DNA level. Significant negative selection values were found for two genes (PITG_08994 and PITG_12737) suggesting active coevolution with the corresponding host resistance proteins. Implications for pathogen virulence mechanisms and disease management are discussed.
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Affiliation(s)
- Juan G. Morales
- Group and Laboratory of Fitotecnia Tropical, Departamento de Ciencias Agronómicas, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia sede Medellín, Medellín, 050034 Antioquia, Colombia; (A.E.G.); (E.G.)
- Correspondence: ; Tel.: +0057-4-4309088
| | - Astrid E. Gaviria
- Group and Laboratory of Fitotecnia Tropical, Departamento de Ciencias Agronómicas, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia sede Medellín, Medellín, 050034 Antioquia, Colombia; (A.E.G.); (E.G.)
| | - Elizabeth Gilchrist
- Group and Laboratory of Fitotecnia Tropical, Departamento de Ciencias Agronómicas, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia sede Medellín, Medellín, 050034 Antioquia, Colombia; (A.E.G.); (E.G.)
- Universidad EAFIT, 050034 Medellín, Colombia
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14
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Yang LN, Liu H, Duan GH, Huang YM, Liu S, Fang ZG, Wu EJ, Shang L, Zhan J. The Phytophthora infestans AVR2 Effector Escapes R2 Recognition Through Effector Disordering. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:921-931. [PMID: 32212906 DOI: 10.1094/mpmi-07-19-0179-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Intrinsic disorder is a common structural characteristic of proteins and a central player in the biochemical processes of species. However, the role of intrinsic disorder in the evolution of plant-pathogen interactions is rarely investigated. Here, we explored the role of intrinsic disorder in the development of the pathogenicity in the RXLR AVR2 effector of Phytophthora infestans. We found AVR2 exhibited high nucleotide diversity generated by point mutation, early-termination, altered start codon, deletion/insertion, and intragenic recombination and is predicted to be an intrinsically disordered protein. AVR2 amino acid sequences conferring a virulent phenotype had a higher disorder tendency in both the N- and C-terminal regions compared with sequences conferring an avirulent phenotype. In addition, we also found virulent AVR2 mutants gained one or two short linear interaction motifs, the critical components of disordered proteins required for protein-protein interactions. Furthermore, virulent AVR2 mutants were predicted to be unstable and have a short protein half-life. Taken together, these results support the notion that intrinsic disorder is important for the effector function of pathogens and demonstrate that SLiM-mediated protein-protein interaction in the C-terminal effector domain might contribute greatly to the evasion of resistance-protein detection in P. infestans.
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Affiliation(s)
- Li-Na Yang
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China
| | - Hao Liu
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China
| | - Guo-Hua Duan
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China
| | - Yan-Mei Huang
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China
| | - Shiting Liu
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhi-Guo Fang
- Xiangyang Academy of Agricultural Sciences, Xiangyang 441057, Hubei, China
| | - E-Jiao Wu
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China
| | - Liping Shang
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agricultural and Forestry University, Fuzhou, Fujian 350002, China
| | - Jiasui Zhan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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15
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Gao F, Chen C, Li B, Weng Q, Chen Q. The Gene Flow Direction of Geographically Distinct Phytophthora infestans Populations in China Corresponds With the Route of Seed Potato Exchange. Front Microbiol 2020; 11:1077. [PMID: 32528452 PMCID: PMC7264822 DOI: 10.3389/fmicb.2020.01077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
Phytophthora infestans is a widespread destructive plant pathogen that causes economic losses worldwide to potato production. In this study, we sequenced four mitochondrial DNA gene sequences of 101 P. infestans isolates from five potato-growing regions in China to investigate the population structure and dispersal pattern of this pathogen. The concatenated mtDNA sequences in the populations showed high haplotype diversity, but low nucleotide diversity. Although there was a degree of spatial structure, our phylogeographic analyses support frequent gene flow between populations and the direction of gene flow, primarily from north to south, corresponds to the route of seed potato transportation, suggesting a role of human activities in the dispersal of P. infestans in China.
