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Murmu S, Archak S. In-silico study of protein-protein interactions in wheat blast using docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2024; 42:5747-5757. [PMID: 37357445 DOI: 10.1080/07391102.2023.2228907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Despite advancements in agricultural research and the introduction of modern biotechnological and farming techniques, food security remains a significant issue. Although the efforts of farmers to meet the demands of a growing population, many plant diseases caused by pathogens, through their effects on cell division and tissue growth, lead to the annual loss of countless food crops. The recently emerged wheat blast fungus Magnaporthe oryzae pathotype Triticum (MoT) poses a significant danger to worldwide wheat cultivation. The fungus is a highly varied lineage of the M. oryzae, responsible for causing rice blast disease. In spite of being a significant challenge to successful wheat production in South America since 1985, the underlying biology of the wheat blast pathogen is still not fully understood. The initial outbreak of the wheat blast in South Asia had a severe impact on wheat production, resulting in a complete loss of yield in affected fields. For the purpose of enhancing disease management, it's vital to acquire a comprehensive comprehension of the infection biology of the fungus and its interaction with wheat plants on molecular levels. Host-pathogen protein interactions (HPIs) have the potential to reveal the pathogens' mechanism for overcoming the host organism. The current study delves into the interactions between the host plant wheat and MoT through protein-protein interactions, molecular docking, and 100 ns molecular dynamic simulations. This research uncovers the structural and functional basis of these proteins, leading to improved plant health and production.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sneha Murmu
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sunil Archak
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Félix C, Meneses R, Gonçalves MFM, Duarte AS, Jorrín-Novo JV, van de Peer Y, Deforce D, Van Nieuwerburgh F, Alves A, Esteves AC. How temperature modulates the expression of pathogenesis-related molecules of the cross-kingdom pathogen Lasiodiplodia hormozganensis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 927:171917. [PMID: 38580127 DOI: 10.1016/j.scitotenv.2024.171917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024]
Abstract
Lasiodiplodia hormozganensis, initially recognized as a fungal plant pathogen, is recognized now acknowledged as a potential threat to humans. However, our understanding of the pathogenesis mechanisms of Lasiodiplodia species remains limited, and the impact of temperature on its pathogenicity is unclear. This study aims to elucidate the effects of temperature on the biology of L. hormozganensis, focusing on the expression of pathogenesis-related molecules and its ability to function as a cross-kingdom pathogen. We conducted experiments at two different temperatures, 25 and 37 °C, analyzing the proteome and transcriptome of L. hormozganensis. Using strain CBS339.90, initially identified as L. theobromae but confirmed through ITS and tef1-α sequence analysis to be L. hormozganensis, we aimed to understand the fungus's protein expression under varying temperature conditions. Results from the functional analysis of the secretome at 25 °C showed a noteworthy presence of proteins related to carbohydrate metabolism, catabolism, plant cell wall degradation, and pathogenesis. However, when grown at 37 °C, the fungus exhibited an increased production of stress response and pathogenesis-related proteins. Our findings identified various pathways crucial for pathogenesis in both plants and humans, suggesting that L. hormozganensis possesses the genetic foundation to infect both hosts. Specific pathogenesis-related proteins, including the phytotoxin snodprot1, aspartic protease aspergillopepsin, and virulence protein SSD1, were also identified. Concluding, we propose a possible mechanism of how L. hormozganensis adapts to different temperatures. The shift in temperature results in the expression of genes that favor human related pathogenesis molecules.
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Affiliation(s)
- Carina Félix
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Present address: MARE - Marine and Environmental Sciences Centre, ESTM, Polytechnic Institute of Leiria, Portugal
| | - Rodrigo Meneses
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052, Belgium
| | - Micael F M Gonçalves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana S Duarte
- Universidade Católica Portuguesa, Center for Interdisciplinary Research in Health (CIIS), Faculty of Dental Medicine, Estrada da Circunvalação, 3504-505, Viseu, Portugal
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, Universidad de Córdoba, Córdoba, Spain
| | - Yves van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Campus Heymans, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Artur Alves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Ana C Esteves
- CESAM and Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
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Dilla-Ermita CJ, Goldman P, Anchieta A, Feldmann MJ, Pincot DDA, Famula RA, Vachev M, Cole GS, Knapp SJ, Klosterman SJ, Henry PM. Secreted in Xylem 6 ( SIX6) Mediates Fusarium oxysporum f. sp. fragariae Race 1 Avirulence on FW1-Resistant Strawberry Cultivars. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:530-541. [PMID: 38552146 DOI: 10.1094/mpmi-02-24-0012-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: 06/25/2024]
Abstract
Fusarium oxysporum f. sp. fragariae (Fof) race 1 is avirulent on cultivars with the dominant resistance gene FW1, while Fof race 2 is virulent on FW1-resistant cultivars. We hypothesized there was a gene-for-gene interaction between a gene at the FW1 locus and an avirulence gene (AvrFW1) in Fof race 1. To identify a candidate AvrFW1, we compared genomes of 24 Fof race 1 and three Fof race 2 isolates. We found one candidate gene that was present in race 1, was absent in race 2, was highly expressed in planta, and was homologous to a known effector, secreted in xylem 6 (SIX6). We knocked out SIX6 in two Fof race 1 isolates by homologous recombination. All SIX6 knockout transformants (ΔSIX6) gained virulence on FW1/fw1 cultivars, whereas ectopic transformants and the wildtype isolates remained avirulent. ΔSIX6 isolates were quantitatively less virulent on FW1/fw1 cultivars Fronteras and San Andreas than fw1/fw1 cultivars. Seedlings from an FW1/fw1 × fw1/fw1 population were genotyped for FW1 and tested for susceptibility to a SIX6 knockout isolate. Results suggested that additional minor-effect quantitative resistance genes could be present at the FW1 locus. This work demonstrates that SIX6 acts as an avirulence factor interacting with a resistance gene at the FW1 locus. The identification of AvrFW1 enables surveillance for Fof race 2 and provides insight into the mechanisms of FW1-mediated resistance. [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)
- Christine Jade Dilla-Ermita
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Polly Goldman
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Amy Anchieta
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Dominique D A Pincot
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Randi A Famula
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Mishi Vachev
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Glenn S Cole
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Steven J Knapp
- Department of Plant Sciences, University of California Davis, One Shields Ave., Davis, CA 95616
| | - Steven J Klosterman
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
| | - Peter M Henry
- Crop Improvement and Protection Research, USDA-ARS, 1636 E. Alisal St., Salinas, CA 93905
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Logachev A, Kanapin A, Rozhmina T, Stanin V, Bankin M, Samsonova A, Orlova E, Samsonova M. Pangenomics of flax fungal parasite Fusarium oxysporum f. sp. lini. FRONTIERS IN PLANT SCIENCE 2024; 15:1383914. [PMID: 38872883 PMCID: PMC11169931 DOI: 10.3389/fpls.2024.1383914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.
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Affiliation(s)
- Anton Logachev
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Alexander Kanapin
- Center for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Rozhmina
- Flax Institute, Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Vladislav Stanin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Mikhail Bankin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Anastasia Samsonova
- Center for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Ekaterina Orlova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
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Ruan Z, Jiao J, Zhao J, Liu J, Liang C, Yang X, Sun Y, Tang G, Li P. Genome sequencing and comparative genomics reveal insights into pathogenicity and evolution of Fusarium zanthoxyli, the causal agent of stem canker in prickly ash. BMC Genomics 2024; 25:502. [PMID: 38773367 PMCID: PMC11110190 DOI: 10.1186/s12864-024-10424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Fusarium zanthoxyli is a destructive pathogen causing stem canker in prickly ash, an ecologically and economically important forest tree. However, the genome lack of F. zanthoxyli has hindered research on its interaction with prickly ash and the development of precise control strategies for stem canker. RESULTS In this study, we sequenced and annotated a relatively high-quality genome of F. zanthoxyli with a size of 43.39 Mb, encoding 11,316 putative genes. Pathogenicity-related factors are predicted, comprising 495 CAZymes, 217 effectors, 156 CYP450s, and 202 enzymes associated with secondary metabolism. Besides, a comparative genomics analysis revealed Fusarium and Colletotrichum diverged from a shared ancestor approximately 141.1 ~ 88.4 million years ago (MYA). Additionally, a phylogenomic investigation of 12 different phytopathogens within Fusarium indicated that F. zanthoxyli originated approximately 34.6 ~ 26.9 MYA, and events of gene expansion and contraction within them were also unveiled. Finally, utilizing conserved domain prediction, the results revealed that among the 59 unique genes, the most enriched domains were PnbA and ULP1. Among the 783 expanded genes, the most enriched domains were PKc_like kinases and those belonging to the APH_ChoK_Like family. CONCLUSION This study sheds light on the genetic basis of F. zanthoxyli's pathogenicity and evolution which provides valuable information for future research on its molecular interactions with prickly ash and the development of effective strategies to combat stem canker.
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Affiliation(s)
- Zhao Ruan
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiahui Jiao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Junchi Zhao
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jiaxue Liu
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Chaoqiong Liang
- Shaanxi Academy of Forestry, Xi'an, Shaanxi, 710082, People's Republic of China
| | - Xia Yang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yan Sun
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peiqin Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio- Disaster, College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Wang Y, Zhang K, Chen D, Liu K, Chen W, He F, Tong Z, Luo Q. Co-expression network analysis and identification of core genes in the interaction between wheat and Puccinia striiformis f. sp. tritici. Arch Microbiol 2024; 206:241. [PMID: 38698267 DOI: 10.1007/s00203-024-03925-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 05/05/2024]
Abstract
The epidemic of stripe rust, caused by the pathogen Puccinia striiformis f. sp. tritici (Pst), would reduce wheat (Triticum aestivum) yields seriously. Traditional experimental methods are difficult to discover the interaction between wheat and Pst. Multi-omics data analysis provides a new idea for efficiently mining the interactions between host and pathogen. We used 140 wheat-Pst RNA-Seq data to screen for differentially expressed genes (DEGs) between low susceptibility and high susceptibility samples, and carried out Gene Ontology (GO) enrichment analysis. Based on this, we constructed a gene co-expression network, identified the core genes and interacted gene pairs from the conservative modules. Finally, we checked the distribution of Nucleotide-binding and leucine-rich repeat (NLR) genes in the co-expression network and drew the wheat NLR gene co-expression network. In order to provide accessible information for related researchers, we built a web-based visualization platform to display the data. Based on the analysis, we found that resistance-related genes such as TaPR1, TaWRKY18 and HSP70 were highly expressed in the network. They were likely to be involved in the biological processes of Pst infecting wheat. This study can assist scholars in conducting studies on the pathogenesis and help to advance the investigation of wheat-Pst interaction patterns.
