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Oliveira-Garcia E, Budot BO, Manangkil J, Lana FD, Angira B, Famoso A, Jia Y. An Efficient Method for Screening Rice Breeding Lines Against Races of Magnaporthe oryzae. PLANT DISEASE 2024; 108:1179-1187. [PMID: 37807096 DOI: 10.1094/pdis-05-23-0922-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: 10/10/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae, is the most destructive rice disease worldwide. The disease symptoms are usually expressed on the leaf and panicle. The leaf disease intensity in controlled environmental conditions is frequently quantified using a 0 to 5 scale, where 0 represents the absence of symptoms, and 5 represents large eyespot lesions. However, this scale restricts the qualitative classification of the varieties into intermediate resistant and susceptible categories. Here, we develop a 0 to 6 scale for blast disease that allows proper assignment of rice breeding lines and varieties into six resistance levels (highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible). We evaluated 40 common rice varieties against four major blast races (IB1, IB17, IB49, and IE1-K). Varieties carrying the Pi-ta gene were either highly resistant, resistant, or moderately resistant to IB17. The IE1-K race was able to break Pi-ta-mediated resistance of the rice varieties. The Pi-z gene conferred resistance to the IB17 and IE1-K races. The varieties M201, Cheniere, and Frontier were highly susceptible (score 6; 100% disease) to the race IE1-K. Moreover, varieties that were resistant or susceptible to all four blast races also showed similar levels of resistance/susceptibility to blast disease in the field. Taken together, our data proved that the 0 to 6 blast scale can efficiently determine the resistance levels of rice varieties against major blast races. This robust method will assist rice breeding programs to incorporate durable resistance against major and emerging blast races.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Ely Oliveira-Garcia
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Bernard Orense Budot
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
- University of the Philippines Los Baños, Los Baños, Philippines
| | - Jennifer Manangkil
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Felipe Dala Lana
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Brijesh Angira
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Adam Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, LA 70578, U.S.A
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR 72160, U.S.A
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Liu M, Wang F, He B, Hu J, Dai Y, Chen W, Yi M, Zhang H, Ye Y, Cui Z, Zheng X, Wang P, Xing W, Zhang Z. Targeting Magnaporthe oryzae effector MoErs1 and host papain-like protease OsRD21 interaction to combat rice blast. NATURE PLANTS 2024; 10:618-632. [PMID: 38409290 PMCID: PMC11162578 DOI: 10.1038/s41477-024-01642-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Effector proteins secreted by plant pathogenic fungi are important artilleries against host immunity, but there is no precedent of such effectors being explored as antifungal targets. Here we demonstrate that MoErs1, a species-specific effector protein secreted by the rice blast fungus Magnaporthe oryzae, inhibits the function of rice papain-like cysteine protease OsRD21 involved in rice immunity. Disrupting MoErs1-OsRD21 interaction effectively controls rice blast. In addition, we show that FY21001, a structure-function-based designer compound, specifically binds to and inhibits MoErs1 function. FY21001 significantly and effectively controls rice blast in field tests. Our study revealed a novel concept of targeting pathogen-specific effector proteins to prevent and manage crop diseases.
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Affiliation(s)
- Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Fangfang Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Bo He
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Jiexiong Hu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Ying Dai
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Weizhong Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Mingxi Yi
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Yonghao Ye
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Zhongli Cui
- College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China
| | - Ping Wang
- Departments of Microbiology, Immunology and Parasitology, and Pediatrics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Weiman Xing
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, and Key Laboratory of Plant Immunity, Ministry of Education, Nanjing, China.
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Meile L, Garrido-Arandia M, Bernasconi Z, Peter J, Schneller A, Bernasconi A, Alassimone J, McDonald BA, Sánchez-Vallet A. Natural variation in Avr3D1 from Zymoseptoria sp. contributes to quantitative gene-for-gene resistance and to host specificity. THE NEW PHYTOLOGIST 2023; 238:1562-1577. [PMID: 36529883 DOI: 10.1111/nph.18690] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Successful host colonization by plant pathogens requires the circumvention of host defense responses, frequently through sequence modifications in secreted pathogen proteins known as avirulence factors (Avrs). Although Avr sequences are often polymorphic, the contribution of these polymorphisms to virulence diversity in natural pathogen populations remains largely unexplored. We used molecular genetic tools to determine how natural sequence polymorphisms of the avirulence factor Avr3D1 in the wheat pathogen Zymoseptoria tritici contributed to adaptive changes in virulence. We showed that there is a continuous distribution in the magnitude of resistance triggered by different Avr3D1 isoforms and demonstrated that natural variation in an Avr gene can lead to a quantitative resistance phenotype. We further showed that homologues of Avr3D1 in two nonpathogenic sister species of Z. tritici are recognized by some wheat cultivars, suggesting that Avr-R gene-for-gene interactions can contribute to nonhost resistance. We suggest that the mechanisms underlying host range, qualitative resistance, and quantitative resistance are not exclusive.
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Affiliation(s)
- Lukas Meile
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
| | - María Garrido-Arandia
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 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 (UPM), 28040, Madrid, Spain
| | - Zoe Bernasconi
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Jules Peter
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Alissa Schneller
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Alessio Bernasconi
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Julien Alassimone
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
| | - Andrea Sánchez-Vallet
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Universitätstrasse 2, Zurich, 8092, Switzerland
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223, Pozuelo de Alarcón, Madrid, Spain
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Thi Le L, Adreit H, Thi Ha L, Milazzo J, Lebrun M, Tharreau D, Hoi Pham X, Thanh Nguyen H, Fournier E, Thi Hoang G. Population structure of Pyricularia oryzae on rice in Vietnam reveals diversified populations with four pandemic and two endemic clusters. Fungal Genet Biol 2023; 166:103794. [PMID: 37003467 DOI: 10.1016/j.fgb.2023.103794] [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: 08/11/2022] [Revised: 02/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
We characterized the genetic structure of 609 strains of Pyricularia oryzae, the fungal pathogen causing rice blast disease, in three main regions in Vietnam using microsatellites (SSR) markers. From the 447 distinct multilocus genotypes identified, six genetic clusters were defined, all of them showing elevated genetic and genotypic diversities. Four of these clusters were related to rice-attacking lineages already described at the worldwide scale, whereas the two remaining clusters were endemic to Vietnam. Strains were unevenly distributed into the six clusters depending on their groups of rice variety (indica / japonica) or type of varieties (traditional / modern) of origin, but none of the clusters was specifically related to these two factors. The highest diversity of blast population was found in Northern mountainous area, and the lowest in Red River Delta in both term of genetic diversity and gene diversity. Hierarchical AMOVAs confirmed that all three factors considered (rice variety group, type of variety origin and geography) significantly contributed to the population structure of P. oryzae in Vietnam, with highest contribution from rice variety group. Mating types were unevenly distributed among clusters. Combined with results of female fertility and linkage disequilibirum, we hypothesized that clonal reproduction probably occurred in all clusters, but that sexual reproduction likely took place at least in some restricted areas in the Northern mountainous area for strains belonging to the cluster related to the previously described recombinant lineage (worldwide lineage 1). Our study pictures the genetic diversity, population structure and reproductive mode of the blast fungus in central and north Vietnam, and shows that the observed population structure is explained by several factors, the most important one being the variability of rice variety. All these new information might help for elaborating appropriate strategies to controlling the blast disease.
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Affiliation(s)
- Lieu Thi Le
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam; University of Science and Technology of Hanoi, Hanoi, Vietnam
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Loan Thi Ha
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam
| | - Joelle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Michel Lebrun
- University of Science and Technology of Hanoi, Hanoi, Vietnam
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Xuan Hoi Pham
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam
| | - Hai Thanh Nguyen
- Vietnam National University of Agriculture, Faculty of Biotechnology, Faculty of Agronomy, Hanoi, Vietnam
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France.
| | - Giang Thi Hoang
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam; Vietnam National University of Agriculture, Faculty of Biotechnology, Faculty of Agronomy, Hanoi, Vietnam.
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Ma J, Morel JB, Riemann M, Nick P. Jasmonic acid contributes to rice resistance against Magnaporthe oryzae. BMC PLANT BIOLOGY 2022; 22:601. [PMID: 36539712 PMCID: PMC9764487 DOI: 10.1186/s12870-022-03948-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The annual yield losses caused by the Rice Blast Fungus, Magnaporthe oryzae, range to the equivalent for feeding 60 million people. To ward off infection by this fungus, rice has evolved a generic basal immunity (so called compatible interaction), which acts in concert with strain-specific defence (so-called incompatible interaction). The plant-defence hormone jasmonic acid (JA) promotes the resistance to M. oryzae, but the underlying mechanisms remain elusive. To get more insight into this open question, we employ the JA-deficient mutants, cpm2 and hebiba, and dissect the JA-dependent defence signalling in rice for both, compatible and incompatible interactions. RESULTS We observe that both JA-deficient mutants are more susceptible to M. oryzae as compared to their wild-type background, which holds true for both types of interactions as verified by cytological staining. Secondly, we observe that transcripts for JA biosynthesis (OsAOS2 and OsOPR7), JA signalling (OsJAZ8, OsJAZ9, OsJAZ11 and OsJAZ13), JA-dependent phytoalexin synthesis (OsNOMT), and JA-regulated defence-related genes, such as OsBBTI2 and OsPR1a, accumulate after fungal infection in a pattern that correlates with the amplitude of resistance. Thirdly, induction of defence transcripts is weaker during compatible interaction. CONCLUSION The study demonstrates the pivotal role of JA in basal immunity of rice in the resistance to M. oryzae in both, compatible and incompatible interactions.