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Affiliation(s)
- Fangluan Gao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Changsheng Chen
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Benjin Li
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Qiyong Weng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Qinghe Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory for Monitoring and Integrated Management of Crop Pests, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, China
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16
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Wu E, Wang Y, Yahuza L, He M, Sun D, Huang Y, Liu Y, Yang L, Zhu W, Zhan J. Rapid adaptation of the Irish potato famine pathogen Phytophthora infestans to changing temperature. Evol Appl 2020; 13:768-780. [PMID: 32211066 PMCID: PMC7086108 DOI: 10.1111/eva.12899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/19/2019] [Accepted: 10/28/2019] [Indexed: 01/06/2023] Open
Abstract
Temperature plays a multidimensional role in host-pathogen interactions. As an important element of climate change, elevated world temperature resulting from global warming presents new challenges to sustainable disease management. Knowledge of pathogen adaptation to global warming is needed to predict future disease epidemiology and formulate mitigating strategies. In this study, 21 Phytophthora infestans isolates originating from seven thermal environments were acclimated for 200 days under stepwise increase or decrease of experimental temperatures and evolutionary responses of the isolates to the thermal changes were evaluated. We found temperature acclimation significantly increased the fitness and genetic adaptation of P. infestans isolates at both low and high temperatures. Low-temperature acclimation enforced the countergradient adaptation of the pathogen to its past selection and enhanced the positive association between the pathogen's intrinsic growth rate and aggressiveness. At high temperatures, we found that pathogen growth collapsed near the maximum temperature for growth, suggesting a thermal niche boundary may exist in the evolutionary adaptation of P. infestans. These results indicate that pathogens can quickly adapt to temperature shifts in global warming. If this is associated with environmental conditions favoring pathogen spread, it will threaten future food security and human health and require the establishment of mitigating actions.
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Affiliation(s)
- E‐Jiao Wu
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
- Jiangsu Key Laboratory for Horticultural Crop Genetic ImprovementInstitute of PomologyJiangsu Academy of Agricultural SciencesNanjingChina
| | - Yan‐Ping Wang
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lurwanu Yahuza
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Meng‐Han He
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouChina
| | - Dan‐Li Sun
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yan‐Mei Huang
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yu‐Chan Liu
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Li‐Na Yang
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wen Zhu
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiasui Zhan
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
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17
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Wang L, Chen H, Li J, Shu H, Zhang X, Wang Y, Tyler BM, Dong S. Effector gene silencing mediated by histone methylation underpins host adaptation in an oomycete plant pathogen. Nucleic Acids Res 2020; 48:1790-1799. [PMID: 31819959 PMCID: PMC7039004 DOI: 10.1093/nar/gkz1160] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/23/2019] [Accepted: 11/29/2019] [Indexed: 12/21/2022] Open
Abstract
The relentless adaptability of pathogen populations is a major obstacle to effective disease control measures. Increasing evidence suggests that gene transcriptional polymorphisms are a strategy deployed by pathogens to evade host immunity. However, the underlying mechanisms of transcriptional plasticity remain largely elusive. Here we found that the soybean root rot pathogen Phytophthora sojae evades the soybean Resistance gene Rps1b through transcriptional polymorphisms in the effector gene Avr1b that occur in the absence of any sequence variation. Elevated levels of histone H3 Lysine27 tri-methylation (H3K27me3) were observed at the Avr1b locus in a naturally occurring Avr1b-silenced strain but not in an Avr1b-expressing strain, suggesting a correlation between this epigenetic modification and silencing of Avr1b. To genetically test this hypothesis, we edited the gene, PsSu(z)12, encoding a core subunit of the H3K27me3 methyltransferase complex by using CRISPR/Cas9, and obtained three deletion mutants. H3K27me3 depletion within the Avr1b genomic region correlated with impaired Avr1b gene silencing in these mutants. Importantly, these mutants lost the ability to evade immune recognition by soybeans carrying Rps1b. These data support a model in which pathogen effector transcriptional polymorphisms are associated with changes in chromatin epigenetic marks, highlighting epigenetic variation as a mechanism of pathogen adaptive plasticity.
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Affiliation(s)
- Liyuan Wang
- Department of Plant Pathology, Nanjing Agriculture University, Nanjing 210095, China
| | - Han Chen
- Department of Plant Pathology, Nanjing Agriculture University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - JiangJiang Li
- Department of Plant Pathology, Nanjing Agriculture University, Nanjing 210095, China
| | - Haidong Shu
- Department of Plant Pathology, Nanjing Agriculture University, Nanjing 210095, China
| | - Xiangxue Zhang
- Department of Plant Pathology, Nanjing Agriculture University, Nanjing 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agriculture University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agriculture University, Nanjing 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing 210095, China
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18
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Temperature-Mediated Plasticity Regulates the Adaptation of Phytophthora infestans to Azoxystrobin Fungicide. SUSTAINABILITY 2020. [DOI: 10.3390/su12031188] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Fungicide is one of the main approaches used in agriculture to manage plant diseases for food production, but their effectiveness can be reduced due to the evolution of plant pathogens. Understanding the genetics and evolutionary processes responsible for the development of fungicide resistance is a key to food production and social sustainability. In this study, we used a common garden experiment to examine the source of genetic variation, natural selection, and temperature contributing to the development of azoxystrobin resistance in Phytophthora infestans and infer sustainable ways of plant disease management in future. We found that plasticity contributed to ~40% of phenotypic variation in azoxystrobin sensitivity while heritability accounted for 16%. Further analysis indicated that overall population differentiation in azoxystrobin sensitivity (QST) was significantly greater than the overall population differentiation in simple sequence repeat (SSR) marker (FST), and the P. infestans isolates demonstrated higher level of azoxystrobin sensitivity at the higher experimental temperature. These results suggest that changes in target gene expression, enzymatic activity, or metabolic rate of P. infestans play a more important role in the adaptation of the pathogen to azoxystrobin resistance than that of mutations in target genes. The development of azoxystrobin resistance in P. infestans is likely driven by diversifying selection for local adaptation, and elevated temperature associated with global warming in the future may increase the effectiveness of using azoxystrobin to manage P. infestans. The sustainable approaches for increasing disease control effectiveness and minimizing the erosion of the fungicide efficacy are proposed.