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Affiliation(s)
- Yibo Wang
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, National Tobacco Genetic Engineering Research Centre, Kunming, 650021, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ke Zhang
- Yunnan Tobacco Quality Inspection & Supervision Station, Kunming, 650106, People's Republic of China
| | - Dan Chen
- Yunnan Tobacco Quality Inspection & Supervision Station, Kunming, 650106, People's Republic of China
| | - Kai Liu
- Yunnan Tobacco Quality Inspection & Supervision Station, Kunming, 650106, People's Republic of China
| | - Wei Chen
- Yunnan Tobacco Quality Inspection & Supervision Station, Kunming, 650106, People's Republic of China
| | - Fei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing, 100101, China
| | - Zhijun Tong
- Key Laboratory of Tobacco Biotechnological Breeding, Yunnan Academy of Tobacco Agricultural Sciences, National Tobacco Genetic Engineering Research Centre, Kunming, 650021, China.
| | - Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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Lahfa M, Barthe P, de Guillen K, Cesari S, Raji M, Kroj T, Le Naour—Vernet M, Hoh F, Gladieux P, Roumestand C, Gracy J, Declerck N, Padilla A. The structural landscape and diversity of Pyricularia oryzae MAX effectors revisited. PLoS Pathog 2024; 20:e1012176. [PMID: 38709846 PMCID: PMC11132498 DOI: 10.1371/journal.ppat.1012176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 05/28/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
Magnaporthe AVRs and ToxB-like (MAX) effectors constitute a family of secreted virulence proteins in the fungus Pyricularia oryzae (syn. Magnaporthe oryzae), which causes blast disease on numerous cereals and grasses. In spite of high sequence divergence, MAX effectors share a common fold characterized by a ß-sandwich core stabilized by a conserved disulfide bond. In this study, we investigated the structural landscape and diversity within the MAX effector repertoire of P. oryzae. Combining experimental protein structure determination and in silico structure modeling we validated the presence of the conserved MAX effector core domain in 77 out of 94 groups of orthologs (OG) identified in a previous population genomic study. Four novel MAX effector structures determined by NMR were in remarkably good agreement with AlphaFold2 (AF2) predictions. Based on the comparison of the AF2-generated 3D models we propose a classification of the MAX effectors superfamily in 20 structural groups that vary in the canonical MAX fold, disulfide bond patterns, and additional secondary structures in N- and C-terminal extensions. About one-third of the MAX family members remain singletons, without strong structural relationship to other MAX effectors. Analysis of the surface properties of the AF2 MAX models also highlights the high variability within the MAX family at the structural level, potentially reflecting the wide diversity of their virulence functions and host targets.
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Affiliation(s)
- Mounia Lahfa
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Philippe Barthe
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Karine de Guillen
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Stella Cesari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Mouna Raji
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Marie Le Naour—Vernet
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - François Hoh
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Christian Roumestand
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Jérôme Gracy
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - Nathalie Declerck
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, Univ Montpellier, CNRS UMR 5048, INSERM U 1054, Montpellier, France
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Dodds PN, Chen J, Outram MA. Pathogen perception and signaling in plant immunity. THE PLANT CELL 2024; 36:1465-1481. [PMID: 38262477 PMCID: PMC11062475 DOI: 10.1093/plcell/koae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/19/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Plant diseases are a constant and serious threat to agriculture and ecological biodiversity. Plants possess a sophisticated innate immunity system capable of detecting and responding to pathogen infection to prevent disease. Our understanding of this system has grown enormously over the past century. Early genetic descriptions of plant disease resistance and pathogen virulence were embodied in the gene-for-gene hypothesis, while physiological studies identified pathogen-derived elicitors that could trigger defense responses in plant cells and tissues. Molecular studies of these phenomena have now coalesced into an integrated model of plant immunity involving cell surface and intracellular detection of specific pathogen-derived molecules and proteins culminating in the induction of various cellular responses. Extracellular and intracellular receptors engage distinct signaling processes but converge on many similar outputs with substantial evidence now for integration of these pathways into interdependent networks controlling disease outcomes. Many of the molecular details of pathogen recognition and signaling processes are now known, providing opportunities for bioengineering to enhance plant protection from disease. Here we provide an overview of the current understanding of the main principles of plant immunity, with an emphasis on the key scientific milestones leading to these insights.
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Affiliation(s)
- Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Jian Chen
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Megan A Outram
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, ACT 2601, Australia
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Alassimone J, Praz C, Lorrain C, De Francesco A, Carrasco-López C, Faino L, Shen Z, Meile L, Sánchez-Vallet A. The Zymoseptoria tritici Avirulence Factor AvrStb6 Accumulates in Hyphae Close to Stomata and Triggers a Wheat Defense Response Hindering Fungal Penetration. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:432-444. [PMID: 38265007 DOI: 10.1094/mpmi-11-23-0181-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: 01/25/2024]
Abstract
Zymoseptoria tritici, the causal agent of Septoria tritici blotch, is one of Europe's most damaging wheat pathogens, causing significant economic losses. Genetic resistance is a common strategy to control the disease, Stb6 being a resistance gene used for more than 100 years in Europe. This study investigates the molecular mechanisms underlying Stb6-mediated resistance. Utilizing confocal microscopy imaging, we determined that Z. tritici epiphytic hyphae mainly accumulate the corresponding avirulence factor AvrStb6 in close proximity to stomata. Consequently, the progression of AvrStb6-expressing avirulent strains is hampered during penetration. The fungal growth inhibition co-occurs with a transcriptional reprogramming in wheat characterized by an induction of immune responses, genes involved in stomatal regulation, and cell wall-related genes. Overall, we shed light on the gene-for-gene resistance mechanisms in the wheat-Z. tritici pathosystem at the cytological and transcriptomic level, and our results highlight that stomatal penetration is a critical process for pathogenicity and resistance. [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)
- Julien Alassimone
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Coraline Praz
- Centro de Biotecnología y Genómica de Plantas (CBGP)/Universidad Politécnica de Madrid-Instituto Nacional de Investigación Agraria y Alimentaria/Centro Superior de Investigaciones Científicas (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
| | - Cécile Lorrain
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Agustina De Francesco
- Centro de Biotecnología y Genómica de Plantas (CBGP)/Universidad Politécnica de Madrid-Instituto Nacional de Investigación Agraria y Alimentaria/Centro Superior de Investigaciones Científicas (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
| | - Cristian Carrasco-López
- Centro de Biotecnología y Genómica de Plantas (CBGP)/Universidad Politécnica de Madrid-Instituto Nacional de Investigación Agraria y Alimentaria/Centro Superior de Investigaciones Científicas (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
| | - Luigi Faino
- Environmental Biology, Sapienza University of Rome, Roma, Italy
| | - Ziqi Shen
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Lukas Meile
- Centro de Biotecnología y Genómica de Plantas (CBGP)/Universidad Politécnica de Madrid-Instituto Nacional de Investigación Agraria y Alimentaria/Centro Superior de Investigaciones Científicas (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
| | - Andrea Sánchez-Vallet
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Centro de Biotecnología y Genómica de Plantas (CBGP)/Universidad Politécnica de Madrid-Instituto Nacional de Investigación Agraria y Alimentaria/Centro Superior de Investigaciones Científicas (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
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10
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Castell-Miller CV, Kono TJ, Ranjan A, Schlatter DC, Samac DA, Kimball JA. Interactive transcriptome analyses of Northern Wild Rice ( Zizania palustris L.) and Bipolaris oryzae show convoluted communications during the early stages of fungal brown spot development. FRONTIERS IN PLANT SCIENCE 2024; 15:1350281. [PMID: 38736448 PMCID: PMC11086184 DOI: 10.3389/fpls.2024.1350281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Fungal diseases, caused mainly by Bipolaris spp., are past and current threats to Northern Wild Rice (NWR) grain production and germplasm preservation in both natural and cultivated settings. Genetic resistance against the pathogen is scarce. Toward expanding our understanding of the global gene communications of NWR and Bipolaris oryzae interaction, we designed an RNA sequencing study encompassing the first 12 h and 48 h of their encounter. NWR activated numerous plant recognition receptors after pathogen infection, followed by active transcriptional reprogramming of signaling mechanisms driven by Ca2+ and its sensors, mitogen-activated protein kinase cascades, activation of an oxidative burst, and phytohormone signaling-bound mechanisms. Several transcription factors associated with plant defense were found to be expressed. Importantly, evidence of diterpenoid phytoalexins, especially phytocassane biosynthesis, among expression of other defense genes was found. In B. oryzae, predicted genes associated with pathogenicity including secreted effectors that could target plant defense mechanisms were expressed. This study uncovered the early molecular communication between the NWR-B. oryzae pathosystem, which could guide selection for allele-specific genes to boost NWR defenses, and overall aid in the development of more efficient selection methods in NWR breeding through the use of the most virulent fungal isolates.
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Affiliation(s)
| | - Thomas J.Y. Kono
- Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, MN, United States
| | - Ashish Ranjan
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
| | - Daniel C. Schlatter
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- United States Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Saint Paul, MN, United States
| | - Deborah A. Samac
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN, United States
- United States Department of Agriculture, Agricultural Research Service, Plant Science Research Unit, Saint Paul, MN, United States
| | - Jennifer A. Kimball
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
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11
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Aparicio Chacón MV, Hernández Luelmo S, Devlieghere V, Robichez L, Leroy T, Stuer N, De Keyser A, Ceulemans E, Goossens A, Goormachtig S, Van Dingenen J. Exploring the potential role of four Rhizophagus irregularis nuclear effectors: opportunities and technical limitations. FRONTIERS IN PLANT SCIENCE 2024; 15:1384496. [PMID: 38736443 PMCID: PMC11085264 DOI: 10.3389/fpls.2024.1384496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) are obligate symbionts that interact with the roots of most land plants. The genome of the AMF model species Rhizophagus irregularis contains hundreds of predicted small effector proteins that are secreted extracellularly but also into the plant cells to suppress plant immunity and modify plant physiology to establish a niche for growth. Here, we investigated the role of four nuclear-localized putative effectors, i.e., GLOIN707, GLOIN781, GLOIN261, and RiSP749, in mycorrhization and plant growth. We initially intended to execute the functional studies in Solanum lycopersicum, a host plant of economic interest not previously used for AMF effector biology, but extended our studies to the model host Medicago truncatula as well as the non-host Arabidopsis thaliana because of the technical advantages of working with these models. Furthermore, for three effectors, the implementation of reverse genetic tools, yeast two-hybrid screening and whole-genome transcriptome analysis revealed potential host plant nuclear targets and the downstream triggered transcriptional responses. We identified and validated a host protein interactors participating in mycorrhization in the host.S. lycopersicum and demonstrated by transcriptomics the effectors possible involvement in different molecular processes, i.e., the regulation of DNA replication, methylglyoxal detoxification, and RNA splicing. We conclude that R. irregularis nuclear-localized effector proteins may act on different pathways to modulate symbiosis and plant physiology and discuss the pros and cons of the tools used.
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Affiliation(s)
- María Victoria Aparicio Chacón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Sofía Hernández Luelmo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Viktor Devlieghere
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Louis Robichez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Toon Leroy
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Naomi Stuer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Annick De Keyser
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Evi Ceulemans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Gent, Belgium
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12
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Romero G, González S, Royero W, González A. Morphological and transcriptional analysis of Colletotrichum lindemuthianum race 7 during early stages of infection in common bean. Genet Mol Biol 2024; 47:e20220263. [PMID: 38593425 PMCID: PMC11003654 DOI: 10.1590/1678-4685-gmb-2022-0263] [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: 09/03/2023] [Accepted: 01/26/2024] [Indexed: 04/11/2024] Open
Abstract
The infection process of the hemibiotrophic fungus Colletotrichum lindemuthianum has been independently studied at the microscopic and genomic levels. However, the relationship between the morphological changes and the pathogenicity mechanisms of the fungus at the early stages of the infection remains uncharacterized. Therefore, this study attempts to bridge this gap by integrating microscopic and transcriptional approaches to understand the infection process of C. lindemuthianum. Fungal structures were followed by fluorescence microscopy for 120 hours. Simultaneously, the transcriptomic profile was made using RNAseq. Morphological characterization shows that appressoria, infective vesicles, and secondary hypha formation occur before 72 hours. Additionally, we assembled 38,206 transcripts with lengths between 201 and 3,548 bp. The secretome annotation revealed the expression of 1,204 CAZymes, of which 17 exhibited secretion domains and were identified as chitinases and β-1,3-glucanases, 27 were effector candidates, and 30 were transport proteins mostly associated with ABC-type. Finally, we confirmed the presence and expression of CAC1 role during the appressoria formation of Clr7. This result represents the first report of adenylate cyclase expression evaluated under three different approaches. In conclusion, C. lindemuthianum colonizes the host through different infection structures complemented with the expression of multiple enzymes, where CAC1 favors disease development.