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Affiliation(s)
- Junning Ma
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jean-Benoît Morel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Michael Riemann
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Peter Nick
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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Pan-Genomics Reveals a New Variation Pattern of Secreted Proteins in Pyricularia oryzae. J Fungi (Basel) 2022; 8:jof8121238. [PMID: 36547571 PMCID: PMC9785059 DOI: 10.3390/jof8121238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/19/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
(1) Background: Pyricularia oryzae, the causal agent of rice blast disease, is one of the major rice pathogens. The complex population structure of P. oryzae facilitates the rapid virulence variations, which make the blast disease a serious challenge for global food security. There is a large body of existing genomics research on P. oryzae, however the population structure at the pan-genome level is not clear, and the mechanism of genetic divergence and virulence variations of different sub-populations is also unknown. (2) Methods: Based on the genome data published in the NCBI, we constructed a pan-genome database of P. oryzae, which consisted of 156 strains (117 isolated from rice and 39 isolated from other hosts). (3) Results: The pan-genome contained a total of 24,100 genes (12,005 novel genes absent in the reference genome 70-15), including 16,911 (~70%) core genes (population frequency ≥95%) and 1378 (~5%) strain-specific genes (population frequency ≤5%). Gene presence-absence variation (PAV) based clustering analysis of the population structure of P. oryzae revealed four subgroups (three from rice and one from other hosts). Interestingly, the cloned avirulence genes and conventional secreted proteins (SPs, with signal peptides) were enriched in the high-frequency regions and significantly associated with transposable elements (TEs), while the unconventional SPs (without signal peptides) were enriched in the low-frequency regions and not associated significantly with TEs. This pan-genome will expand the breadth and depth of the rice blast fungus reference genome, and also serve as a new blueprint for scientists to further study the pathogenic mechanism and virulence variation of the rice blast fungus.
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Rao MJ, Duan M, Wei X, Zuo H, Ma L, Tahir Ul Qamar M, Li M, Han S, Hu L, Wang L. LC-MS/MS-based metabolomics approach revealed novel phytocompounds from sugarcane rind with promising pharmacological value. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:6632-6642. [PMID: 35603546 DOI: 10.1002/jsfa.12030] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 04/23/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Sugarcane provides many secondary metabolites for the pharmacological and cosmetic industries. Secondary metabolites, such as phenolic compounds, flavonoids, and anthocyanins, have been studied, but few reports focus on the identification of alkaloid and non-alkaloid phytocompounds in sugarcane. RESULTS In this study, we identified 40 compounds in total from the rinds of cultivated sugarcane varieties (including eight alkaloids, 24 non-alkaloids, and eight others) by using the liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach. Among these compounds, 31 were novel and are reported for the first time in sugarcane. Some alkaloids such as 3-indoleacrylic acid, N,N-dimethyl-5-methoxytryptamine, tryptamine, 6-hydroxynicotinic acid, and 6-deoxyfagomine are identified the first time in sugarcane rind. Four alkaloids such as trigonelline, piperidine, 3-indoleacrylic acid, and 6-deoxyfagomine are found abundantly in sugarcane rind and these compounds have promising pharmaceutical value. Some phytocompounds such as choline and acetylcholine (non-alkaloid compounds) were most common in the rind of ROC22 and Yuetang93/159 (YT93/159). Hierarchical cluster analysis and principal component analysis revealed that the ROC22, Taitang172 (F172), and Yuetang71/210 (YT71/210) varieties were quite similar in alkaloid composition when compared with other sugarcane varieties. We have also characterized the biosynthesis pathway of sugarcane alkaloids. The rind of F172, ROC22, and YT71/210 showed the highest total alkaloid content, whereas the rind of ROC16 revealed a minimum level. Interestingly, the rind extract from YT71/210 and F172 showed maximum antioxidant activity, followed by ROC22. CONCLUSION Our results showed the diversity of alkaloid and non-alkaloid compounds in the rind of six cultivated sugarcanes and highlighted the promising phytocompounds that can be extracted, isolated, and utilized by the pharmacological industry. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Muhammad Junaid Rao
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Mingzheng Duan
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Xiaoshuang Wei
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Hou Zuo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Ministry of Agriculture), Huazhong Agricultural University, Wuhan, China
| | - Li Ma
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Muhammad Tahir Ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Min Li
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Shijian Han
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Lingqiang Wang
- Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
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Ma X, Duan G, Chen H, Tang P, Su S, Wei Z, Yang J. Characterization of infected process and primary mechanism in rice Acuce defense against rice blast fungus, Magnaporthe oryzae. PLANT MOLECULAR BIOLOGY 2022; 110:219-234. [PMID: 35759052 DOI: 10.1007/s11103-022-01296-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Identification of infection process and defense response during M. oryzae infecting Acuce. Magnaporthe oryzae is a destructive rice pathogen. Recent studies have focused on the initial infectious stage, with a few studies conducted to elucidate the characteristics of the late infectious stages. This study aims to decipher the characteristics at different stages (biotrophic, biotrophy-necrotrophy switch (BNS), and necrotrophic) between the interaction of two M. oryzae-rice combinations and investigate the resistance mechanisms of rice to M. oryzae using cytological and molecular methods. The biotrophic phase of M. oryzae-LTH compatible interaction was found to be longer than that of M. oryzae-Acuce incompatible interaction. We also found that jasmonic acid (JA) signaling plays an important role in defense by regulating antimicrobial compound accumulation in infected Acuce via a synergistic interaction of JA-salicylic acid (SA) and JA-ethylene (ET). In infected LTH, JA-ET/JA-SA showed antagonistic interaction. Ibuprofen (IBU) is a JA inhibitor. Despite the above findings, we found that exogenous JA-Ile and IBU significantly alleviated blast symptoms in infected LTH at 36 hpi (biotrophic) and 72 hpi (BNS), indicating these two-time points may be critical for managing blast disease in the compatible interaction. Conversely, IBU significantly increased blast symptoms on the infected Acuce at 36 hpi, confirming that the JA signal plays a central role in the defense response in infected Acuce. According to transcriptional analysis, the number of genes enriched in the plant hormone signal pathway was significantly higher than in other pathways. Our findings suggested that JA-mediated defense mechanism is essential in regulating Acuce resistance, particularly during the biotrophic and BNS phases.
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Affiliation(s)
- Xiaoqing Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Guihua Duan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongfeng Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Tang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Shunyu Su
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Zhaoxia Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China
| | - Jing Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, 650201, China.
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Rao MJ, Tahir ul Qamar M, Wang D, Ali Q, Ma L, Han S, Duan M, Hu L, Wang L. A high-throughput lipidomics and transcriptomic approach reveals novel compounds from sugarcane linked with promising therapeutic potential against COVID-19. Front Nutr 2022; 9:988249. [PMID: 36118771 PMCID: PMC9480494 DOI: 10.3389/fnut.2022.988249] [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: 07/07/2022] [Accepted: 08/11/2022] [Indexed: 11/23/2022] Open
Abstract
Sugarcane (Saccharum ssp., Poaceae) provides enormous metabolites such as sugars, lipid, and other dietary metabolites to humans. Among them, lipids are important metabolites that perform various functions and have promising pharmacological value. However, in sugarcane, few studies are focusing on lipidomics and few lipid compounds were reported, and their pharmacological values are not explored yet. The transcriptomic and widely targeted lipidomics approach quantified 134 lipid compounds from the rind of six sugarcane genotypes. These lipid compounds include 57 fatty acids, 30 lysophosphatidylcholines, 23 glycerol esters, 21 lysophosphatidylethanolamines, 2 phosphatidylcholines, and 1 sphingolipid. Among them, 119 compounds were first time reported in sugarcane rind. Seventeen lipids compounds including 12 fatty acids, 2 glycerol lipids, LysoPC 16:0, LysoPE 16:0, and choline alfoscerate were abundantly found in the rind of sugarcane genotypes. From metabolic and transcriptomic results, we have developed a comprehensive lipid metabolic pathway and highlighted key genes that are differentially expressed in sugarcane. Several genes associated with α-linolenic acid and linoleic acid biosynthesis pathways were highly expressed in the rind of the ROC22 genotype. ROC22 has a high level of α-linolenic acid (an essential fatty acid) followed by ROC16. Moreover, we have explored pharmacological values of lipid compounds and found that the 2-linoleoylglycerol and gingerglycolipid C have strong binding interactions with 3CLpro of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and these compounds can be utilized against SARS-CoV-2 as therapeutic agents. The transcriptome, metabolome, and bioinformatics analysis suggests that the sugarcane cultivars have a diversity of lipid compounds having promising therapeutic potential, and exploring the lipid metabolism will help to know more compounds that have promising cosmetic and pharmacological value.
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Affiliation(s)
- Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | | | - Dongxin Wang
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Qurban Ali
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Li Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Shijian Han
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Mingzheng Duan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- College of Life Science and Technology, Guangxi University, Nanning, China
- Lihua Hu
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- *Correspondence: Lingqiang Wang
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Thierry M, Charriat F, Milazzo J, Adreit H, Ravel S, Cros-Arteil S, borron S, Sella V, Kroj T, Ioos R, Fournier E, Tharreau D, Gladieux P. Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation, loss of sex and post-mating genetic incompatibilities. PLoS Pathog 2022; 18:e1010687. [PMID: 35877779 PMCID: PMC9352207 DOI: 10.1371/journal.ppat.1010687] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/04/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.
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Affiliation(s)
- Maud Thierry
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Florian Charriat
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Joëlle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sébastien Ravel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sandrine Cros-Arteil
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia borron
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Violaine Sella
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- * E-mail: (DT); (PG)
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- * E-mail: (DT); (PG)
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11
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Gibson AK. Genetic diversity and disease: The past, present, and future of an old idea. Evolution 2022; 76:20-36. [PMID: 34796478 PMCID: PMC9064374 DOI: 10.1111/evo.14395] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/03/2021] [Accepted: 10/08/2021] [Indexed: 01/21/2023]
Abstract
Why do infectious diseases erupt in some host populations and not others? This question has spawned independent fields of research in evolution, ecology, public health, agriculture, and conservation. In the search for environmental and genetic factors that predict variation in parasitism, one hypothesis stands out for its generality and longevity: genetically homogeneous host populations are more likely to experience severe parasitism than genetically diverse populations. In this perspective piece, I draw on overlapping ideas from evolutionary biology, agriculture, and conservation to capture the far-reaching implications of the link between genetic diversity and disease. I first summarize the development of this hypothesis and the results of experimental tests. Given the convincing support for the protective effect of genetic diversity, I then address the following questions: (1) Where has this idea been put to use, in a basic and applied sense, and how can we better use genetic diversity to limit disease spread? (2) What new hypotheses does the established disease-diversity relationship compel us to test? I conclude that monitoring, preserving, and augmenting genetic diversity is one of our most promising evolutionarily informed strategies for buffering wild, domesticated, and human populations against future outbreaks.