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19
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Wang Y, Xie J, Wu E, Yahuza L, Duan G, Shen L, Liu H, Zhou S, Nkurikiyimfura O, Andersson B, Yang L, Shang L, Zhu W, Zhan J. Lack of gene flow between Phytophthora infestans populations of two neighboring countries with the largest potato production. Evol Appl 2020; 13:318-329. [PMID: 31993079 PMCID: PMC6976962 DOI: 10.1111/eva.12870] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 08/23/2019] [Accepted: 08/29/2019] [Indexed: 12/18/2022] Open
Abstract
Gene flow is an important evolutionary force that enables adaptive responses of plant pathogens in response to changes in the environment and plant disease management strategies. In this study, we made a direct inference concerning gene flow in the Irish famine pathogen Phytophthora infestans between two of its hosts (potato and tomato) as well as between China and India. This was done by comparing sequence characteristics of the eukaryotic translation elongation factor 1 alpha (eEF-1α) gene, generated from 245 P. infestans isolates sampled from two countries and hosts. Consistent with previous results, we found that eEF-1α gene was highly conserved and point mutation was the only mechanism generating any sequence variation. Higher genetic variation was found in the eEF-1α sequences in the P. infestans populations sampled from tomato compared to those sampled from potato. We also found the P. infestans population from India displayed a higher genetic variation in the eEF-1α sequences compared to China. No gene flow was detected between the pathogen populations from the two countries, which is possibly attributed to the geographic barrier caused by Himalaya Plateau and the minimum cross-border trade of potato and tomato products. The implications of these results for a sustainable management of late blight diseases are discussed.
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Affiliation(s)
- Yan‐Ping Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jia‐Hui Xie
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - E‐Jiao Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lurwanu Yahuza
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Guo‐Hua Duan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lin‐Lin Shen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Hao Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shi‐Hao Zhou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Oswald Nkurikiyimfura
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Björn Andersson
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Li‐Na Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Li‐Ping Shang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wen Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiasui Zhan
- Key Lab for Biopesticide and Chemical BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
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20
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Elnahal ASM, Li J, Wang X, Zhou C, Wen G, Wang J, Lindqvist-Kreuze H, Meng Y, Shan W. Identification of Natural Resistance Mediated by Recognition of Phytophthora infestans Effector Gene Avr3aEM in Potato. FRONTIERS IN PLANT SCIENCE 2020; 11:919. [PMID: 32636869 PMCID: PMC7318898 DOI: 10.3389/fpls.2020.00919] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/05/2020] [Indexed: 05/13/2023]
Abstract
Late blight is considered the most renowned devastating potato disease worldwide. Resistance gene (R)-based resistance to late blight is the most effective method to inhibit infection by the causal agent Phytophthora infestans. However, the limited availability of resistant potato varieties and the rapid loss of R resistance, caused by P. infestans virulence variability, make disease control rely on fungicide application. We employed an Agrobacterium tumefaciens-mediated transient gene expression assay and effector biology approach to understand late blight resistance of Chinese varieties that showed years of promising field performance. We are particularly interested in PiAvr3aEM , the most common virulent allele of PiAvr3aKI that triggers a R3a-mediated hypersensitive response (HR) and late blight resistance. Through our significantly improved A. tumefaciens-mediated transient gene expression assay in potato using cultured seedlings, we characterized two dominant potato varieties, Qingshu9 and Longshu7, in China by transient expression of P. infestans effector genes. Transient expression of 10 known avirulence genes showed that PiAvr4 and PiAvr8 (PiAvrsmira2) could induce HR in Qingshu9, and PiAvrvnt1.1 in Longshu7, respectively. Our study also indicated that PiAvr3aEM is recognized by these two potato varieties, and is likely involved in their significant field performance of late blight resistance. The identification of natural resistance mediated by PiAvr3aEM recognition in Qingshu9 and Longshu7 will facilitate breeding for improved potato resistance against P. infestans.
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Affiliation(s)
- Ahmed S. M. Elnahal
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
- Plant Pathology Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jinyang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xiaoxia Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Chenyao Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, China
| | - Guohong Wen
- Institute of Potato Research, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Jian Wang
- Institute of Biotechnology, Qinghai Academy of Agricultural Sciences, Xining, China
| | | | - Yuling Meng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- *Correspondence: Weixing Shan,
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