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Affiliation(s)
- German Romero
- Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Bogotá, Colombia
| | - Sandra González
- Universidad Nacional de Colombia, Instituto de Biotecnología, Bogotá, Colombia
| | - Wendy Royero
- Universidad Nacional de Colombia, Instituto de Biotecnología, Bogotá, Colombia
| | - Adriana González
- Universidad Nacional de Colombia, Facultad de Ciencias Agrarias, Bogotá, Colombia
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13
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Nallathambi P, Umamaheswari C, Reddy B, Aarthy B, Javed M, Ravikumar P, Watpade S, Kashyap PL, Boopalakrishnan G, Kumar S, Sharma A, Kumar A. Deciphering the Genomic Landscape and Virulence Mechanisms of the Wheat Powdery Mildew Pathogen Blumeria graminis f. sp. tritici Wtn1: Insights from Integrated Genome Assembly and Conidial Transcriptomics. J Fungi (Basel) 2024; 10:267. [PMID: 38667938 PMCID: PMC11051031 DOI: 10.3390/jof10040267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
A high-quality genome sequence from an Indian isolate of Blumeria graminis f. sp. tritici Wtn1, a persistent threat in wheat farming, was obtained using a hybrid method. The assembly of over 9.24 million DNA-sequence reads resulted in 93 contigs, totaling a 140.61 Mb genome size, potentially encoding 8480 genes. Notably, more than 73.80% of the genome, spanning approximately 102.14 Mb, comprises retro-elements, LTR elements, and P elements, influencing evolution and adaptation significantly. The phylogenomic analysis placed B. graminis f. sp. tritici Wtn1 in a distinct monocot-infecting clade. A total of 583 tRNA anticodon sequences were identified from the whole genome of the native virulent strain B. graminis f. sp. tritici, which comprises distinct genome features with high counts of tRNA anticodons for leucine (70), cysteine (61), alanine (58), and arginine (45), with only two stop codons (Opal and Ochre) present and the absence of the Amber stop codon. Comparative InterProScan analysis unveiled "shared and unique" proteins in B. graminis f. sp. tritici Wtn1. Identified were 7707 protein-encoding genes, annotated to different categories such as 805 effectors, 156 CAZymes, 6102 orthologous proteins, and 3180 distinct protein families (PFAMs). Among the effectors, genes like Avra10, Avrk1, Bcg-7, BEC1005, CSEP0105, CSEP0162, BEC1016, BEC1040, and HopI1 closely linked to pathogenesis and virulence were recognized. Transcriptome analysis highlighted abundant proteins associated with RNA processing and modification, post-translational modification, protein turnover, chaperones, and signal transduction. Examining the Environmental Information Processing Pathways in B. graminis f. sp. tritici Wtn1 revealed 393 genes across 33 signal transduction pathways. The key pathways included yeast MAPK signaling (53 genes), mTOR signaling (38 genes), PI3K-Akt signaling (23 genes), and AMPK signaling (21 genes). Additionally, pathways like FoxO, Phosphatidylinositol, the two-component system, and Ras signaling showed significant gene representation, each with 15-16 genes, key SNPs, and Indels in specific chromosomes highlighting their relevance to environmental responses and pathotype evolution. The SNP and InDel analysis resulted in about 3.56 million variants, including 3.45 million SNPs, 5050 insertions, and 5651 deletions within the whole genome of B. graminis f. sp. tritici Wtn1. These comprehensive genome and transcriptome datasets serve as crucial resources for understanding the pathogenicity, virulence effectors, retro-elements, and evolutionary origins of B. graminis f. sp. tritici Wtn1, aiding in developing robust strategies for the effective management of wheat powdery mildew.
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Affiliation(s)
- Perumal Nallathambi
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Chandrasekaran Umamaheswari
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Bhaskar Reddy
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
| | - Balakrishnan Aarthy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Mohammed Javed
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
| | - Priya Ravikumar
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643231, Tamil Nadu, India; (P.N.); (C.U.); (B.A.); (P.R.)
| | - Santosh Watpade
- ICAR-Indian Agricultural Research Institute, Regional Station, Shimla 171004, Himachal Pradesh, India;
| | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | | | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | - Anju Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, Haryana, India; (P.L.K.); (S.K.); (A.S.)
| | - Aundy Kumar
- ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, Delhi, India; (M.J.); (G.B.)
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14
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Joubert PM, Krasileva KV. Distinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae. Genetics 2024; 226:iyae012. [PMID: 38290434 PMCID: PMC10990425 DOI: 10.1093/genetics/iyae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 11/28/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.
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Affiliation(s)
- Pierre M Joubert
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California-Berkeley, Berkeley, CA 94720, USA
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15
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Nishmitha K, Bashyal BM, Dubey SC, Kamil D. Molecular characterization of Indian races of Fusarium oxysporum f. sp. lentis (Fol) based on secreted in Xylem (SIX) effector genes and development of a SIX11 gene-based molecular marker for specific detection of Fol. Arch Microbiol 2024; 206:200. [PMID: 38564016 DOI: 10.1007/s00203-024-03945-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Fusarium wilt of lentil caused by Fusarium oxysporum f. sp. lentis (Fol) is a destructive pathogen limiting lentil production in India. In the present study, Secreted in Xylem (SIX) effectors genes were explored in Indian races of Fol and also a diagnostic tool for reliable detection of the disease was developed. Four SIX effectors genes, SIX11, SIX13, SIX6 and SIX2 were identified in 12 isolates of Fol belonging to seven races. SIX11 was present in all the races while SIX 13 was absent in race 6 and SIX6 was present only in race 4. The phylogenetic analysis revealed the conserved nature of the SIX genes within the forma specialis and showed sequence homology with F. oxysporum f. sp. pisi. The presence of three effectors, SIX11, SIX13 and SIX6 in race 4 correlates with high disease incidence in lentil germplasms. The in-silico characterization revealed the presence of signal peptide and localization of the effectors. Further SIX11 effector gene present in all the isolates was used to develop Fol-specific molecular marker for accurate detection. The marker developed could differentiate F. oxysporum f. sp. lycopersici, F. solani, F. oxysporum, Rhizoctonia solani and Sclerotium rolfsii and had a detection limit of 0.01ng μL- 1. The effector-based marker detection helps in the unambiguous detection of the pathogen under field conditions.
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Affiliation(s)
- K Nishmitha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Bishnu Maya Bashyal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S C Dubey
- Birsa Agricultural University, Jharkhand, 834006, India
| | - Deeba Kamil
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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16
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Arndell T, Chen J, Sperschneider J, Upadhyaya NM, Blundell C, Niesner N, Outram MA, Wang A, Swain S, Luo M, Ayliffe MA, Figueroa M, Vanhercke T, Dodds PN. Pooled effector library screening in protoplasts rapidly identifies novel Avr genes. NATURE PLANTS 2024; 10:572-580. [PMID: 38409291 PMCID: PMC11035141 DOI: 10.1038/s41477-024-01641-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
Crop breeding for durable disease resistance is challenging due to the rapid evolution of pathogen virulence. While progress in resistance (R) gene cloning and stacking has accelerated in recent years1-3, the identification of corresponding avirulence (Avr) genes in many pathogens is hampered by the lack of high-throughput screening options. To address this technology gap, we developed a platform for pooled library screening in plant protoplasts to allow rapid identification of interacting R-Avr pairs. We validated this platform by isolating known and novel Avr genes from wheat stem rust (Puccinia graminis f. sp. tritici) after screening a designed library of putative effectors against individual R genes. Rapid Avr gene identification provides molecular tools to understand and track pathogen virulence evolution via genotype surveillance, which in turn will lead to optimized R gene stacking and deployment strategies. This platform should be broadly applicable to many crop pathogens and could potentially be adapted for screening genes involved in other protoplast-selectable traits.
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Affiliation(s)
- Taj Arndell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jian Chen
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Cheryl Blundell
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Nathalie Niesner
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Megan A Outram
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Aihua Wang
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Steve Swain
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Ming Luo
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michael A Ayliffe
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
| | - Peter N Dodds
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia.
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17
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Rozano L, Jones DAB, Hane JK, Mancera RL. Template-Based Modelling of the Structure of Fungal Effector Proteins. Mol Biotechnol 2024; 66:784-813. [PMID: 36940017 PMCID: PMC11043172 DOI: 10.1007/s12033-023-00703-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/14/2023] [Indexed: 03/21/2023]
Abstract
The discovery of new fungal effector proteins is necessary to enable the screening of cultivars for disease resistance. Sequence-based bioinformatics methods have been used for this purpose, but only a limited number of functional effector proteins have been successfully predicted and subsequently validated experimentally. A significant obstacle is that many fungal effector proteins discovered so far lack sequence similarity or conserved sequence motifs. The availability of experimentally determined three-dimensional (3D) structures of a number of effector proteins has recently highlighted structural similarities amongst groups of sequence-dissimilar fungal effectors, enabling the search for similar structural folds amongst effector sequence candidates. We have applied template-based modelling to predict the 3D structures of candidate effector sequences obtained from bioinformatics predictions and the PHI-BASE database. Structural matches were found not only with ToxA- and MAX-like effector candidates but also with non-fungal effector-like proteins-including plant defensins and animal venoms-suggesting the broad conservation of ancestral structural folds amongst cytotoxic peptides from a diverse range of distant species. Accurate modelling of fungal effectors were achieved using RaptorX. The utility of predicted structures of effector proteins lies in the prediction of their interactions with plant receptors through molecular docking, which will improve the understanding of effector-plant interactions.
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Affiliation(s)
- Lina Rozano
- Curtin Medical School, Curtin Health Innovation Research Institute, GPO Box U1987, Perth, WA, 6845, Australia
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Darcy A B Jones
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - James K Hane
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia
| | - Ricardo L Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, GPO Box U1987, Perth, WA, 6845, Australia.
- Curtin Institute for Computation, Curtin University, GPO Box U1987, Perth, WA, 6845, Australia.
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18
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Baudin M, Le Naour‐Vernet M, Gladieux P, Tharreau D, Lebrun M, Lambou K, Leys M, Fournier E, Césari S, Kroj T. Pyricularia oryzae: Lab star and field scourge. MOLECULAR PLANT PATHOLOGY 2024; 25:e13449. [PMID: 38619508 PMCID: PMC11018116 DOI: 10.1111/mpp.13449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/16/2024]
Abstract
Pyricularia oryzae (syn. Magnaporthe oryzae), is a filamentous ascomycete that causes a major disease called blast on cereal crops, as well as on a wide variety of wild and cultivated grasses. Blast diseases have a tremendous impact worldwide particularly on rice and on wheat, where the disease emerged in South America in the 1980s, before spreading to Asia and Africa. Its economic importance, coupled with its amenability to molecular and genetic manipulation, have inspired extensive research efforts aiming at understanding its biology and evolution. In the past 40 years, this plant-pathogenic fungus has emerged as a major model in molecular plant-microbe interactions. In this review, we focus on the clarification of the taxonomy and genetic structure of the species and its host range determinants. We also discuss recent molecular studies deciphering its lifecycle. TAXONOMY Kingdom: Fungi, phylum: Ascomycota, sub-phylum: Pezizomycotina, class: Sordariomycetes, order: Magnaporthales, family: Pyriculariaceae, genus: Pyricularia. HOST RANGE P. oryzae has the ability to infect a wide range of Poaceae. It is structured into different host-specialized lineages that are each associated with a few host plant genera. The fungus is best known to cause tremendous damage to rice crops, but it can also attack other economically important crops such as wheat, maize, barley, and finger millet. DISEASE SYMPTOMS P. oryzae can cause necrotic lesions or bleaching on all aerial parts of its host plants, including leaf blades, sheaths, and inflorescences (panicles, spikes, and seeds). Characteristic symptoms on leaves are diamond-shaped silver lesions that often have a brown margin and whose appearance is influenced by numerous factors such as the plant genotype and environmental conditions. USEFUL WEBSITES Resources URL Genomic data repositories http://genome.jouy.inra.fr/gemo/ Genomic data repositories http://openriceblast.org/ Genomic data repositories http://openwheatblast.net/ Genome browser for fungi (including P. oryzae) http://fungi.ensembl.org/index.html Comparative genomics database https://mycocosm.jgi.doe.gov/mycocosm/home T-DNA mutant database http://atmt.snu.kr/ T-DNA mutant database http://www.phi-base.org/ SNP and expression data https://fungidb.org/fungidb/app/.