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Affiliation(s)
- Amanda Kyle Gibson
- Department of Biology University of Virginia Charlottesville Virginia 22903
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12
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NLRs guard metabolism to coordinate pattern- and effector-triggered immunity. Nature 2022; 601:245-251. [PMID: 34912119 DOI: 10.1038/s41586-021-04219-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/09/2021] [Indexed: 01/09/2023]
Abstract
Pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) in plants enable them to respond to pathogens by activating the production of defence metabolites that orchestrate immune responses1-4. How the production of defence metabolites is promoted by immune receptors and coordinated with broad-spectrum resistance remains elusive. Here we identify the deubiquitinase PICI1 as an immunity hub for PTI and ETI in rice (Oryza sativa). PICI1 deubiquitinates and stabilizes methionine synthetases to activate methionine-mediated immunity principally through biosynthesis of the phytohormone ethylene. PICI1 is targeted for degradation by blast fungal effectors, including AvrPi9, to dampen PTI. Nucleotide-binding domain, leucine-rich-repeat-containing receptors (NLRs) in the plant immune system, such as PigmR, protect PICI1 from effector-mediated degradation to reboot the methionine-ethylene cascade. Natural variation in the PICI1 gene contributes to divergence in basal blast resistance between the rice subspecies indica and japonica. Thus, NLRs govern an arms race with effectors, using a competitive mode that hinges on a critical defence metabolic pathway to synchronize PTI with ETI and ensure broad-spectrum resistance.
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Wu Q, Wang Y, Liu LN, Shi K, Li CY. Comparative Genomics and Gene Pool Analysis Reveal the Decrease of Genome Diversity and Gene Number in Rice Blast Fungi by Stable Adaption with Rice. J Fungi (Basel) 2021; 8:jof8010005. [PMID: 35049945 PMCID: PMC8778285 DOI: 10.3390/jof8010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/12/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Magnaporthe oryzae caused huge losses in rice and wheat production worldwide. Comparing to long-term co-evolution history with rice, wheat-infecting isolates were new-emerging. To reveal the genetic differences between rice and wheat blast on global genomic scale, 109 whole-genome sequences of M. oryzae from rice, wheat, and other hosts were reanalyzed in this study. We found that the rice lineage had gone through stronger selective sweep and fewer conserved genes than those of Triticum and Lolium lineages, which indicated that rice blast fungi adapted to rice by gene loss and rapid evolution of specific loci. Furthermore, 228 genes associated with host adaptation of M. oryzae were found by presence/absence variation (PAV) analyses. The functional annotation of these genes found that the fine turning of genes gain/loss involved with transport and transcription factor, thiol metabolism, and nucleotide metabolism respectively are major mechanisms for rice adaption. This result implies that genetic base of specific host plant may lead to gene gain/loss variation of pathogens, so as to enhance their adaptability to host. Further characterization of these specific loci and their roles in adaption and evaluation of the fungi may eventually lead to understanding of interaction mechanism and develop new strategies of the disease management.
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Affiliation(s)
- Qi Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- College of Science, Yunnan Agricultural University, Kunming 650201, China
- Yunnan Organic Tea Industry Intelligent Engineering Research Center, Key Laboratory of Intelligent Organic Tea Garden Construction in Universities of Yunnan Province, Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
| | - Li-Na Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests of Yunnan Province, Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming 650201, China
| | - Kai Shi
- School of Foreign Language, Yunnan Agricultural University, Kunming 650201, China;
| | - Cheng-Yun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.W.); (L.-N.L.)
- Correspondence:
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14
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Gao J, Xu G, Xu P. Whole-genome resequencing of three Coilia nasus population reveals genetic variations in genes related to immune, vision, migration, and osmoregulation. BMC Genomics 2021; 22:878. [PMID: 34872488 PMCID: PMC8647404 DOI: 10.1186/s12864-021-08182-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Background Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea. Based on morphological and ecological researches of C. nasus, two ecotypes were identified. One is the anadromous population (AP). The sexually mature fish run thousands of kilometers from marine to river for spawning. Another one is the resident population which cannot migrate. Based on their different habitats, they were classified into landlocked population (LP) and sea population (SP) which were resident in the freshwater lake and marine during the entire lifetime, respectively. However, they have never been systematically studied. Moreover, C. nasus is declining sharply due to overfishing and pollution recently. Therefore, further understandings of C. nasus populations are needed for germplasm protection. Results Whole-genome resequencing of AP, LP, and SP were performed to enrich the understanding of different populations of C. nasus. At the genome level, 3,176,204, 3,307,069, and 3,207,906 single nucleotide polymorphisms (SNPs) and 1,892,068, 2,002,912, and 1,922,168 insertion/deletion polymorphisms (InDels) were generated in AP, LP, and SP, respectively. Selective sweeping analysis showed that 1022 genes were selected in AP vs LP; 983 genes were selected in LP vs SP; 116 genes were selected in AP vs SP. Among them, selected genes related to immune, vision, migration, and osmoregulation were identified. Furthermore, their expression profiles were detected by quantitative real-time PCR. Expression levels of selected genes related to immune, and vision in LP were significantly lower than AP and SP. Selected genes related to migration in AP were expressed significantly more highly than LP. Expression levels of selected genes related to osmoregulation were also detected. The expression of NKAα and NKCC1 in LP were significantly lower than SP, while expression of NCC, SLC4A4, NHE3, and V-ATPase in LP was significantly higher than SP. Conclusions Combined to life history of C. nasus populations, our results revealed that the molecular mechanisms of their differences of immune, vision, migration, and osmoregulation. Our findings will provide a further understanding of different populations of C. nasus and will be beneficial for wild C. nasus protection. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08182-0.
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Affiliation(s)
- Jun Gao
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China
| | - Gangchun Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China. .,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, Jiangsu, China.
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, Jiangsu, China. .,Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, Jiangsu, China.
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15
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Boufleur TR, Massola Júnior NS, Tikami Í, Sukno SA, Thon MR, Baroncelli R. Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean. Pathogens 2021; 10:pathogens10111520. [PMID: 34832675 PMCID: PMC8625359 DOI: 10.3390/pathogens10111520] [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: 10/18/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
Colletotrichum is one of the most important plant pathogenic genus of fungi due to its scientific and economic impact. A wide range of hosts can be infected by Colletotrichum spp., which causes losses in crops of major importance worldwide, such as soybean. Soybean anthracnose is mainly caused by C. truncatum, but other species have been identified at an increasing rate during the last decade, becoming one of the most important limiting factors to soybean production in several regions. To gain a better understanding of the evolutionary origin of soybean anthracnose, we compared the repertoire of effector candidates of four Colletotrichum species pathogenic to soybean and eight species not pathogenic. Our results show that the four species infecting soybean belong to two lineages and do not share any effector candidates. These results strongly suggest that two Colletotrichum lineages have acquired the capability to infect soybean independently. This study also provides, for each lineage, a set of candidate effectors encoding genes that may have important roles in pathogenicity towards soybean offering a new resource useful for further research on soybean anthracnose management.
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Affiliation(s)
- Thaís R. Boufleur
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
- Correspondence: (T.R.B.); (R.B.)
| | - Nelson S. Massola Júnior
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
| | - Ísis Tikami
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba 13418-900, São Paulo, Brazil; (N.S.M.J.); (Í.T.)
| | - Serenella A. Sukno
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
| | - Michael R. Thon
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
| | - Riccardo Baroncelli
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185 Villamayor, Salamanca, Spain; (S.A.S.); (M.R.T.)
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale Fanin 44, 40126 Bologna, Italy
- Correspondence: (T.R.B.); (R.B.)
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16
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Gao M, He Y, Yin X, Zhong X, Yan B, Wu Y, Chen J, Li X, Zhai K, Huang Y, Gong X, Chang H, Xie S, Liu J, Yue J, Xu J, Zhang G, Deng Y, Wang E, Tharreau D, Wang GL, Yang W, He Z. Ca 2+ sensor-mediated ROS scavenging suppresses rice immunity and is exploited by a fungal effector. Cell 2021; 184:5391-5404.e17. [PMID: 34597584 DOI: 10.1016/j.cell.2021.09.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/23/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Plant immunity is activated upon pathogen perception and often affects growth and yield when it is constitutively active. How plants fine-tune immune homeostasis in their natural habitats remains elusive. Here, we discover a conserved immune suppression network in cereals that orchestrates immune homeostasis, centering on a Ca2+-sensor, RESISTANCE OF RICE TO DISEASES1 (ROD1). ROD1 promotes reactive oxygen species (ROS) scavenging by stimulating catalase activity, and its protein stability is regulated by ubiquitination. ROD1 disruption confers resistance to multiple pathogens, whereas a natural ROD1 allele prevalent in indica rice with agroecology-specific distribution enhances resistance without yield penalty. The fungal effector AvrPiz-t structurally mimics ROD1 and activates the same ROS-scavenging cascade to suppress host immunity and promote virulence. We thus reveal a molecular framework adopted by both host and pathogen that integrates Ca2+ sensing and ROS homeostasis to suppress plant immunity, suggesting a principle for breeding disease-resistant, high-yield crops.
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Affiliation(s)
- Mingjun Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yang He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Yin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbin Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Bingxiao Yan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yue Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jin Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaoyuan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Keran Zhai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yifeng Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiangyu Gong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huizhong Chang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shenghan Xie
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiaxing Yue
- Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Jianlong Xu
- Insititute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guiquan Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Didier Tharreau
- PHIM, CIRAD, INRAE, IRD, Montpellier SupAgro, MUSE, Montpellier Cedex 05, France
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, OH 43210, USA
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; CAS-JIC Center of Excellence for Plant and Microbial Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Ramu VS, Oh S, Lee HK, Nandety RS, Oh Y, Lee S, Nakashima J, Tang Y, Senthil-Kumar M, Mysore KS. A Novel Role of Salt- and Drought-Induced RING 1 Protein in Modulating Plant Defense Against Hemibiotrophic and Necrotrophic Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:297-308. [PMID: 33231502 DOI: 10.1094/mpmi-09-20-0257-r] [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: 06/11/2023]
Abstract
Many plant-encoded E3 ligases are known to be involved in plant defense. Here, we report a novel role of E3 ligase SALT- AND DROUGHT-INDUCED RING FINGER1 (SDIR1) in plant immunity. Even though SDIR1 is reasonably well-characterized, its role in biotic stress response is not known. The silencing of SDIR1 in Nicotiana benthamiana reduced the multiplication of the virulent bacterial pathogen Pseudomonas syringae pv. tabaci. The Arabidopsis sdir1 mutant is resistant to virulent pathogens, whereas SDIR1 overexpression lines are susceptible to both host and nonhost hemibiotrophic bacterial pathogens. However, sdir1 mutant and SDIR1 overexpression lines showed hypersusceptibility and resistance, respectively, against the necrotrophic pathogen Erwinia carotovora. The mutant of SDIR1 target protein, i.e., SDIR-interacting protein 1 (SDIR1P1), also showed resistance to host and nonhost pathogens. In SDIR1 overexpression plants, transcripts of NAC transcription factors were less accumulated and the levels of jasmonic acid (JA) and abscisic acid were increased. In the sdir1 mutant, JA signaling genes JAZ7 and JAZ8 were downregulated. These data suggest that SDIR1 is a susceptibility factor and its activation or overexpression enhances disease caused by P. syringae pv. tomato DC3000 in Arabidopsis. Our results show a novel role of SDIR1 in modulating plant defense gene expression and plant immunity.[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)
- Vemanna S Ramu
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Laboratory of Plant Functional Genomics, Regional Center for Biotechnology, Faridabad, India
| | - Sunhee Oh
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Hee-Kyung Lee
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Youngjae Oh
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL 33598, U.S.A
| | - Seonghee Lee
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Science, University of Florida, Wimauma, FL 33598, U.S.A
| | - Jin Nakashima
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Yuhong Tang
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
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18
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Ebbole DJ, Chen M, Zhong Z, Farmer N, Zheng W, Han Y, Lu G, Wang Z. Evolution and Regulation of a Large Effector Family of Pyricularia oryzae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:255-269. [PMID: 33211639 DOI: 10.1094/mpmi-07-20-0210-r] [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: 06/11/2023]
Abstract
Plant pathogen effectors play important roles in parasitism, including countering plant immunity. However, investigations of the emergence and diversification of fungal effectors across host-adapted populations has been limited. We previously identified a gene encoding a suppressor of plant cell death in Pyricularia oryzae (syn. Magnaporthe oryzae). Here, we report the gene is one of a 21-member gene family and we characterize sequence diversity in different populations. Within the rice pathogen population, nucleotide diversity is low, however; the majority of gene family members display presence-absence polymorphism or other null alleles. Gene family allelic diversity is greater between host-adapted populations and, thus, we named them host-adapted genes (HAGs). Multiple copies of HAGs were found in some genome assemblies and sequence divergence between the alleles in two cases suggested they were the result of repeat-induced point mutagenesis. Transfer of family members between populations and novel HAG haplotypes resulting from apparent recombination were observed. HAG family transcripts were induced in planta and a subset of HAGs are dependent on a key regulator of pathogenesis, PMK1. We also found differential intron splicing for some HAGs that would prevent ex planta protein expression. For some genes, spliced transcript was expressed in antiphase with an overlapping antisense transcript. Characterization of HAG expression patterns and allelic diversity reveal novel mechanisms for HAG regulation and mechanisms generating sequence diversity and novel allele combinations. This evidence of strong in planta-specific expression and selection operating on the HAG family is suggestive of a role in parasitism.[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)
- Daniel J Ebbole
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, U.S.A
| | - Meilian Chen
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, U.S.A
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Nicholas Farmer
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, U.S.A
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Yijuan Han
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Zonghua Wang
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
- Fujian Universities Key Laboratory of Plant-Microbe Interactions, College of Life Science, Fujian Agriculture and Forestry University, Fujian 350002, China
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19
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Lv Z, He Z, Hao L, Kang X, Ma B, Li H, Luo Y, Yuan J, He N. Genome Sequencing Analysis of Scleromitrula shiraiana, a Causal Agent of Mulberry Sclerotial Disease With Narrow Host Range. Front Microbiol 2021; 11:603927. [PMID: 33519746 PMCID: PMC7840784 DOI: 10.3389/fmicb.2020.603927] [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: 09/08/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
Scleromitrula shiraiana is a necrotrophic fungus with a narrow host range, and is one of the main causal pathogens of mulberry sclerotial disease. However, its molecular mechanisms and pathogenesis are unclear. Here, we report a 39.0 Mb high-quality genome sequence for S. shiraiana strain SX-001. The S. shiraiana genome contains 11,327 protein-coding genes. The number of genes and genome size of S. shiraiana are similar to most other Ascomycetes. The cross-similarities and differences of S. shiraiana with the closely related Sclerotinia sclerotiorum and Botrytis cinerea indicated that S. shiraiana differentiated earlier from their common ancestor. A comparative genomic analysis showed that S. shiraiana has fewer genes encoding cell wall-degrading enzymes (CWDEs) and effector proteins than that of S. sclerotiorum and B. cinerea, as well as many other Ascomycetes. This is probably a key factor in the weaker aggressiveness of S. shiraiana to other plants. S. shiraiana has many species-specific genes encoding secondary metabolism core enzymes. The diversity of secondary metabolites may be related to the adaptation of these pathogens to specific ecological niches. However, melanin and oxalic acid are conserved metabolites among many Sclerotiniaceae fungi, and may be essential for survival and infection. Our results provide insights into the narrow host range of S. shiraiana and its adaptation to mulberries.
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Affiliation(s)
- Zhiyuan Lv
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ziwen He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Lijuan Hao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Xin Kang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Hongshun Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Yiwei Luo
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Jianglian Yuan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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20
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Arroyo-Velez N, González-Fuente M, Peeters N, Lauber E, Noël LD. From effectors to effectomes: Are functional studies of individual effectors enough to decipher plant pathogen infectious strategies? PLoS Pathog 2020; 16:e1009059. [PMID: 33270803 PMCID: PMC7714205 DOI: 10.1371/journal.ppat.1009059] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Noe Arroyo-Velez
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Nemo Peeters
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | - Laurent D. Noël
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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21
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Volante A, Tondelli A, Desiderio F, Abbruscato P, Menin B, Biselli C, Casella L, Singh N, McCouch SR, Tharreau D, Zampieri E, Cattivelli L, Valè G. Genome wide association studies for japonica rice resistance to blast in field and controlled conditions. RICE (NEW YORK, N.Y.) 2020; 13:71. [PMID: 33030605 PMCID: PMC7544789 DOI: 10.1186/s12284-020-00431-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/24/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority. Given these assumptions, a Genome Wide Association Study (GWAS) for rice blast resistance was undertaken using a panel of 311 temperate/tropical japonica and indica accessions adapted to temperate conditions and genotyped with 37,423 SNP markers. The panel was evaluated for blast resistance in field, under the pressure of the natural blast population, and in growth chamber, using a mixture of three different fungal strains. RESULTS The parallel screening identified 11 accessions showing high levels of resistance in the two conditions, representing potential donors of resistance sources harbored in rice genotypes adapted to temperate conditions. A general higher resistance level was observed in tropical japonica and indica with respect to temperate japonica varieties. The GWAS identified 14 Marker-Traits Associations (MTAs), 8 of which discovered under field conditions and 6 under growth chamber screening. Three MTAs were identified in both conditions; five MTAs were specifically detected under field conditions while three for the growth chamber inoculation. Comparative analysis of physical/genetic positions of the MTAs showed that most of them were positionally-related with cloned or mapped blast resistance genes or with candidate genes whose functions were compatible for conferring pathogen resistance. However, for three MTAs, indicated as BRF10, BRF11-2 and BRGC11-3, no obvious candidate genes or positional relationships with blast resistance QTLs were identified, raising the possibility that they represent new sources of blast resistance. CONCLUSIONS We identified 14 MTAs for blast resistance using both field and growth chamber screenings. A total of 11 accessions showing high levels of resistance in both conditions were discovered. Combinations of loci conferring blast resistance were identified in rice accessions adapted to temperate conditions, thus allowing the genetic dissection of affordable resistances present in the panel. The obtained information will provide useful bases for both resistance breeding and further characterization of the highlighted resistance loci.
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Affiliation(s)
- Andrea Volante
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy.
- Present Address: CREA Research Centre for Vegetable and Ornamental Crops, Corso Inglesi 508, 18038, Sanremo, IM, Italy.
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Pamela Abbruscato
- PTP Science Park, Rice Genomics Unit, via Einstein, 26900, Lodi, Italy
| | - Barbara Menin
- PTP Science Park, Rice Genomics Unit, via Einstein, 26900, Lodi, Italy
- Centre for Sustainable Future Technologies, Istituto Italiano di Tecnologia, Via Livorno 60, 10144, Torino, Italy
| | - Chiara Biselli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Laura Casella
- SA.PI.SE. Coop. Agricola, via G. Mameli 7, 13100, Vercelli, Italy
| | - Namrata Singh
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, 14850, USA
| | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics section, Cornell University, Ithaca, New York, 14850, USA
| | - Didier Tharreau
- UMR BGPI, CIRAD, TA A54/K, F 34398, Montpellier, France
- BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Elisa Zampieri
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy
- Present Address: Institute for Sustainable Plant Protection, National Research Council, Turin, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100, Vercelli, Italy.
- Dipartimento di Scienze e Innovazione Tecnologica, Complesso Universitario S. Giuseppe, University of Piemonte Orientale, Piazza S. Eusebio 5, 13100, Vercelli, Italy.