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Affiliation(s)
- Maël Baudin
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
- Present address:
Université Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Marie Le Naour‐Vernet
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
- CIRAD, UMR PHIMMontpellierFrance
| | - Marc‐Henri Lebrun
- UMR 1290 BIOGER – Campus Agro Paris‐Saclay – INRAE‐AgroParisTechPalaiseauFrance
| | - Karine Lambou
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Marie Leys
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Stella Césari
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRDMontpellierFrance
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19
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Dobbs JT, Caballero JRI, Ata JP, Babiker E, Copes WE, Stewart JE. Genomic and Transcriptomic Comparisons of the Twig Blight Pathogen, Passalora sequoiae, with Mycosphaerellaceae Foliar and Conifer Pathogens. PHYTOPATHOLOGY 2024; 114:732-742. [PMID: 37942864 DOI: 10.1094/phyto-08-23-0271-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: 11/10/2023]
Abstract
Passalora sequoiae is a foliar pathogen to conifer tree species. In this study, we conducted whole-genome and transcriptome analyses on isolates of P. sequoiae collected from symptomatic Leyland cypress leaves from a Christmas tree farm in Mississippi. The objectives for this research were to elucidate the pathogenicity mechanisms of P. sequoiae by characterizing the genome and transcriptome and possibly identify unique and shared predicted genes in comparison with non-conifer/canker and foliar pathogens in the family Mycosphaerellaceae. P. sequoiae was found to be similar to other foliar Mycosphaerellaceae pathogens and likely represents a hemibiotrophic lifestyle based on comparisons across pathogens. The genome and in planta transcriptome highlighted some unique features of P. sequoiae: the significant presence of chitin synthases and fructose-degrading carbohydrate-degrading enzymes, trans-AT PKS genes, and antibiotic gene clusters that were unique to P. sequoiae compared with the other Mycosphaerellaceae species genomes. Several transcripts that were highly expressed in planta were identified as effectors, yet the functions were not characterized. These targets provide ample resources to continue to characterize pathogen-conifer host interactions in conifer foliar pathogens. Furthermore, this research helps build genomic resources for an important plant pathogen on Leyland cypress that will further our ability to develop novel management practices that could begin with breeding for resistance.
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Affiliation(s)
- John T Dobbs
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
| | | | - Jessa P Ata
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
- Department of Forest Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines
| | - Ebrahiem Babiker
- Thad Cochran Southern Horticultural Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, U.S.A
| | - Warren E Copes
- Thad Cochran Southern Horticultural Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, U.S.A
| | - Jane E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
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20
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Yang D, Zhang X, Ming Y, Liu C, Zhang X, Liu S, Zhu L. Characterization of the High-Quality Genome Sequence and Virulence Factors of Fusarium oxysporum f. sp. vasinfectum Race 7. J Fungi (Basel) 2024; 10:242. [PMID: 38667913 PMCID: PMC11051352 DOI: 10.3390/jof10040242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Fusarium oxysporum f. sp. vasinfectum (Fov) is a common soilborne fungal pathogen that causes Fusarium wilt (FW) disease in cotton. Although considerable progress has been made in cotton disease-resistance breeding against FW in China, and the R gene conferring resistance to Fov race 7 (FOV) in Upland cotton (Gossypium hirsutum) has been identified, knowledge regarding the evolution of fungal pathogenicity and virulence factors in Fov remains limited. In this study, we present a reference-scale genome assembly and annotation for FOV7, created through the integration of single-molecule real-time sequencing (PacBio) and high-throughput chromosome conformation capture (Hi-C) techniques. Comparative genomics analysis revealed the presence of six supernumerary scaffolds specific to FOV7. The genes or sequences within this region can potentially serve as reliable diagnostic markers for distinguishing Fov race 7. Furthermore, we conducted an analysis of the xylem sap proteome of FOV7-infected cotton plants, leading to the identification of 19 proteins that are secreted in xylem (FovSIX). Through a pathogenicity test involving knockout mutants, we demonstrated that FovSIX16 is crucial for the full virulence of FOV7. Overall, this study sheds light on the underlying mechanisms of Fov's pathogenicity and provides valuable insights into potential management strategies for controlling FW.
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Affiliation(s)
- Dingyi Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.Y.); (X.Z.); (Y.M.); (C.L.); (X.Z.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaojun Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.Y.); (X.Z.); (Y.M.); (C.L.); (X.Z.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing Ming
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.Y.); (X.Z.); (Y.M.); (C.L.); (X.Z.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Chenglin Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.Y.); (X.Z.); (Y.M.); (C.L.); (X.Z.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.Y.); (X.Z.); (Y.M.); (C.L.); (X.Z.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Shiming Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.Y.); (X.Z.); (Y.M.); (C.L.); (X.Z.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.Y.); (X.Z.); (Y.M.); (C.L.); (X.Z.)
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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21
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Zong X, Lou Y, Xia M, Zhao K, Chen J, Huang J, Yang S, Wang L. Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae. J Genet Genomics 2024:S1673-8527(24)00056-0. [PMID: 38490361 DOI: 10.1016/j.jgg.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops worldwide. Evidence shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates host-jumping. However, the pervasive clonal lineages of M. oryzae observed in natural fields contradict this expectation. A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation (RIP) in shaping its evolutionary trajectory is essential to bridge this knowledge gap. Here we systematically investigate the RIP and recombination landscapes in M. oryzae using a whole genome sequencing data from 252 population samples and 92 cross progenies. Our data reveal that the RIP can robustly capture the population history of M. oryzae, and we provide accurate estimations of the recombination and RIP rates across different M. oryzae clades. Significantly, our results highlight a parent-of-origin bias in both recombination and RIP rates, tightly associating with their sexual potential and variations of effector proteins. This bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host coevolution. These findings provide unique insights into understanding the evolution of blast fungus.
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Affiliation(s)
- Xifang Zong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Yaxin Lou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Mengshuang Xia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Kunyang Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Jingxuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210000, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210000, China.
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China.
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22
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Murmu S, Sinha D, Chaurasia H, Sharma S, Das R, Jha GK, Archak S. A review of artificial intelligence-assisted omics techniques in plant defense: current trends and future directions. FRONTIERS IN PLANT SCIENCE 2024; 15:1292054. [PMID: 38504888 PMCID: PMC10948452 DOI: 10.3389/fpls.2024.1292054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024]
Abstract
Plants intricately deploy defense systems to counter diverse biotic and abiotic stresses. Omics technologies, spanning genomics, transcriptomics, proteomics, and metabolomics, have revolutionized the exploration of plant defense mechanisms, unraveling molecular intricacies in response to various stressors. However, the complexity and scale of omics data necessitate sophisticated analytical tools for meaningful insights. This review delves into the application of artificial intelligence algorithms, particularly machine learning and deep learning, as promising approaches for deciphering complex omics data in plant defense research. The overview encompasses key omics techniques and addresses the challenges and limitations inherent in current AI-assisted omics approaches. Moreover, it contemplates potential future directions in this dynamic field. In summary, AI-assisted omics techniques present a robust toolkit, enabling a profound understanding of the molecular foundations of plant defense and paving the way for more effective crop protection strategies amidst climate change and emerging diseases.
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Affiliation(s)
- Sneha Murmu
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Dipro Sinha
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Himanshushekhar Chaurasia
- Central Institute for Research on Cotton Technology, Indian Council of Agricultural Research (ICAR), Mumbai, India
| | - Soumya Sharma
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Ritwika Das
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Girish Kumar Jha
- Indian Agricultural Statistics Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Sunil Archak
- National Bureau of Plant Genetic Resources, Indian Council of Agricultural Research (ICAR), New Delhi, India
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23
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Amezrou R, Ducasse A, Compain J, Lapalu N, Pitarch A, Dupont L, Confais J, Goyeau H, Kema GHJ, Croll D, Amselem J, Sanchez-Vallet A, Marcel TC. Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing. Nat Commun 2024; 15:1933. [PMID: 38431601 PMCID: PMC10908820 DOI: 10.1038/s41467-024-46191-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/14/2024] [Indexed: 03/05/2024] Open
Abstract
Knowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the genetic architecture of fungal pathogenicity often focus on large-effect effector genes triggering strong, qualitative resistance. It is not clear how this translates to predominately quantitative interactions. Here, we use the Zymoseptoria tritici-wheat model to elucidate the genetic architecture of quantitative pathogenicity and mechanisms mediating host adaptation. With a multi-host genome-wide association study, we identify 19 high-confidence candidate genes associated with quantitative pathogenicity. Analysis of genetic diversity reveals that sequence polymorphism is the main evolutionary process mediating differences in quantitative pathogenicity, a process that is likely facilitated by genetic recombination and transposable element dynamics. Finally, we use functional approaches to confirm the role of an effector-like gene and a methyltransferase in phenotypic variation. This study highlights the complex genetic architecture of quantitative pathogenicity, extensive diversifying selection and plausible mechanisms facilitating pathogen adaptation.
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Affiliation(s)
- Reda Amezrou
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France.