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22
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Karasov TL, Shirsekar G, Schwab R, Weigel D. What natural variation can teach us about resistance durability. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:89-98. [PMID: 32535454 DOI: 10.1016/j.pbi.2020.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/08/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Breeding a crop variety to be resistant to a pathogen usually takes years. This is problematic because pathogens, with short generation times and fluid genomes, adapt quickly to overcome resistance. The triumph of the pathogen is not inevitable, however, as there are numerous examples of durable resistance, particularly in wild plants. Which factors then contribute to such resistance stability over millennia? We review current knowledge of wild and agricultural pathosystems, detailing the importance of genetic, species and spatial heterogeneity in the prevention of pathogen outbreaks. We also highlight challenges associated with increasing resistance diversity in crops, both in light of pathogen (co-)evolution and breeding practices. Historically it has been difficult to incorporate heterogeneity into agriculture due to reduced efficiency in harvesting. Recent advances implementing computer vision and automation in agricultural production may improve our ability to harvest mixed genotype and mixed species plantings, thereby increasing resistance durability.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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23
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Badet T, Croll D. The rise and fall of genes: origins and functions of plant pathogen pangenomes. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:65-73. [PMID: 32480355 DOI: 10.1016/j.pbi.2020.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 06/11/2023]
Abstract
Plant pathogens can rapidly overcome resistance of their hosts by mutating key pathogenicity genes encoding for effectors. Pathogen adaptation is fuelled by extensive genetic variability in populations and different strains may not share the same set of genes. Recently, such an intra-specific variation in gene content became formalized as pangenomes distinguishing core genes (i.e. shared) and accessory genes (i.e. lineage or strain-specific). Across pathogens species, key effectors tend to be part of the rapidly evolving accessory genome. Here, we show how the construction and analysis of pathogen pangenomes provide deep insights into the dynamic host adaptation process. We also discuss how pangenomes should ideally be built and how geography, niche and lifestyle likely determine pangenome sizes.
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Affiliation(s)
- Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland.
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24
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Alonso P, Blondin L, Gladieux P, Mahé F, Sanguin H, Ferdinand R, Filloux D, Desmarais E, Cerqueira F, Jin B, Huang H, He X, Morel JB, Martin DP, Roumagnac P, Vernière C. Heterogeneity of the rice microbial community of the Chinese centuries-old Honghe Hani rice terraces system. Environ Microbiol 2020; 22:3429-3445. [PMID: 32510843 PMCID: PMC7497281 DOI: 10.1111/1462-2920.15114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 11/30/2022]
Abstract
The Honghe Hani rice terraces system (HHRTS) is a traditional rice cultivation system where Hani people cultivate remarkably diverse rice varieties. Recent introductions of modern rice varieties to the HHRTS have significantly increased the severity of rice diseases within the terraces. Here, we determine the impacts of these recent introductions on the composition of the rice-associated microbial communities. We confirm that the HHRTS contains a range of both traditional HHRTS landraces and introduced modern rice varieties and find differences between the microbial communities of these two groups. However, this introduction of modern rice varieties has not strongly impacted the overall diversity of the HHRTS rice microbial community. Furthermore, we find that the rice varieties (i.e. groups of closely related genotypes) have significantly structured the rice microbial community composition (accounting for 15%-22% of the variance) and that the core microbial community of HHRTS rice plants represents less than 3.3% of all the microbial taxa identified. Collectively, our study suggests a highly diverse HHRTS rice holobiont (host with its associated microbes) where the diversity of rice hosts mirrors the diversity of their microbial communities. Further studies will be needed to better determine how such changes might impact the sustainability of the HHRTS.
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Affiliation(s)
- Pascal Alonso
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Laurence Blondin
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Pierre Gladieux
- BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France.,INRA, BGPI, Montpellier, France
| | - Frédéric Mahé
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Hervé Sanguin
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Romain Ferdinand
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Denis Filloux
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Eric Desmarais
- ISEM, CNRS, University of Montpellier, IRD, EPHE, Montpellier, France
| | | | - Baihui Jin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,Southwest Forestry University, Kunming, China
| | - Jean-Benoit Morel
- BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France.,INRA, BGPI, Montpellier, France
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, 4579, South Africa
| | - Philippe Roumagnac
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Christian Vernière
- CIRAD, BGPI, Montpellier, France.,BGPI, INRAE, CIRAD, Institut Agro, Univ Montpellier, Montpellier, France
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25
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Liu M, Kang H, Xu Y, Peng Y, Wang D, Gao L, Wang X, Ning Y, Wu J, Liu W, Li C, Liu B, Wang G. Genome-wide association study identifies an NLR gene that confers partial resistance to Magnaporthe oryzae in rice. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1376-1383. [PMID: 31742855 PMCID: PMC7206997 DOI: 10.1111/pbi.13300] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/30/2019] [Accepted: 11/08/2019] [Indexed: 05/09/2023]
Abstract
Because of the frequent breakdown of major resistance (R) genes, identification of new partial R genes against rice blast disease is an important goal of rice breeding. In this study, we used a core collection of the Rice Diversity Panel II (C-RDP-II), which contains 584 rice accessions and are genotyped with 700 000 single-nucleotide polymorphism (SNP) markers. The C-RDP-II accessions were inoculated with three blast strains collected from different rice-growing regions in China. Genome-wide association study identified 27 loci associated with rice blast resistance (LABRs). Among them, 22 LABRs were not associated with any known blast R genes or QTLs. Interestingly, a nucleotide-binding site leucine-rich repeat (NLR) gene cluster exists in the LABR12 region on chromosome 4. One of the NLR genes is highly conserved in multiple partially resistant rice cultivars, and its expression is significantly up-regulated at the early stages of rice blast infection. Knockout of this gene via CRISPR-Cas9 in transgenic plants partially reduced blast resistance to four blast strains. The identification of this new non-strain specific partial R gene, tentatively named rice blast Partial Resistance gene 1 (PiPR1), provides genetic material that will be useful for understanding the partial resistance mechanism and for breeding durably resistant cultivars against blast disease of rice.
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Affiliation(s)
- Ming‐Hao Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yucheng Xu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of AgronomyHunan Agricultural UniversityChangshaHunanChina
| | - Ye Peng
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Dan Wang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and College of AgronomyHunan Agricultural UniversityChangshaHunanChina
| | - Lijun Gao
- Guangxi Crop Genetic Improvement and Biotechnology LaboratoryGuangxi Academy of Agricultural SciencesNanningChina
| | - Xuli Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Jun Wu
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CentreChangshaHunanChina
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Chengyun Li
- The Ministry of Education Key Laboratory for Agricultural Biodiversity and Pest ManagementYunnan Agricultural UniversityKunmingChina
| | - Bin Liu
- Guangdong Key Laboratory of New Technology in Rice BreedingRice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Guo‐Liang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect PestsInstitute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
- Department of Plant PathologyOhio State UniversityColumbusOHUSA
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26
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Kim KT, Ko J, Song H, Choi G, Kim H, Jeon J, Cheong K, Kang S, Lee YH. Evolution of the Genes Encoding Effector Candidates Within Multiple Pathotypes of Magnaporthe oryzae. Front Microbiol 2019; 10:2575. [PMID: 31781071 PMCID: PMC6851232 DOI: 10.3389/fmicb.2019.02575] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/24/2019] [Indexed: 01/08/2023] Open
Abstract
Magnaporthe oryzae infects rice, wheat, and many grass species in the Poaceae family by secreting protein effectors. Here, we analyzed the distribution, sequence variation, and genomic context of effector candidate (EFC) genes in 31 isolates that represent five pathotypes of M. oryzae, three isolates of M. grisea, a sister species of M. oryzae, and one strain each for eight species in the family Magnaporthaceae to investigate how the host range expansion of M. oryzae has likely affected the evolution of effectors. We used the EFC genes of M. oryzae strain 70-15, whose genome has served as a reference for many comparative genomics analyses, to identify their homologs in these strains. We also analyzed the previously characterized avirulence (AVR) genes and single-copy orthologous (SCO) genes in these strains, which showed that the EFC and AVR genes evolved faster than the SCO genes. The EFC and AVR repertoires among M. oryzae pathotypes varied widely probably because adaptation to individual hosts exerted different types of selection pressure. Repetitive DNA elements appeared to have caused the variation of some EFC genes. Lastly, we analyzed expression patterns of the AVR and EFC genes to test the hypothesis that such genes are preferentially expressed during host infection. This comprehensive dataset serves as a foundation for future studies on the genetic basis of the evolution and host specialization in M. oryzae.
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Affiliation(s)
- Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Jaeho Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, PA, United States
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea.,Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea.,Plant Immunity Research Center, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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27
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Alonso P, Gladieux P, Moubset O, Shih PJ, Mournet P, Frouin J, Blondin L, Ferdinand R, Fernandez E, Julian C, Filloux D, Adreit H, Fournier E, Ducasse A, Grosbois V, Morel JB, Huang H, Jin B, He X, Martin DP, Vernière C, Roumagnac P. Emergence of Southern Rice Black-Streaked Dwarf Virus in the Centuries-Old Chinese Yuanyang Agrosystem of Rice Landraces. Viruses 2019; 11:v11110985. [PMID: 31731529 PMCID: PMC6893465 DOI: 10.3390/v11110985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 01/17/2023] Open
Abstract
Southern rice black-streaked dwarf virus (SRBSDV), which causes severe disease symptoms in rice (Oriza sativa L.) has been emerging in the last decade throughout northern Vietnam, southern Japan and southern, central and eastern China. Here we attempt to quantify the prevalence of SRBSDV in the Honghe Hani rice terraces system (HHRTS)-a Chinese 1300-year-old traditional rice production system. We first confirm that genetically diverse rice varieties are still being cultivated in the HHRTS and categorize these varieties into three main genetic clusters, including the modern hybrid varieties group (MH), the Hongyang improved modern variety group (HY) and the traditional indica landraces group (TIL). We also show over a 2-year period that SRBSDV remains prevalent in the HHRTS (20.1% prevalence) and that both the TIL (17.9% prevalence) and the MH varieties (5.1% prevalence) were less affected by SRBSDV than were the HY varieties (30.2% prevalence). Collectively we suggest that SRBSDV isolates are freely moving within the HHRTS and that TIL, HY and MH rice genetic clusters are not being preferentially infected by particular SRBSDV lineages. Given that SRBSDV can cause 30-50% rice yield losses, our study emphasizes both the need to better monitor the disease in the HHRTS, and the need to start considering ways to reduce its burden on rice production.