| | - Aurélie Ducasse
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Jérôme Compain
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | - Anais Pitarch
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Laetitia Dupont
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Johann Confais
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | | | - Gert H J Kema
- Plant Research International B.V., Wageningen, The Netherlands
| | - Daniel Croll
- Department of Ecology and Evolution, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Joëlle Amselem
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
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24
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Figueroa M, Coaker G, Kanyuka K. Focus on the Effectors at the Interface of Plant-Microbe Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:168-170. [PMID: 38573845 DOI: 10.1094/mpmi-02-24-0010-cm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Affiliation(s)
- Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, ACT 2600, Australia
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Kostya Kanyuka
- National Institute of Agricultural Botany (NIAB), Cambridge, CB3 0LE, U.K
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25
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Parada-Rojas CH, Stahr M, Childs KL, Quesada-Ocampo LM. Effector Repertoire of the Sweetpotato Black Rot Fungal Pathogen Ceratocystis fimbriata. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:315-326. [PMID: 38353601 DOI: 10.1094/mpmi-09-23-0146-fi] [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: 04/04/2024]
Abstract
In 2015, sweetpotato producers in the United States experienced one of the worst outbreaks of black rot recorded in history, with up to 60% losses reported in the field and packing houses and at shipping ports. Host resistance remains the ideal management tool to decrease crop losses. Lack of knowledge of Ceratocystis fimbriata biology represents a critical barrier for the deployment of resistance to black rot in sweetpotato. In this study, we scanned the recent near chromosomal-level assembly for putative secreted effectors in the sweetpotato C. fimbriata isolate AS236 using a custom fungal effector annotation pipeline. We identified a set of 188 putative effectors on the basis of secretion signal and in silico prediction in EffectorP. We conducted a deep RNA time-course sequencing experiment to determine whether C. fimbriata modulates effectors in planta and to define a candidate list of effectors expressed during infection. We examined the expression profile of two C. fimbriata isolates, a pre-epidemic (1990s) isolate and a post-epidemic (2015) isolate. Our in planta expression profiling revealed clusters of co-expressed secreted effector candidates. Based on fold-change differences of putative effectors in both isolates and over the course of infection, we suggested prioritization of 31 effectors for functional characterization. Among this set, we identified several effectors that provide evidence for a marked biotrophic phase in C. fimbriata during infection of sweetpotato storage roots. Our study revealed a catalog of effector proteins that provide insight into C. fimbriata infection mechanisms and represent a core catalog to implement effector-assisted breeding in sweetpotato. [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)
- Camilo H Parada-Rojas
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27606, U.S.A
| | - Madison Stahr
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27606, U.S.A
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27606, U.S.A
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26
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Hewitt TC, Henningsen EC, Pereira D, McElroy K, Nazareno ES, Dugyala S, Nguyen-Phuc H, Li F, Miller ME, Visser B, Pretorius ZA, Boshoff WHP, Sperschneider J, Stukenbrock EH, Kianian SF, Dodds PN, Figueroa M. Genome-Enabled Analysis of Population Dynamics and Virulence-Associated Loci in the Oat Crown Rust Fungus Puccinia coronata f. sp. avenae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:290-303. [PMID: 37955552 DOI: 10.1094/mpmi-09-23-0126-fi] [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: 11/14/2023]
Abstract
Puccinia coronata f. sp. avenae (Pca) is an important fungal pathogen causing crown rust that impacts oat production worldwide. Genetic resistance for crop protection against Pca is often overcome by the rapid virulence evolution of the pathogen. This study investigated the factors shaping adaptive evolution of Pca using pathogen populations from distinct geographic regions within the United States and South Africa. Phenotypic and genome-wide sequencing data of these diverse Pca collections, including 217 isolates, uncovered phylogenetic relationships and established distinct genetic composition between populations from northern and southern regions from the United States and South Africa. The population dynamics of Pca involve a bidirectional movement of inoculum between northern and southern regions of the United States and contributions from clonality and sexuality. The population from South Africa is solely clonal. A genome-wide association study (GWAS) employing a haplotype-resolved Pca reference genome was used to define 11 virulence-associated loci corresponding to 25 oat differential lines. These regions were screened to determine candidate Avr effector genes. Overall, the GWAS results allowed us to identify the underlying genetic factors controlling pathogen recognition in an oat differential set used in the United States to assign pathogen races (pathotypes). Key GWAS findings support complex genetic interactions in several oat lines, suggesting allelism among resistance genes or redundancy of genes included in the differential set, multiple resistance genes recognizing genetically linked Avr effector genes, or potentially epistatic relationships. A careful evaluation of the composition of the oat differential set accompanied by the development or implementation of molecular markers is recommended. [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)
- Tim C Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eva C Henningsen
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Danilo Pereira
- Christian Albrechts University of Kiel, 24118 Kiel, Germany
- Max Planck Institute of Evolutionary Biology, 24306 Plön, Germany
| | - Kerensa McElroy
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Sheshanka Dugyala
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Hoa Nguyen-Phuc
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Feng Li
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Botma Visser
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Zacharias A Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Willem H P Boshoff
- Department of Plant Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Eva H Stukenbrock
- Christian Albrechts University of Kiel, 24118 Kiel, Germany
- Max Planck Institute of Evolutionary Biology, 24306 Plön, Germany
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
- USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108, U.S.A
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2600, Australia
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27
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John E, Chau MQ, Hoang CV, Chandrasekharan N, Bhaskar C, Ma LS. Fungal Cell Wall-Associated Effectors: Sensing, Integration, Suppression, and Protection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:196-210. [PMID: 37955547 DOI: 10.1094/mpmi-09-23-0142-fi] [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: 11/14/2023]
Abstract
The cell wall (CW) of plant-interacting fungi, as the direct interface with host plants, plays a crucial role in fungal development. A number of secreted proteins are directly associated with the fungal CW, either through covalent or non-covalent interactions, and serve a range of important functions. In the context of plant-fungal interactions many are important for fungal development in the host environment and may therefore be considered fungal CW-associated effectors (CWAEs). Key CWAE functions include integrating chemical/physical signals to direct hyphal growth, interfering with plant immunity, and providing protection against plant defenses. In recent years, a diverse range of mechanisms have been reported that underpin their roles, with some CWAEs harboring conserved motifs or functional domains, while others are reported to have novel features. As such, the current understanding regarding fungal CWAEs is systematically presented here from the perspective of their biological functions in plant-fungal interactions. An overview of the fungal CW architecture and the mechanisms by which proteins are secreted, modified, and incorporated into the CW is first presented to provide context for their biological roles. Some CWAE functions are reported across a broad range of pathosystems or symbiotic/mutualistic associations. Prominent are the chitin interacting-effectors that facilitate fungal CW modification, protection, or suppression of host immune responses. However, several alternative functions are now reported and are presented and discussed. CWAEs can play diverse roles, some possibly unique to fungal lineages and others conserved across a broad range of plant-interacting fungi. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Evan John
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Minh-Quang Chau
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Cuong V Hoang
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo UPM, 28223 Pozuelo de Alarcón, Spain
| | | | - Chibbhi Bhaskar
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Lay-Sun Ma
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
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28
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Oliveira-Garcia E, Yan X, Oses-Ruiz M, de Paula S, Talbot NJ. Effector-triggered susceptibility by the rice blast fungus Magnaporthe oryzae. THE NEW PHYTOLOGIST 2024; 241:1007-1020. [PMID: 38073141 DOI: 10.1111/nph.19446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024]
Abstract
Rice blast, the most destructive disease of cultivated rice world-wide, is caused by the filamentous fungus Magnaporthe oryzae. To cause disease in plants, M. oryzae secretes a diverse range of effector proteins to suppress plant defense responses, modulate cellular processes, and support pathogen growth. Some effectors can be secreted by appressoria even before host penetration, while others accumulate in the apoplast, or enter living plant cells where they target specific plant subcellular compartments. During plant infection, the blast fungus induces the formation of a specialized plant structure known as the biotrophic interfacial complex (BIC), which appears to be crucial for effector delivery into plant cells. Here, we review recent advances in the cell biology of M. oryzae-host interactions and show how new breakthroughs in disease control have stemmed from an increased understanding of effector proteins of M. oryzae are deployed and delivered into plant cells to enable pathogen invasion and host susceptibility.
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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, USA
| | - Xia Yan
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Miriam Oses-Ruiz
- IMAB, Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Navarra, Spain
| | - Samuel de Paula
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
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Huamán-Pilco AF, Ramos-Carrasco TA, Franco MEE, Tineo-Flores D, Estrada-Cañari R, Romero PE, Aguilar-Rafael V, Ramírez-Orrego LA, Tincopa-Marca R, Márquez FR, Oliva-Cruz M, Díaz-Valderrama JR. Morphological, phylogenetic, and genomic evidence reveals the causal agent of thread blight disease of cacao in Peru is a new species of Marasmius in the section Neosessiles, Marasmius infestans sp. nov. F1000Res 2024; 12:1327. [PMID: 38680601 PMCID: PMC11053350 DOI: 10.12688/f1000research.140405.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 05/01/2024] Open
Abstract
The thread blight disease (TBD) of cacao ( Theobroma cacao) in the department of Amazonas, Peru was recently reported to be caused by Marasmius tenuissimus (sect. Neosessiles). This same species is known to be the main causal agent of TBD in West Africa. However, some morphological characteristics, such as the presence of rhizomorphs, the almost exclusively white color, and pileus sizes less than 5 mm, among others, differ to the description of M. tenuissimus. Therefore, we aimed to conduct a taxonomic revision of the cacao-TBD causal agent in Peru, by using thorough micro and macro morphological, phylogenetic, and nuclear and mitochondrial genomic approaches. We showed that the causal agent of TBD of cacao in Amazonas, Peru, belongs to a new species, Marasmius infestans sp. nov. This study enriches our knowledge of species in the sect. Neosessiles, and strongly suggests that the M. tenuissimus species complex is highly diverse.
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Affiliation(s)
- Angel Fernando Huamán-Pilco
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Tito Ademir Ramos-Carrasco
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Mario Emilio Ernesto Franco
- Sustainable Plant Protection Programme, Institute of Agrifood Research and Technology (IRTA), 25198 Lieda, Spain
- Department of Soil, Plant and Food Sciences, Universita degli Studi di Bari Aldo Moro, Bari, Apulia, 70126, Italy
| | - Daniel Tineo-Flores
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
- Centro Experimental Yanayacu, Dirección de Supervisión y Monitoreo en las Estaciones Experimentales Agrarias, Instituto Nacional de Innovación Agraria, Jaén 06801, Calamarca, Peru
| | - Richard Estrada-Cañari
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria, Lima, Lima, Peru
| | - Pedro Eduardo Romero
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima District, Lima Region, Peru
| | - Vilma Aguilar-Rafael
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Lourdes Adriana Ramírez-Orrego
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Rosalina Tincopa-Marca
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Fanny-Rosario Márquez
- Escuela Profesional de Ingeniería Agronómica Tropical, Universidad Nacional Intercultural de Quillabamba, Quillabamba, Cusco, Peru
| | - Manuel Oliva-Cruz
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
| | - Jorge Ronny Díaz-Valderrama
- Grupo de Investigación en Fitopatología y Micología, Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
- Facultad de Ingeniería y Ciencias Agrarias, National University Toribio Rodriguez de Mendoza of Amazonas, Chachapoyas, Amazonas, 01001, Peru
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Zhao M, Lei C, Zhou K, Huang Y, Fu C, Yang S, Zhang Z. POOE: predicting oomycete effectors based on a pre-trained large protein language model. mSystems 2024; 9:e0100423. [PMID: 38078741 PMCID: PMC10804963 DOI: 10.1128/msystems.01004-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/23/2023] [Indexed: 01/24/2024] Open
Abstract
Oomycetes are fungus-like eukaryotic microorganisms which can cause catastrophic diseases in many plants. Successful infection of oomycetes depends highly on their effector proteins that are secreted into plant cells to subvert plant immunity. Thus, systematic identification of effectors from the oomycete proteomes remains an initial but crucial step in understanding plant-pathogen relationships. However, the number of experimentally identified oomycete effectors is still limited. Currently, only a few bioinformatics predictors exist to detect potential effectors, and their prediction performance needs to be improved. Here, we used the sequence embeddings from a pre-trained large protein language model (ProtTrans) as input and developed a support vector machine-based method called POOE for predicting oomycete effectors. POOE could achieve a highly accurate performance with an area under the precision-recall curve of 0.804 (area under the receiver operating characteristic curve = 0.893, accuracy = 0.874, precision = 0.777, recall = 0.684, and specificity = 0.936) in the fivefold cross-validation, considerably outperforming various combinations of popular machine learning algorithms and other commonly used sequence encoding schemes. A similar prediction performance was also observed in the independent test. Compared with the existing oomycete effector prediction methods, POOE provided very competitive and promising performance, suggesting that ProtTrans effectively captures rich protein semantic information and dramatically improves the prediction task. We anticipate that POOE can accelerate the identification of oomycete effectors and provide new hints to systematically understand the functional roles of effectors in plant-pathogen interactions. The web server of POOE is freely accessible at http://zzdlab.com/pooe/index.php. The corresponding source codes and data sets are also available at https://github.com/zzdlabzm/POOE.IMPORTANCEIn this work, we use the sequence representations from a pre-trained large protein language model (ProtTrans) as input and develop a Support Vector Machine-based method called POOE for predicting oomycete effectors. POOE could achieve a highly accurate performance in the independent test set, considerably outperforming existing oomycete effector prediction methods. We expect that this new bioinformatics tool will accelerate the identification of oomycete effectors and further guide the experimental efforts to interrogate the functional roles of effectors in plant-pathogen interaction.
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Affiliation(s)
- Miao Zhao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenping Lei
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kewei Zhou
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yan Huang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chen Fu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China
| | - Shiping Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ziding Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, China
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Wei H, Zhong Z, Li Z, Zhang Y, Stukenbrock EH, Tang B, Yang N, Baroncelli R, Peng L, Liu Z, He X, Yang Y, Yuan Z. Loss of the accessory chromosome converts a pathogenic tree-root fungus into a mutualistic endophyte. PLANT COMMUNICATIONS 2024; 5:100672. [PMID: 37563834 PMCID: PMC10811371 DOI: 10.1016/j.xplc.2023.100672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
Some fungal accessory chromosomes (ACs) may contribute to virulence in plants. However, the mechanisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic continuum are not clear. Here we delineated the genetic divergence in two sympatric but considerably variable isolates (16B and 16W) of the poplar-associated fungus Stagonosporopsis rhizophilae. We identified a ∼0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in plants. Complete deletion of the AC (Δ16W) significantly altered the fungal phenotype. Specifically, Δ16W was morphologically more similar to 16B, showed enhanced melanization, and established beneficial interactions with poplar plants, thereby acting as a dark septate endophyte. RNA sequencing (RNA-seq) analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and melanin. We observed that the AC maintained a more open status of chromatin across the genome, indicating an impressive remodeling of cis-regulatory elements upon AC loss, which potentially enhanced symbiotic effectiveness. We demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum- and Arabidopsis-fungus associations. Furthermore, the three isolates generated symbiotic interactions with a nonvascular liverwort. In summary, our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the AC. We speculate that AC-situated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence.
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Affiliation(s)
- Huanshen Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongfeng Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yuwei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University, 24118 Kiel, Germany; Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng 224002, China
| | - Ningning Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Long Peng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhuo Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xinghua He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yuzhan Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
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Chen C, Keunecke H, Bemm F, Gyetvai G, Neu E, Kopisch‐Obuch FJ, McDonald BA, Stapley J. GWAS reveals a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogen. MOLECULAR PLANT PATHOLOGY 2024; 25:e13407. [PMID: 38009399 PMCID: PMC10799204 DOI: 10.1111/mpp.13407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
The major resistance gene BvCR4 recently bred into sugar beet hybrids provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogen Cercospora beticola. The occurrence of pathogen strains that overcome BvCR4 was studied using field trials in Switzerland conducted under natural disease pressure. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a new C. beticola reference genome and mapped whole genome sequences of 256 isolates collected in Switzerland and Germany. These were combined with virulence phenotypes to conduct three separate genome-wide association studies (GWAS) to identify candidate avirulence genes. We identified a locus associated with avirulence containing a putative avirulence effector gene named AvrCR4. All virulent isolates either lacked AvrCR4 or had nonsynonymous mutations within the gene. AvrCR4 was present in all 74 isolates from non-BvCR4 hybrids, whereas 33 of 89 isolates from BvCR4 hybrids carried a deletion. We also mapped genomic data from 190 publicly available US isolates to our new reference genome. The AvrCR4 deletion was found in only one of 95 unique isolates from non-BvCR4 hybrids in the United States. AvrCR4 presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment of BvCR4. Identification of AvrCR4 will enable real-time screening of C. beticola populations for the emergence and spread of virulent isolates.
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Affiliation(s)
- Chen Chen
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
| | | | | | | | - Enzo Neu
- KWS SAAT SE & Co. KGaAEinbeckGermany
| | | | - Bruce A. McDonald
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
| | - Jessica Stapley
- Plant Pathology GroupInstitute of Integrative Biology, ETH ZurichZürichSwitzerland
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Dvorianinova EM, Sigova EA, Mollaev TD, Rozhmina TA, Kudryavtseva LP, Novakovskiy RO, Turba AA, Zhernova DA, Borkhert EV, Pushkova EN, Melnikova NV, Dmitriev AA. Comparative Genomic Analysis of Colletotrichum lini Strains with Different Virulence on Flax. J Fungi (Basel) 2023; 10:32. [PMID: 38248942 PMCID: PMC10817032 DOI: 10.3390/jof10010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/04/2023] [Accepted: 12/24/2023] [Indexed: 01/23/2024] Open
Abstract
Colletotrichum lini is a flax fungal pathogen. The genus comprises differently virulent strains, leading to significant yield losses. However, there were no attempts to investigate the molecular mechanisms of C. lini pathogenicity from high-quality genome assemblies until this study. In this work, we sequenced the genomes of three C. lini strains of high (#390-1), medium (#757), and low (#771) virulence. We obtained more than 100× genome coverage with Oxford Nanopore Technologies reads (N50 = 12.1, 6.1, 5.0 kb) and more than 50× genome coverage with Illumina data (150 + 150 bp). Several assembly strategies were tested. The final assemblies were obtained using the Canu-Racon ×2-Medaka-Polca scheme. The assembled genomes had a size of 54.0-55.3 Mb, 26-32 contigs, N50 values > 5 Mb, and BUSCO completeness > 96%. A comparative genomic analysis showed high similarity among mitochondrial and nuclear genomes. However, a rearrangement event and the loss of a 0.7 Mb contig were revealed. After genome annotation with Funannotate, secreting proteins were selected using SignalP, and candidate effectors were predicted among them using EffectorP. The analysis of the InterPro annotations of predicted effectors revealed unique protein categories in each strain. The assembled genomes and the conducted comparative analysis extend the knowledge of the genetic diversity of C. lini and form the basis for establishing the molecular mechanisms of its pathogenicity.
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Affiliation(s)
- Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
- Moscow Institute of Physics and Technology, Moscow 141701, Russia
| | - Timur D. Mollaev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
- Agrarian and Technological Institute, Peoples Friendship University of Russia (RUDN University), Moscow 117198, Russia
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, Torzhok 172002, Russia; (T.A.R.); (L.P.K.)
| | | | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (E.A.S.); (T.D.M.); (R.O.N.); (A.A.T.); (D.A.Z.); (E.V.B.); (E.N.P.); (N.V.M.)
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Chakraborty A, Hussain A, Sabnam N. Uncovering the structural stability of Magnaporthe oryzae effectors: a secretome-wide in silico analysis. J Biomol Struct Dyn 2023:1-22. [PMID: 38109060 DOI: 10.1080/07391102.2023.2292795] [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: 05/07/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is a deadly disease and a major threat to global food security. The pathogen secretes small proteinaceous effectors, virulence factors, inside the host to manipulate and perturb the host immune system, allowing the pathogen to colonize and establish a successful infection. While the molecular functions of several effectors are characterized, very little is known about the structural stability of these effectors. We analyzed a total of 554 small secretory proteins (SSPs) from the M. oryzae secretome to decipher key features of intrinsic disorder (ID) and the structural dynamics of the selected putative effectors through thorough and systematic in silico studies. Our results suggest that out of the total SSPs, 66% were predicted as effector proteins, released either into the apoplast or cytoplasm of the host cell. Of these, 68% were found to be intrinsically disordered effector proteins (IDEPs). Among the six distinct classes of disordered effectors, we observed peculiar relationships between the localization of several effectors in the apoplast or cytoplasm and the degree of disorder. We determined the degree of structural disorder and its impact on protein foldability across all the putative small secretory effector proteins from the blast pathogen, further validated by molecular dynamics simulation studies. This study provides definite clues toward unraveling the mystery behind the importance of structural distortions in effectors and their impact on plant-pathogen interactions. The study of these dynamical segments may help identify new effectors as well.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Afzal Hussain
- Department of Bioinformatics, Maulana Azad National Institute of Technology, Bhopal, India
| | - Nazmiara Sabnam
- Department of Life Sciences, Presidency University, Kolkata, India
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Nakamoto AA, Joubert PM, Krasileva KV. Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes. Genome Biol Evol 2023; 15:evad206. [PMID: 37975814 PMCID: PMC10691877 DOI: 10.1093/gbe/evad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.
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Affiliation(s)
- Anne A Nakamoto
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Pierre M Joubert
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
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36
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Sankari S, Lovelace AH. Unveiling the Molecular Arsenal: Identification and Characterization of Sphaerulina musiva Effectors Targeting Populus Genotypes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:752-753. [PMID: 38153816 DOI: 10.1094/mpmi-11-23-0186-cm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Affiliation(s)
- Siva Sankari
- Stowers Institute for Medical Research, Kansas City, MO 64110, U.S.A
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Kariyawasam GK, Nelson AC, Williams SJ, Solomon PS, Faris JD, Friesen TL. The Necrotrophic Pathogen Parastagonospora nodorum Is a Master Manipulator of Wheat Defense. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:764-773. [PMID: 37581456 DOI: 10.1094/mpmi-05-23-0067-irw] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2023]
Abstract
Parastagonospora nodorum is a necrotrophic pathogen of wheat that is particularly destructive in major wheat-growing regions of the United States, northern Europe, Australia, and South America. P. nodorum secretes necrotrophic effectors that target wheat susceptibility genes to induce programmed cell death (PCD), resulting in increased colonization of host tissue and, ultimately, sporulation to complete its pathogenic life cycle. Intensive research over the last two decades has led to the functional characterization of five proteinaceous necrotrophic effectors, SnTox1, SnToxA, SnTox267, SnTox3, and SnTox5, and three wheat susceptibility genes, Tsn1, Snn1, and Snn3D-1. Functional characterization has revealed that these effectors, in addition to inducing PCD, have additional roles in pathogenesis, including chitin binding that results in protection from wheat chitinases, blocking defense response signaling, and facilitating plant colonization. There are still large gaps in our understanding of how this necrotrophic pathogen is successfully manipulating wheat defense to complete its life cycle. This review summarizes our current knowledge, identifies knowledge gaps, and provides a summary of well-developed tools and resources currently available to study the P. nodorum-wheat interaction, which has become a model for necrotrophic specialist interactions. Further functional characterization of the effectors involved in this interaction and work toward a complete understanding of how P. nodorum manipulates wheat defense will provide fundamental knowledge about this and other necrotrophic interactions. Additionally, a broader understanding of this interaction will contribute to the successful management of Septoria nodorum blotch disease on wheat. [Formula: see text] Copyright © 2023 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)
- Gayan K Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Ashley C Nelson
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Simon J Williams
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Peter S Solomon
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Justin D Faris
- Cereal Crops Research Unit, USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
| | - Timothy L Friesen
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
- Cereal Crops Research Unit, USDA-ARS, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, U.S.A
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Liu Z, Zhu Z, Huang Y, Nong S, Jiang M, Yi S, Xie D, Hu H. Identification of gene modules and hub genes associated with Colletotrichum siamense infection in mango using weighted gene co-expression network analysis. BMC Genomics 2023; 24:710. [PMID: 37996781 PMCID: PMC10668491 DOI: 10.1186/s12864-023-09811-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
Colletotrichum siamense is a hemibiotrophic ascomycetous fungus responsible for mango anthracnose. The key genes involved in C. siamense infection remained largely unknown. In this study, we conducted weighted gene co-expression network analysis (WGCNA) of RNA-seq data to mine key genes involved in Colletotrichum siamense-mango interactions. Gene modules of Turquoise and Salmon, containing 1039 and 139 respectively, were associated with C. siamense infection, which were conducted for further analysis. GO enrichment analysis revealed that protein synthesis, organonitrogen compound biosynthetic and metabolic process, and endoplasmic reticulum-related genes were associated with C. siamense infection. A total of 568 proteins had homologs in the PHI database, 370 of which were related to virulence. The hub genes in each module were identified, which were annotated as O-methyltransferase (Salmon) and Clock-controlled protein 6 (Turquoise). A total of 24 proteins exhibited characteristics of SCRPs. By using transient expression in Nicotiana benthamiana, the SCRPs of XM_036637681.1 could inhibit programmed cell death (PCD) that induced by BAX (BCL-2-associated X protein), suggesting that it may play important roles in C. siamense infection. A mango-C. siamense co-expression network was constructed, and the mango gene of XM_044632979.1 (auxin-induced protein 15A-like) was positively associated with 5 SCRPs. These findings help to deepen the current understanding of necrotrophic stage in C. siamense infection.
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Affiliation(s)
- Zongling Liu
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, 533000, China.