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Affiliation(s)
- Pascal Alonso
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Pierre Gladieux
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
- INRA, BGPI, 34398 Montpellier, France
| | - Oumaima Moubset
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Pei-Jung Shih
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
- Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan
| | - Pierre Mournet
- CIRAD, UMR AGAP, 34398 Montpellier, France; (P.M.); (J.F.)
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier, France
| | - Julien Frouin
- CIRAD, UMR AGAP, 34398 Montpellier, France; (P.M.); (J.F.)
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34398 Montpellier, France
| | - Laurence Blondin
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Romain Ferdinand
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Emmanuel Fernandez
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Charlotte Julian
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Denis Filloux
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Henry Adreit
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Elisabeth Fournier
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
- INRA, BGPI, 34398 Montpellier, France
| | - Aurélie Ducasse
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
- INRA, BGPI, 34398 Montpellier, France
| | | | - Jean-Benoit Morel
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
- INRA, BGPI, 34398 Montpellier, France
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (H.H.); (X.H.)
| | - Baihui Jin
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (H.H.); (X.H.)
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; (H.H.); (X.H.)
- Southwest Forestry University, Kunming 650224, China
| | - Darren P. Martin
- Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 4579, South Africa;
| | - Christian Vernière
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
| | - Philippe Roumagnac
- CIRAD, BGPI, 34398 Montpellier, France; (P.A.); (O.M.); (P.-J.S.); (L.B.); (R.F.); (E.F.); (C.J.); (D.F.); (H.A.); (C.V.)
- BGPI, INRA, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France; (P.G.); (E.F.); (A.D.); (J.-B.M.)
- Correspondence: ; Tel.: +33(0)-4-99-62-48-53; Fax: +33(0)-4-99-62-48-48
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28
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Phosphorylation-guarded light-harvesting complex II contributes to broad-spectrum blast resistance in rice. Proc Natl Acad Sci U S A 2019; 116:17572-17577. [PMID: 31405986 DOI: 10.1073/pnas.1905123116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Environmental conditions are key factors in the progression of plant disease epidemics. Light affects the outbreak of plant diseases, but the underlying molecular mechanisms are not well understood. Here, we report that the light-harvesting complex II protein, LHCB5, from rice is subject to light-induced phosphorylation during infection by the rice blast fungus Magnaporthe oryzae We demonstrate that single-nucleotide polymorphisms (SNPs) in the LHCB5 promoter control the expression of LHCB5, which in turn correlates with the phosphorylation of LHCB5. LHCB5 phosphorylation enhances broad-spectrum resistance of rice to M. oryzae through the accumulation of reactive oxidative species (ROS) in the chloroplast. We also show that LHCB5 phosphorylation-induced resistance is inheritable. Our results uncover an immunity mechanism mediated by phosphorylation of light-harvesting complex II.
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29
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Ayliffe M, Sørensen CK. Plant nonhost resistance: paradigms and new environments. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:104-113. [PMID: 31075541 DOI: 10.1016/j.pbi.2019.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/08/2019] [Accepted: 03/25/2019] [Indexed: 05/25/2023]
Abstract
Nonhost resistance (NHR) protects plants from a large and diverse array of potential phytopathogens. Each phytopathogen can parasitise some plant species, but most plant species are nonhosts that are innately immune due to a series of physical, chemical and inducible defenses these nonadapted pathogens cannot overcome. New evidence supports the NHR paradigm that posits the inability of potential pathogens to colonise nonhost plants is frequently due to molecular incompatibility between pathogen virulence factors and plant cellular targets. While NHR is durable, it is not insurmountable. Environmental changes can facilitate pathogen host jumps or alternatively result in new encounters between previously isolated plant species and pathogens. Climate change is predicted to substantially alter the current distribution of plants and their pathogens which could result in parasitism of new plant species.
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Affiliation(s)
- Michael Ayliffe
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra, ACT 2601, Australia.
| | - Chris K Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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30
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Gómez Luciano LB, Tsai IJ, Chuma I, Tosa Y, Chen YH, Li JY, Li MY, Lu MYJ, Nakayashiki H, Li WH. Blast Fungal Genomes Show Frequent Chromosomal Changes, Gene Gains and Losses, and Effector Gene Turnover. Mol Biol Evol 2019; 36:1148-1161. [PMID: 30835262 DOI: 10.1093/molbev/msz045] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Pyricularia is a fungal genus comprising several pathogenic species causing the blast disease in monocots. Pyricularia oryzae, the best-known species, infects rice, wheat, finger millet, and other crops. As past comparative and population genomics studies mainly focused on isolates of P. oryzae, the genomes of the other Pyricularia species have not been well explored. In this study, we obtained a chromosomal-level genome assembly of the finger millet isolate P. oryzae MZ5-1-6 and also highly contiguous assemblies of Pyricularia sp. LS, P. grisea, and P. pennisetigena. The differences in the genomic content of repetitive DNA sequences could largely explain the variation in genome size among these new genomes. Moreover, we found extensive gene gains and losses and structural changes among Pyricularia genomes, including a large interchromosomal translocation. We searched for homologs of known blast effectors across fungal taxa and found that most avirulence effectors are specific to Pyricularia, whereas many other effectors share homologs with distant fungal taxa. In particular, we discovered a novel effector family with metalloprotease activity, distinct from the well-known AVR-Pita family. We predicted 751 gene families containing putative effectors in 7 Pyricularia genomes and found that 60 of them showed differential expression in the P. oryzae MZ5-1-6 transcriptomes obtained under experimental conditions mimicking the pathogen infection process. In summary, this study increased our understanding of the structural, functional, and evolutionary genomics of the blast pathogen and identified new potential effector genes, providing useful data for developing crops with durable resistance.
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Affiliation(s)
- Luis B Gómez Luciano
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan
| | | | - Izumi Chuma
- Obihiro University of Agriculture and Veterinary Medicine, Hokkaido, Japan
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jeng-Yi Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Meng-Yun Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.,Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung-Hsing University, Taipei, Taiwan.,Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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31
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Bourras S, Kunz L, Xue M, Praz CR, Müller MC, Kälin C, Schläfli M, Ackermann P, Flückiger S, Parlange F, Menardo F, Schaefer LK, Ben-David R, Roffler S, Oberhaensli S, Widrig V, Lindner S, Isaksson J, Wicker T, Yu D, Keller B. The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nat Commun 2019; 10:2292. [PMID: 31123263 PMCID: PMC6533294 DOI: 10.1038/s41467-019-10274-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/03/2019] [Indexed: 12/25/2022] Open
Abstract
The wheat Pm3 resistance gene against the powdery mildew pathogen occurs as an allelic series encoding functionally different immune receptors which induce resistance upon recognition of isolate-specific avirulence (AVR) effectors from the pathogen. Here, we describe the identification of five effector proteins from the mildew pathogens of wheat, rye, and the wild grass Dactylis glomerata, specifically recognized by the PM3B, PM3C and PM3D receptors. Together with the earlier identified AVRPM3A2/F2, the recognized AVRs of PM3B/C, (AVRPM3B2/C2), and PM3D (AVRPM3D3) belong to a large group of proteins with low sequence homology but predicted structural similarities. AvrPm3b2/c2 and AvrPm3d3 are conserved in all tested isolates of wheat and rye mildew, and non-host infection assays demonstrate that Pm3b, Pm3c, and Pm3d are also restricting the growth of rye mildew on wheat. Furthermore, divergent AVR homologues from non-adapted rye and Dactylis mildews are recognized by PM3B, PM3C, or PM3D, demonstrating their involvement in host specificity.
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Affiliation(s)
- Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.
| | - Lukas Kunz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Coraline Rosalie Praz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Carol Kälin
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Michael Schläfli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Patrick Ackermann
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | | | - Roi Ben-David
- Institute of Plant Science, ARO-Volcani Center, 50250, Bet Dagan, Israel
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Victoria Widrig
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Stefan Lindner
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Jonatan Isaksson
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China.
- College of Life Science, Wuhan University, Wuhan, 430072, China.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
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32
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Mohd-Assaad N, McDonald BA, Croll D. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses. Environ Microbiol 2019; 21:2677-2695. [PMID: 30838748 DOI: 10.1111/1462-2920.14583] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 01/28/2023]
Abstract
Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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33
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Gladieux P. What makes a specialized endophyte special? Mol Ecol 2019; 27:3037-3039. [PMID: 30133874 DOI: 10.1111/mec.14775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/08/2018] [Indexed: 02/05/2023]
Abstract
Fungal plant symbionts can be highly specialized on a limited range of host genotypes and species. Understanding the genetic basis of this specialization, the mechanisms governing its establishment and the relationship between specialization and speciation is a major challenge for evolutionary biologists (Timms & Read, ). A deeper knowledge of evolutionary plant-microbe interactions could be exploited to improve agricultural management, by bringing fungal biodiversity and fungal biomass under greater and more durable human control. Previous studies on pathogens have shown that effectors, that is, small secreted proteins that modulate plant physiology to favour host colonization, play a key role in infection of novel hosts (e.g., Inoue et al., ) or in host specialization (e.g., Liao et al. ()). Like pathogens, endophytes also manipulate the physiology of their hosts and colonize novel hosts to which they specialize (Hardoim et al., ). These biological characteristics of endophytes raise the question of similarities in the protein arsenal contributing to the specialization of pathogens and endophytes. In this issue of Molecular Ecology, Schirrmann et al. () used a combination of divergence genome scans and tests for positive selection to investigate the genetic basis of specialization of two subspecies of the symbiont Epichloë typhina occurring on two different grass hosts. Their analyses suggest a key role of effectors as determinants of host specialization. This study paves the way towards the comparative analysis of the genomics of speciation among plant symbionts.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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34
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Zhong Z, Lin L, Chen M, Lin L, Chen X, Lin Y, Chen X, Wang Z, Norvienyeku J, Zheng H. Expression Divergence as an Evolutionary Alternative Mechanism Adopted by Two Rice Subspecies Against Rice Blast Infection. RICE (NEW YORK, N.Y.) 2019; 12:12. [PMID: 30825020 PMCID: PMC6397267 DOI: 10.1186/s12284-019-0270-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/18/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide. Some important agronomic traits that allow rice to cope with numerous abiotic and biotic stresses have been selected and fixed during domestication. Knowledge on how expression divergence of genes gradually contributes to phenotypic differentiation in response to biotic stress and their contribution to rice population speciation is still limited. RESULTS Here, we explored gene expression divergence between a japonica rice cultivar Nipponbare and an indica rice cultivar 93-11 in response to invasion by the filamentous ascomycete fungus Magnaporthe oryzae (Pyricularia oryzae), a plant pathogen that causes significant loss to rice production worldwide. We investigated differentially expressed genes in the two cultivars and observed that evolutionarily conserved orthologous genes showed highly variable expression patterns under rice blast infection. Analysis of promoter region of these differentially expressed orthologous genes revealed the existence of cis-regulatory elements associated with the differentiated expression pattern of these genes in the two rice cultivars. Further comparison of these regions in global rice population indicated their fixation and close relationship with rice population divergence. CONCLUSION We proposed that variation in the expression patterns of these orthologous genes mediated by cis-regulatory elements in the two rice cultivars, may constitute an alternative evolutionary mechanism that distinguishes these two genetically and ecologically divergent rice cultivars in response to M. oryzae infection.