- Guangxi Key Laboratory of Biology for Mango, Baise, 533000, China.
| | - Zhengjie Zhu
- Guangxi Key Laboratory of Biology for Mango, Baise, 533000, China
| | - Yuanhe Huang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, 533000, China
| | - Song Nong
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, 533000, China
| | - Minli Jiang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, 533000, China
| | - Sangui Yi
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, 533000, China
| | - Delong Xie
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, 533000, China
| | - Hongliu Hu
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, 533000, China
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Lin HC, de Ulzurrun GVD, Chen SA, Yang CT, Tay RJ, Iizuka T, Huang TY, Kuo CY, Gonçalves AP, Lin SY, Chang YC, Stajich JE, Schwarz EM, Hsueh YP. Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus. PLoS Biol 2023; 21:e3002400. [PMID: 37988381 PMCID: PMC10662756 DOI: 10.1371/journal.pbio.3002400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
Nutritional deprivation triggers a switch from a saprotrophic to predatory lifestyle in soil-dwelling nematode-trapping fungi (NTF). In particular, the NTF Arthrobotrys oligospora secretes food and sex cues to lure nematodes to its mycelium and is triggered to develop specialized trapping devices. Captured nematodes are then invaded and digested by the fungus, thus serving as a food source. In this study, we examined the transcriptomic response of A. oligospora across the stages of sensing, trap development, and digestion upon exposure to the model nematode Caenorhabditis elegans. A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. Two-thirds of the predicted secretome of A. oligospora was up-regulated in the presence of C. elegans at all time points examined, and among these secreted proteins, 38.5% are predicted to be effector proteins. Furthermore, functional studies disrupting the t-SNARE protein Sso2 resulted in impaired ability to capture nematodes. Additionally, genes of the DUF3129 family, which are expanded in the genomes of several NTF, were highly up-regulated upon nematode exposure. We observed the accumulation of highly expressed DUF3129 proteins in trap cells, leading us to name members of this gene family as Trap Enriched Proteins (TEPs). Gene deletion of the most highly expressed TEP gene, TEP1, impairs the function of traps and prevents the fungus from capturing prey efficiently. In late stages of predation, we observed up-regulation of a variety of proteases, including metalloproteases. Following penetration of nematodes, these metalloproteases facilitate hyphal growth required for colonization of prey. These findings provide insights into the biology of the predatory lifestyle switch in a carnivorous fungus and provide frameworks for other fungal-nematode predator-prey systems.
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Affiliation(s)
- Hung-Che Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | | | - Sheng-An Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Ching-Ting Yang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Rebecca J. Tay
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tomoyo Iizuka
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tsung-Yu Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Yen Kuo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - A. Pedro Gonçalves
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Siou-Ying Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Erich M. Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
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40
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Sperschneider J, Yildirir G, Rizzi YS, Malar C M, Mayrand Nicol A, Sorwar E, Villeneuve-Laroche M, Chen ECH, Iwasaki W, Brauer EK, Bosnich W, Gutjahr C, Corradi N. Arbuscular mycorrhizal fungi heterokaryons have two nuclear populations with distinct roles in host-plant interactions. Nat Microbiol 2023; 8:2142-2153. [PMID: 37884816 DOI: 10.1038/s41564-023-01495-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) are prominent root symbionts that can carry thousands of nuclei deriving from two parental strains in a large syncytium. These co-existing genomes can also vary in abundance with changing environmental conditions. Here we assemble the nuclear genomes of all four publicly available AMF heterokaryons using PacBio high-fidelity and Hi-C sequencing. We find that the two co-existing genomes of these strains are phylogenetically related but differ in structure, content and epigenetics. We confirm that AMF heterokaryon genomes vary in relative abundance across conditions and show this can lead to nucleus-specific differences in expression during interactions with plants. Population analyses also reveal signatures of genetic exchange indicative of past events of sexual reproduction in these strains. This work uncovers the origin and contribution of two nuclear genomes in AMF heterokaryons and opens avenues for the improvement and environmental application of these strains.
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Affiliation(s)
- Jana Sperschneider
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Gokalp Yildirir
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Yanina S Rizzi
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mathu Malar C
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Essam Sorwar
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Eric C H Chen
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Elizabeth K Brauer
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Whynn Bosnich
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada.
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41
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Welgemoed T, Duong TA, Barnes I, Stukenbrock EH, Berger DK. Population genomic analyses suggest recent dispersal events of the pathogen Cercospora zeina into East and Southern African maize cropping systems. G3 (BETHESDA, MD.) 2023; 13:jkad214. [PMID: 37738420 PMCID: PMC10627275 DOI: 10.1093/g3journal/jkad214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/03/2023] [Accepted: 09/06/2023] [Indexed: 09/24/2023]
Abstract
A serious factor hampering global maize production is gray leaf spot disease. Cercospora zeina is one of the causative pathogens, but population genomics analysis of C. zeina is lacking. We conducted whole-genome Illumina sequencing of a representative set of 30 C. zeina isolates from Kenya and Uganda (East Africa) and Zambia, Zimbabwe, and South Africa (Southern Africa). Selection of the diverse set was based on microsatellite data from a larger collection of the pathogen. Pangenome analysis of the C. zeina isolates was done by (1) de novo assembly of the reads with SPAdes, (2) annotation with BRAKER, and (3) protein clustering with OrthoFinder. A published long-read assembly of C. zeina (CMW25467) from Zambia was included and annotated using the same pipeline. This analysis revealed 790 non-shared accessory and 10,677 shared core orthogroups (genes) between the 31 isolates. Accessory gene content was largely shared between isolates from all countries, with a few genes unique to populations from Southern Africa (32) or East Africa (6). There was a significantly higher proportion of effector genes in the accessory secretome (44%) compared to the core secretome (24%). PCA, ADMIXTURE, and phylogenetic analysis using a neighbor-net network indicated a population structure with a geographical subdivision between the East African isolates and the Southern African isolates, although gene flow was also evident. The small pangenome and partial population differentiation indicated recent dispersal of C. zeina into Africa, possibly from 2 regional founder populations, followed by recurrent gene flow owing to widespread maize production across sub-Saharan Africa.
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Affiliation(s)
- Tanya Welgemoed
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-11, Kiel 24118, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön 24306, Germany
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
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42
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Bouqellah NA, Farag PF. In Silico Evaluation, Phylogenetic Analysis, and Structural Modeling of the Class II Hydrophobin Family from Different Fungal Phytopathogens. Microorganisms 2023; 11:2632. [PMID: 38004644 PMCID: PMC10672791 DOI: 10.3390/microorganisms11112632] [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: 09/18/2023] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The class II hydrophobin group (HFBII) is an extracellular group of proteins that contain the HFBII domain and eight conserved cysteine residues. These proteins are exclusively secreted by fungi and have multiple functions with a probable role as effectors. In the present study, a total of 45 amino acid sequences of hydrophobin class II proteins from different phytopathogenic fungi were retrieved from the NCBI database. We used the integration of well-designed bioinformatic tools to characterize and predict their physicochemical parameters, novel motifs, 3D structures, multiple sequence alignment (MSA), evolution, and functions as effector proteins through molecular docking. The results revealed new features for these protein members. The ProtParam tool detected the hydrophobicity properties of all proteins except for one hydrophilic protein (KAI3335996.1). Out of 45 proteins, six of them were detected as GPI-anchored proteins by the PredGPI server. Different 3D structure templates with high pTM scores were designed by Multifold v1, AlphaFold2, and trRosetta. Most of the studied proteins were anticipated as apoplastic effectors and matched with the ghyd5 gene of Fusarium graminearum as virulence factors. A protein-protein interaction (PPI) analysis unraveled the molecular function of this group as GTP-binding proteins, while a molecular docking analysis detected a chitin-binding effector role. From the MSA analysis, it was observed that the HFBII sequences shared conserved 2 Pro (P) and 2 Gly (G) amino acids besides the known eight conserved cysteine residues. The evolutionary analysis and phylogenetic tree provided evidence of episodic diversifying selection at the branch level using the aBSREL tool. A detailed in silico analysis of this family and the present findings will provide a better understanding of the HFBII characters and evolutionary relationships, which could be very useful in future studies.
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Affiliation(s)
- Nahla A. Bouqellah
- Department of Biology, College of Science, Taibah University, P.O. Box 344, Al Madinah Al Munawwarah 42317-8599, Saudi Arabia
| | - Peter F. Farag
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo 11566, Egypt;
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43
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Xie Y, Shi L, Cheng K, Li Y, Yu S. Host Recognition and Specific Infection of Endomelanconiopsis endophytica during Early Infection. J Fungi (Basel) 2023; 9:1040. [PMID: 37888296 PMCID: PMC10607883 DOI: 10.3390/jof9101040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Coevolution between the pathogen and host plant drives pathogenic effector diversity. However, the molecular mechanism behind host-specific pathogenesis remains to be explored. Here, we present a 43 Mb whole-genome sequence of Endomelanconiopsis endophytica strain LS29, a host-specific pathogen of the common subtropical tree Castanopsis fissa. We described its genome annotations and identified its effector candidates. By performing temporal transcriptome sequencing of E. endophytica on C. fissa during early infection, we found that E. endophytica repressed other microbes in order to attack the tissue of the host by producing antibiotics earlier than 24 h post-inoculation (hpi). Simultaneously, a variety of effectors were secreted to recognize the host plant, but most of them showed a significantly opposing expression regulation trend after 24 hpi, indicating that 24 hpi represents a key time point between host recognition and specific infection. Furthermore, a comparison of isoenzymes showed that only a few effectors were identified as specific effectors, which were involved in hydrolyzing the compounds of the plant cell wall and releasing fatty acids during the early infection of C. fissa. Our results determined host recognition timing and identified a specific catalog of effectors, which are crucial for revealing the molecular mechanism of host-specific pathogenesis.
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Affiliation(s)
- Yan Xie
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Liuqing Shi
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Keke Cheng
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yang Li
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Shixiao Yu
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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44
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Rozano L, Hane JK, Mancera RL. The Molecular Docking of MAX Fungal Effectors with Plant HMA Domain-Binding Proteins. Int J Mol Sci 2023; 24:15239. [PMID: 37894919 PMCID: PMC10607590 DOI: 10.3390/ijms242015239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Fungal effector proteins are important in mediating disease infections in agriculturally important crops. These secreted small proteins are known to interact with their respective host receptor binding partners in the host, either inside the cells or in the apoplastic space, depending on the localisation of the effector proteins. Consequently, it is important to understand the interactions between fungal effector proteins and their target host receptor binding partners, particularly since this can be used for the selection of potential plant resistance or susceptibility-related proteins that can be applied to the breeding of new cultivars with disease resistance. In this study, molecular docking simulations were used to characterise protein-protein interactions between effector and plant receptors. Benchmarking was undertaken using available experimental structures of effector-host receptor complexes to optimise simulation parameters, which were then used to predict the structures and mediating interactions of effector proteins with host receptor binding partners that have not yet been characterised experimentally. Rigid docking was applied for both the so-called bound and unbound docking of MAX effectors with plant HMA domain protein partners. All bound complexes used for benchmarking were correctly predicted, with 84% being ranked as the top docking pose using the ZDOCK scoring function. In the case of unbound complexes, a minimum of 95% of known residues were predicted to be part of the interacting interface on the host receptor binding partner, and at least 87% of known residues were predicted to be part of the interacting interface on the effector protein. Hydrophobic interactions were found to dominate the formation of effector-plant protein complexes. An optimised set of docking parameters based on the use of ZDOCK and ZRANK scoring functions were established to enable the prediction of near-native docking poses involving different binding interfaces on plant HMA domain proteins. Whilst this study was limited by the availability of the experimentally determined complexed structures of effectors and host receptor binding partners, we demonstrated the potential of molecular docking simulations to predict the likely interactions between effectors and their respective host receptor binding partners. This computational approach may accelerate the process of the discovery of putative interacting plant partners of effector proteins and contribute to effector-assisted marker discovery, thereby supporting the breeding of disease-resistant crops.