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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
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, 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
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Meilian Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lili 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
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaofeng Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yahong 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
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xi Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - 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
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Institute of Oceanography, Minjiang University, Fuzhou, 350108 China
| | - Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, 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
- Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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35
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Kale SD. PenSeq: coverage you can count on. THE NEW PHYTOLOGIST 2019; 221:1177-1179. [PMID: 30644579 DOI: 10.1111/nph.15608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Shiv D Kale
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, 24060, USA
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36
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Zheng H, Zhong Z, Shi M, Zhang L, Lin L, Hong Y, Fang T, Zhu Y, Guo J, Zhang L, Fang J, Lin H, Norvienyeku J, Chen X, Lu G, Hu H, Wang Z. Comparative genomic analysis revealed rapid differentiation in the pathogenicity-related gene repertoires between Pyricularia oryzae and Pyricularia penniseti isolated from a Pennisetum grass. BMC Genomics 2018; 19:927. [PMID: 30545292 PMCID: PMC6293661 DOI: 10.1186/s12864-018-5222-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 11/05/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND A number of Pyricularia species are known to infect different grass species. In the case of Pyricularia oryzae (syn. Magnaporthe oryzae), distinct populations are known to be adapted to a wide variety of grass hosts, including rice, wheat and many other grasses. The genome sizes of Pyricularia species are typical for filamentous ascomycete fungi [~ 40 Mbp for P. oryzae, and ~ 45 Mbp for P. grisea]. Genome plasticity, mediated in part by deletions promoted by recombination between repetitive elements [Genome Res 26:1091-1100, 2016, Nat Rev Microbiol 10:417-430,2012] and transposable elements [Annu Rev Phytopathol 55:483-503,2017] contributes to host adaptation. Therefore, comparisons of genome structure of individual species will provide insight into the evolution of host specificity. However, except for the P. oryzae subgroup, little is known about the gene content or genome organization of other Pyricularia species, such as those infecting Pennisetum grasses. RESULTS Here, we report the genome sequence of P. penniseti strain P1609 isolated from a Pennisetum grass (JUJUNCAO) using PacBio SMRT sequencing technology. Phylogenomic analysis of 28 Magnaporthales species and 5 non-Magnaporthales species indicated that P1609 belongs to a Pyricularia subclade, which is genetically distant from P. oryzae. Comparative genomic analysis revealed that the pathogenicity-related gene repertoires had diverged between P1609 and the P. oryzae strain 70-15, including the known avirulence genes, other putative secreted proteins, as well as some other predicted Pathogen-Host Interaction (PHI) genes. Genomic sequence comparison also identified many genomic rearrangements relative to P. oryzae. CONCLUSION Our results suggested that the genomic sequence of the P. penniseti P1609 could be a useful resource for the genetic study of the Pennisetum-infecting Pyricularia species and provide new insight into evolution of pathogen genomes during host adaptation.
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Affiliation(s)
- Huakun Zheng
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - 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
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Mingyue Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 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
- 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
- College of life science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yonghe Hong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of life science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Tian Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yangyan Zhu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Limin 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
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jie Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of life science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hui Lin
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of life science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaofeng Chen
- Institute of Oceanography, Minjiang University, Fuzhou, 350108 China
| | - Guodong Lu
- National Engineering Research Center of JUNCAO Technology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hongli Hu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - 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
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of life science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Tanaka S, Schweizer G, Rössel N, Fukada F, Thines M, Kahmann R. Neofunctionalization of the secreted Tin2 effector in the fungal pathogen Ustilago maydis. Nat Microbiol 2018; 4:251-257. [PMID: 30510169 DOI: 10.1038/s41564-018-0304-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/24/2018] [Indexed: 01/23/2023]
Abstract
Plant-pathogenic fungi hijack their hosts by secreting effector proteins. Effectors serve to suppress plant immune responses and modulate the host metabolism to benefit the pathogen. Smut fungi are biotrophic pathogens that also parasitize important cereals, including maize1. Symptom development is usually restricted to the plant inflorescences. Ustilago maydis is an exception in its ability to cause tumours in both inflorescences and leaves of maize, and in inducing anthocyanin biosynthesis through the secreted Tin2 effector2,3. How the unique lifestyle of U. maydis has evolved remains to be elucidated. Here we show that Tin2 in U. maydis has been neofunctionalized. We functionally compared Tin2 effectors of U. maydis and the related smut Sporisorium reilianum, which results in symptoms only in the inflorescences of maize and fails to induce anthocyanin. We show that Tin2 effectors from both fungi target distinct paralogues of a maize protein kinase, leading to stabilization and inhibition, respectively. An ancestral Tin2 effector functionally replaced the virulence function of S. reilianum Tin2 but failed to induce anthocyanin, and was unable to substitute for Tin2 in U. maydis. This shows that Tin2 in U. maydis has acquired a specialized function, probably connected to the distinct pathogenic lifestyle of this fungus.
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Affiliation(s)
- Shigeyuki Tanaka
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gabriel Schweizer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,University of Zurich, Department of Evolutionary Biology and Environmental Studies, Zurich, Switzerland
| | - Nicole Rössel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Fumi Fukada
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marco Thines
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Center, Frankfurt am Main, Germany
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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Rimbaud L, Papaïx J, Barrett LG, Burdon JJ, Thrall PH. Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy to deploy major gene resistance? Evol Appl 2018; 11:1791-1810. [PMID: 30459830 PMCID: PMC6231482 DOI: 10.1111/eva.12681] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/14/2018] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
Once deployed uniformly in the field, genetically controlled plant resistance is often quickly overcome by pathogens, resulting in dramatic losses. Several strategies have been proposed to constrain the evolutionary potential of pathogens and thus increase resistance durability. These strategies can be classified into four categories, depending on whether resistance sources are varied across time (rotations) or combined in space in the same cultivar (pyramiding), in different cultivars within a field (cultivar mixtures) or among fields (mosaics). Despite their potential to differentially affect both pathogen epidemiology and evolution, to date the four categories of deployment strategies have never been directly compared together within a single theoretical or experimental framework, with regard to efficiency (ability to reduce disease impact) and durability (ability to limit pathogen evolution and delay resistance breakdown). Here, we used a spatially explicit stochastic demogenetic model, implemented in the R package landsepi, to assess the epidemiological and evolutionary outcomes of these deployment strategies when two major resistance genes are present. We varied parameters related to pathogen evolutionary potential (mutation probability and associated fitness costs) and landscape organization (mostly the relative proportion of each cultivar in the landscape and levels of spatial or temporal aggregation). Our results, broadly focused on qualitative resistance to rust fungi of cereal crops, show that evolutionary and epidemiological control are not necessarily correlated and that no deployment strategy is universally optimal. Pyramiding two major genes offered the highest durability, but at high mutation probabilities, mosaics, mixtures and rotations can perform better in delaying the establishment of a universally infective superpathogen. All strategies offered the same short-term epidemiological control, whereas rotations provided the best long-term option, after all sources of resistance had broken down. This study also highlights the significant impact of landscape organization and pathogen evolutionary ability in considering the optimal design of a deployment strategy.
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Affiliation(s)
- Loup Rimbaud
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | | | - Luke G. Barrett
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | - Jeremy J. Burdon
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | - Peter H. Thrall
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
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Besset-Manzoni Y, Rieusset L, Joly P, Comte G, Prigent-Combaret C. Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:29953-29970. [PMID: 29313197 DOI: 10.1007/s11356-017-1152-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 12/26/2017] [Indexed: 05/23/2023]
Abstract
The rhizosphere hosts a considerable microbial community. Among that community, bacteria called plant growth-promoting rhizobacteria (PGPR) can promote plant growth and defense against diseases using diverse distinct plant-beneficial functions. Crop inoculation with PGPR could allow to reduce the use of pesticides and fertilizers in agrosystems. However, microbial crop protection and growth stimulation would be more efficient if cooperation between rhizosphere bacterial populations was taken into account when developing biocontrol agents and biostimulants. Rhizospheric bacteria live in multi-species biofilms formed all along the root surface or sometimes inside the plants (i.e., endophyte). PGPR cooperate with their host plants and also with other microbial populations inside biofilms. These interactions are mediated by a large diversity of microbial metabolites and physical signals that trigger cell-cell communication and appropriate responses. A better understanding of bacterial behavior and microbial cooperation in the rhizosphere could allow for a more successful use of bacteria in sustainable agriculture. This review presents an ecological view of microbial cooperation in agrosystems and lays the emphasis on the main microbial metabolites involved in microbial cooperation, plant health protection, and plant growth stimulation. Eco-friendly inoculant consortia that will foster microbe-microbe and microbe-plant cooperation can be developed to promote crop growth and restore biodiversity and functions lost in agrosystems.
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Affiliation(s)
- Yoann Besset-Manzoni
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
- Biovitis, 15 400, Saint Etienne-de-Chomeil, France
| | - Laura Rieusset
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
| | - Pierre Joly
- Biovitis, 15 400, Saint Etienne-de-Chomeil, France
| | - Gilles Comte
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France
| | - Claire Prigent-Combaret
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, 43 bd du 11 Novembre 1918, F-69622, Villeurbanne cedex, France.
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40
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Abstract
The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae) is both a threat to global food security and a model for plant pathology. Molecular pathologists need an accurate understanding of the origins and line of descent of M. oryzae populations in order to identify the genetic and functional bases of pathogen adaptation and to guide the development of more effective control strategies. We used a whole-genome sequence analysis of samples from different times and places to infer details about the genetic makeup of M. oryzae from a global collection of isolates. Analyses of population structure identified six lineages within M. oryzae, including two pandemic on japonica and indica rice, respectively, and four lineages with more restricted distributions. Tip-dating calibration indicated that M. oryzae lineages separated about a millennium ago, long after the initial domestication of rice. The major lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and evidence of DNA acquisition from multiple lineages. Tests for weak natural selection revealed that the pandemic spread of clonal lineages entailed an evolutionary “cost,” in terms of the accumulation of deleterious mutations. Our findings reveal the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen. The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae) is a textbook example of a rapidly adapting pathogen, and it is responsible for one of the most damaging diseases of rice. Improvements in our understanding of Magnaporthe oryzae’s diversity and evolution are required to guide the development of more effective control strategies. We used genome sequencing data for samples from around the world to infer the evolutionary history of M. oryzae. We found that M. oryzae diversified about 1,000 years ago, separating into six main lineages: two pandemic on japonica and indica rice, respectively, and four with more restricted distributions. We also found that a lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and the acquisition of genetic material from multiple lineages. This work provides a population-level genomic framework for defining molecular markers for the control of rice blast and investigations of the molecular basis of differences in pathogenicity between M. oryzae lineages.
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41
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Zhong Z, Chen M, Lin L, Han Y, Bao J, Tang W, Lin L, Lin Y, Somai R, Lu L, Zhang W, Chen J, Hong Y, Chen X, Wang B, Shen WC, Lu G, Norvienyeku J, Ebbole DJ, Wang Z. Population genomic analysis of the rice blast fungus reveals specific events associated with expansion of three main clades. ISME JOURNAL 2018; 12:1867-1878. [PMID: 29568114 PMCID: PMC6051997 DOI: 10.1038/s41396-018-0100-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 02/10/2018] [Accepted: 02/20/2018] [Indexed: 12/30/2022]
Abstract
We examined the genomes of 100 isolates of Magnaporthe oryzae (Pyricularia oryzae), the causal agent of rice blast disease. We grouped current field populations of M. oryzae into three major globally distributed groups. A genetically diverse group, clade 1, which may represent a group of closely related lineages, contains isolates of both mating types. Two well-separated clades, clades 2 and 3, appear to have arisen as clonal lineages distinct from the genetically diverse clade. Examination of genes involved in mating pathways identified clade-specific diversification of several genes with orthologs involved in mating behavior in other fungi. All isolates within each clonal lineage are of the same mating type. Clade 2 is distinguished by a unique deletion allele of a gene encoding a small cysteine-rich protein that we determined to be a virulence factor. Clade 3 isolates have a small deletion within the MFA2 pheromone precursor gene, and this allele is shared with an unusual group of isolates we placed within clade 1 that contain AVR1-CO39 alleles. These markers could be used for rapid screening of isolates and suggest specific events in evolution that shaped these populations. Our findings are consistent with the view that M. oryzae populations in Asia generate diversity through recombination and may have served as the source of the clades 2 and 3 isolates that comprise a large fraction of the global population.
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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.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meilian Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, 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.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yijuan Han
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, 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.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, 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.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lili 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.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yahong 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.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rewish Somai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjing 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.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jian Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yonghe Hong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaofeng Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baohua 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.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei-Chiang Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Republic of China.
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Daniel J Ebbole
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,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. .,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Institute of Ocean Science, Minjiang University, Fuzhou, 350108, China.
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Navaud O, Barbacci A, Taylor A, Clarkson JP, Raffaele S. Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens. Mol Ecol 2018; 27:1309-1323. [PMID: 29421852 PMCID: PMC5900718 DOI: 10.1111/mec.14523] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 01/26/2018] [Accepted: 01/29/2018] [Indexed: 01/07/2023]
Abstract
The range of hosts that a parasite can infect in nature is a trait determined by its own evolutionary history and that of its potential hosts. However, knowledge on host range diversity and evolution at the family level is often lacking. Here, we investigate host range variation and diversification trends within the Sclerotiniaceae, a family of Ascomycete fungi. Using a phylogenetic framework, we associate diversification rates, the frequency of host jump events and host range variation during the evolution of this family. Variations in diversification rate during the evolution of the Sclerotiniaceae define three major macro-evolutionary regimes with contrasted proportions of species infecting a broad range of hosts. Host-parasite cophylogenetic analyses pointed towards parasite radiation on distant hosts long after host speciation (host jump or duplication events) as the dominant mode of association with plants in the Sclerotiniaceae. The intermediate macro-evolutionary regime showed a low diversification rate, high frequency of duplication events and the highest proportion of broad host range species. Our findings suggest that the emergence of broad host range fungal pathogens results largely from host jumps, as previously reported for oomycete parasites, probably combined with low speciation rates. These results have important implications for our understanding of fungal parasites evolution and are of particular relevance for the durable management of disease epidemics.
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Affiliation(s)
- Olivier Navaud
- LIPM, Université de Toulouse, INRA, CNRSCastanet‐TolosanFrance
| | - Adelin Barbacci
- LIPM, Université de Toulouse, INRA, CNRSCastanet‐TolosanFrance
| | - Andrew Taylor
- Warwick Crop CentreSchool of Life SciencesUniversity of WarwickCoventryUK
| | - John P. Clarkson
- Warwick Crop CentreSchool of Life SciencesUniversity of WarwickCoventryUK
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Praz CR, Menardo F, Robinson MD, Müller MC, Wicker T, Bourras S, Keller B. Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen. FRONTIERS IN PLANT SCIENCE 2018; 9:49. [PMID: 29441081 PMCID: PMC5797619 DOI: 10.3389/fpls.2018.00049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/10/2018] [Indexed: 05/20/2023]
Abstract
Powdery mildew is an important disease of cereals. It is caused by one species, Blumeria graminis, which is divided into formae speciales each of which is highly specialized to one host. Recently, a new form capable of growing on triticale (B.g. triticale) has emerged through hybridization between wheat and rye mildews (B.g. tritici and B.g. secalis, respectively). In this work, we used RNA sequencing to study the molecular basis of host adaptation in B.g. triticale. We analyzed gene expression in three B.g. tritici isolates, two B.g. secalis isolates and two B.g. triticale isolates and identified a core set of putative effector genes that are highly expressed in all formae speciales. We also found that the genes differentially expressed between isolates of the same form as well as between different formae speciales were enriched in putative effectors. Their coding genes belong to several families including some which contain known members of mildew avirulence (Avr) and suppressor (Svr) genes. Based on these findings we propose that effectors play an important role in host adaptation that is mechanistically based on Avr-Resistance gene-Svr interactions. We also found that gene expression in the B.g. triticale hybrid is mostly conserved with the parent-of-origin, but some genes inherited from B.g. tritici showed a B.g. secalis-like expression. Finally, we identified 11 unambiguous cases of putative effector genes with hybrid-specific, non-parent of origin gene expression, and we propose that they are possible determinants of host specialization in triticale mildew. These data suggest that altered expression of multiple effector genes, in particular Avr and Svr related factors, might play a role in mildew host adaptation based on hybridization.
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Affiliation(s)
- Coraline R. Praz
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Mark D. Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Marion C. Müller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- *Correspondence: Salim Bourras
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- Beat Keller
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Dong L, Liu S, Xu P, Deng W, Li X, Tharreau D, Li J, Zhou J, Wang Q, Tao D, Yang Q. Fine mapping of Pi57(t) conferring broad spectrum resistance against Magnaporthe oryzae in introgression line IL-E1454 derived from Oryza longistaminata. PLoS One 2017; 12:e0186201. [PMID: 29016662 PMCID: PMC5634632 DOI: 10.1371/journal.pone.0186201] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 09/27/2017] [Indexed: 01/22/2023] Open
Abstract
Wild species of the genus Oryza are excellent gene pools for improvement of agronomic traits of Asian cultivated rice. The blast resistance gene Pi57(t) in the introgression line IL-E1454 derived from Oryza longistaminata was previously mapped on rice chromosome 12. Inoculation with 322 Magnaporthe oryzae isolates collected from 6 countries indicated that Pi57(t) conferred broad spectrum resistance against M. oryzae. Two mapping populations consisting of 29070 and 10375 F2 plants derived from the crosses of resistant donor IL-E1454 with susceptible parents RD23 and Lijiangxintuanheigu respectively, were used for fine mapping of Pi57(t) locus. Based on genotyping and phenotyping results of recombinants screened from the two crosses, Pi57(t) was finally mapped to a 51.7-kb region flanked by two molecular markers (STS57-320 and STS57-372) on the short arm and close to the centromere of chromosome 12. Six candidate resistance genes were predicted in the target region according to the reference sequence of Nipponbare. These results could facilitate both marker-assisted selection for disease-resistant breeding and gene cloning.
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Affiliation(s)
- Liying Dong
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Shufang Liu
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Peng Xu
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Kunming, Yunnan, China
| | - Wei Deng
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Xundong Li
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Didier Tharreau
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR BGPI, Montpellier, France
| | - Jing Li
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Jiawu Zhou
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Qun Wang
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Dayun Tao
- Food Crops Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- * E-mail: (DT); (QY)
| | - Qinzhong Yang
- Agricultural Environment and Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
- * E-mail: (DT); (QY)
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