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Affiliation(s)
- Lina Rozano
- Curtin Medical School, Curtin Health Innovation Research Institute, GPO Box U1987, Perth, WA 6845, Australia
- Curtin Institute for Data Science, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - James K. Hane
- Curtin Institute for Data Science, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
| | - Ricardo L. Mancera
- Curtin Medical School, Curtin Health Innovation Research Institute, GPO Box U1987, Perth, WA 6845, Australia
- Curtin Institute for Data Science, Curtin University, GPO Box U1987, Perth, WA 6845, Australia
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45
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Searight J, Famoso AN, Zhou XG, Doyle VP, Richards JK. A High-Quality Genome Assembly for Cercospora janseana, Causal Agent of Narrow Brown Leaf Spot of Rice. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:666-669. [PMID: 37129280 DOI: 10.1094/mpmi-10-22-0222-a] [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: 05/03/2023]
Abstract
Cercospora janseana causes narrow brown leaf spot of rice. A nearly complete telomere-to-telomere reference genome was assembled with a combination of Oxford Nanopore and Illumina sequences. The genome assembly has a total length of 39,075,509 bp and consists of 15 chromosomes, 14 of which have telomeric repeats at both ends. The assembly N50 is 2.97 Mb and the L50 is five contigs. RNA-seq-mediated gene annotation identified 10,850 genes, including 955 predicted secreted proteins and 361 predicted effector proteins. This highly contiguous and almost complete C. janseana reference genome will be a vital resource for further investigation of host-pathogen interactions and genome evolution within this pathosystem. [Formula: see text] Copyright © 2023 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)
- Jacob Searight
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Adam N Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, Crowley, LA, U.S.A
| | - Xin-Gen Zhou
- Texas A&M University System, AgriLife Research and Extension Center, Beaumont, TX, U.S.A
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - Jonathan K Richards
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
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Bao J, Su J, Wang Y, Liang X, Yu H, Zhu X, Li L, Hu H. High-Quality Genome Assembly and Annotation Resource of Elsinoë annonae, Causing Fruit Scab on Camellia oleifera. PLANT DISEASE 2023; 107:3264-3268. [PMID: 36935384 DOI: 10.1094/pdis-10-22-2322-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Elsinoë annonae is a fungal pathogen that causes fruit scab disease in the edible-oil (tea oil) plant (Camellia oleifera Abel). The absence of genome resources for this fungus hampers functional genetic studies of the pathogenesis mechanism of E. annonae. This study reports the genome assembly of E. annonae strain SM-YC-2 collected from tea oil tree fruit with scab disease in Fujian Province, China. Combining 16.44 Gb of PacBio Sequel II long reads and 5.13 Gb of Illumina NovaSeq reads, we generated a 25.93-Mb (99.19% of expected genome size) high-quality genome assembly with 52.66% GC content, 5.05% repeats, and over 98% Benchmarking Universal Single-Copy Orthologs completeness for E. annonae strain SM-YC-2. These high-quality genome assembly resources will facilitate functional genomic characterization studies, enhance insights into the pathogenicity mechanism of E. annonae, and support the development of molecular-based control strategies.
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Affiliation(s)
- Jiandong Bao
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiyu Su
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yinping Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinyu Liang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hao Yu
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xueming Zhu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lin Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hongli Hu
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Sarkar D, Majumder S, Giri K, Sabnam N. In silico characterization, molecular docking, and dynamic simulation of a novel fungal cell-death suppressing effector, MoRlpA as potential cathepsin B-like cysteine protease inhibitor during rice blast infection. J Biomol Struct Dyn 2023; 41:9039-9056. [PMID: 36345772 DOI: 10.1080/07391102.2022.2139763] [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: 08/20/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022]
Abstract
The blast fungus Magnaporthe oryzae is one of the most notorious pathogens affecting rice production worldwide. The cereal killer employs a special class of small secreted proteins called effectors to manipulate and perturb the host metabolism. In turn, the host plants trigger effector-triggered immunity (ETI) via localized cell death and hypersensitive response (HR). We have identified and characterized a novel secreted effector MoRlpA from M. oryzae by extensive in silico methods. The localization studies suggested that it is exclusively secreted in the host apoplasts. Interestingly, MoRlpA interacts with a protease, cathepsin B from rice with highest affinity. The 3D structural models of both the proteins were generated. Cathepsin B-like cysteine proteases are usually involved in programmed cell death (PCD) and autophagy in plants which lead to generation of HR upon infection. Our results suggest that MoRlpA interacts with rice cathepsin B-like cysteine protease and demolish the host counter-attack by suppressing cell death and HR during an active blast infection. This was further validated by molecular docking and molecular dynamic simulation analyses. The important residues involved in the rice-blast pathogen interactions were deciphered. Overall, this research highlights stable interactions between MoRlpA-OsCathB during rice blast pathogenesis and providing an insight into how this novel RlpA protease inhibitor-cum-effector modulates the host's apoplast to invade the host tissues and establish a successful infection. Thus, this research will help to develop potential fungicide to block the binding region of MoRlpA target so that the cryptic pathogen would be recognized by the host. HIGHLIGHTSFor the first time, a novel secreted effector protein, MoRlpA has been identified and characterised from M. oryzae in silicoMoRlpA contains a rare lipoprotein A-like DPBB domain which is often an enzymatic domain in other systemsMoRlpA as an apoplastic effector interacts with the rice protease OsCathB to suppress the cell death and hypersensitive response during rice blast infectionThe three-dimensional structures of both the MoRlpA and OsCathB proteins were predictedMoRlpA-OsCathB interactions were analysed by molecular docking and molecular dynamic simulation studiesCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debrup Sarkar
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Kalyan Giri
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Nazmiara Sabnam
- Department of Life Sciences, Presidency University, Kolkata, India
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Ramos-Lizardo GN, Mucherino-Muñoz JJ, Aguiar ERGR, Pirovani CP, Corrêa RX. A repertoire of candidate effector proteins of the fungus Ceratocystis cacaofunesta. Sci Rep 2023; 13:16368. [PMID: 37773261 PMCID: PMC10542334 DOI: 10.1038/s41598-023-43117-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
The genus Ceratocystis includes many phytopathogenic fungi that affect different plant species. One of these is Ceratocystis cacaofunesta, which is pathogenic to the cocoa tree and causes Ceratocystis wilt, a lethal disease for the crop. However, little is known about how this pathogen interacts with its host. The knowledge and identification of possible genes encoding effector proteins are essential to understanding this pathosystem. The present work aimed to predict genes that code effector proteins of C. cacaofunesta from a comparative analysis of the genomes of five Ceratocystis species available in databases. We performed a new genome annotation through an in-silico analysis. We analyzed the secretome and effectorome of C. cacaofunesta using the characteristics of the peptides, such as the presence of signal peptide for secretion, absence of transmembrane domain, and richness of cysteine residues. We identified 160 candidate effector proteins in the C. cacaofunesta proteome that could be classified as cytoplasmic (102) or apoplastic (58). Of the total number of candidate effector proteins, 146 were expressed, presenting an average of 206.56 transcripts per million. Our database was created using a robust bioinformatics strategy, followed by manual curation, generating information on pathogenicity-related genes involved in plant interactions, including CAZymes, hydrolases, lyases, and oxidoreductases. Comparing proteins already characterized as effectors in Sordariomycetes species revealed five groups of protein sequences homologous to C. cacaofunesta. These data provide a valuable resource for studying the infection mechanisms of these pathogens in their hosts.
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Affiliation(s)
- Gabriela N Ramos-Lizardo
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Jonathan J Mucherino-Muñoz
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Eric R G R Aguiar
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Carlos Priminho Pirovani
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil
| | - Ronan Xavier Corrêa
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, 45662-900, Brazil.
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Poudel RS, Belay K, Nelson B, Brueggeman R, Underwood W. Population and genome-wide association studies of Sclerotinia sclerotiorum isolates collected from diverse host plants throughout the United States. Front Microbiol 2023; 14:1251003. [PMID: 37829452 PMCID: PMC10566370 DOI: 10.3389/fmicb.2023.1251003] [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: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 10/14/2023] Open
Abstract
Introduction Sclerotinia sclerotiorum is a necrotrophic fungal pathogen causing disease and economic loss on numerous crop plants. This fungus has a broad host range and can infect over 400 plant species, including important oilseed crops such as soybean, canola, and sunflower. S. sclerotiorum isolates vary in aggressiveness of lesion formation on plant tissues. However, the genetic basis for this variation remains to be determined. The aims of this study were to evaluate a diverse collection of S. sclerotiorum isolates collected from numerous hosts and U.S. states for aggressiveness of stem lesion formation on sunflower, to evaluate the population characteristics, and to identify loci associated with isolate aggressiveness using genome-wide association mapping. Methods A total of 219 S. sclerotiorum isolates were evaluated for stem lesion formation on two sunflower inbred lines and genotyped using genotyping-by-sequencing. DNA markers were used to assess population differentiation across hosts, regions, and climatic conditions and to perform a genome-wide association study of isolate aggressiveness. Results and discussion We observed a broad range of aggressiveness for lesion formation on sunflower stems, and only a moderate correlation between aggressiveness on the two lines. Population genetic evaluations revealed differentiation between populations from warmer climate regions compared to cooler regions. Finally, a genome-wide association study of isolate aggressiveness identified three loci significantly associated with aggressiveness on sunflower. Functional characterization of candidate genes at these loci will likely improve our understanding of the virulence strategies used by this pathogen to cause disease on a wide array of agriculturally important host plants.
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Affiliation(s)
- Roshan Sharma Poudel
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Kassaye Belay
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Berlin Nelson
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - William Underwood
- Edward T. Schafer Agricultural Research Center, Sunflower and Plant Biology Research Unit, USDA Agricultural Research Service, Fargo, ND, United States
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Prasad P, Jain N, Chaudhary J, Thakur RK, Savadi S, Bhardwaj SC, Gangwar OP, Lata C, Adhikari S, Kumar S, Balyan HS, Gupta PK. Candidate effectors for leaf rust resistance gene Lr28 identified through transcriptome and in-silico analysis. Front Microbiol 2023; 14:1143703. [PMID: 37789861 PMCID: PMC10543267 DOI: 10.3389/fmicb.2023.1143703] [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: 01/13/2023] [Accepted: 07/31/2023] [Indexed: 10/05/2023] Open
Abstract
Puccinia spp. causing rust diseases in wheat and other cereals secrete several specialized effector proteins into host cells. Characterization of these proteins and their interaction with host's R proteins could greatly help to limit crop losses due to diseases. Prediction of effector proteins by combining the transcriptome analysis and multiple in-silico approaches is gaining importance in revealing the pathogenic mechanism. The present study involved identification of 13 Puccinia triticina (Pt) coding sequences (CDSs), through transcriptome analysis, that were differentially expressed during wheat-leaf rust interaction; and prediction of their effector like features using different in-silico tools. NCBI-BLAST and pathogen-host interaction BLAST (PHI-BLAST) tools were used to annotate and classify these sequences based on their most closely matched counterpart in both the databases. Homology between CDSs and the annotated sequences in the NCBI database ranged from 79 to 94% and with putative effectors of other plant pathogens in PHI-BLAST from 24.46 to 54.35%. Nine of the 13 CDSs had effector-like features according to EffectorP 3.0 (≥0.546 probability of these sequences to be effector). The qRT-PCR expression analysis revealed that the relative expression of all CDSs in compatible interaction (HD2329) was maximum at 11 days post inoculation (dpi) and that in incompatible interactions (HD2329 + Lr28) was maximum at 3 dpi in seven and 9 dpi in five CDSs. These results suggest that six CDSs (>0.8 effector probability as per EffectorP 3.0) could be considered as putative Pt effectors. The molecular docking and MD simulation analysis of these six CDSs suggested that candidate Lr28 protein binds more strongly to candidate effector c14094_g1_i1 to form more stable complex than the remaining five. Further functional characterization of these six candidate effectors should prove useful for a better understanding of wheat-leaf rust interaction. In turn, this should facilitate effector-based leaf rust resistance breeding in wheat.
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Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Rajni Kant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | | | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Charu Lata
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Sneha Adhikari
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
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