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Wang J, Xu Y, Peng Y, Wang Y, Kang Z, Zhao J. A fully haplotype-resolved and nearly gap-free genome assembly of wheat stripe rust fungus. Sci Data 2024; 11:508. [PMID: 38755209 PMCID: PMC11099153 DOI: 10.1038/s41597-024-03361-6] [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: 10/18/2023] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
Stripe rust fungus Puccinia striiformis f. sp. tritici (Pst) is a destructive pathogen of wheat worldwide. Pst has a macrocyclic-heteroecious lifecycle, in which one-celled urediniospores are dikaryotic, each nucleus containing one haploid genome. We successfully generated the first fully haplotype-resolved and nearly gap-free chromosome-scale genome assembly of Pst by combining PacBio HiFi sequencing and trio-binning strategy. The genome size of the two haploid assemblies was 75.59 Mb and 75.91 Mb with contig N50 of 4.17 Mb and 4.60 Mb, and both had 18 pseudochromosomes. The high consensus quality values of 55.57 and 59.02 for both haplotypes confirmed the correctness of the assembly. Of the total 18 chromosomes, 15 and 16 were gapless while there were only five and two gaps for the remaining chromosomes of the two haplotypes, respectively. In total, 15,046 and 15,050 protein-coding genes were predicted for the two haplotypes, and the complete BUSCO scores achieved 97.7% and 97.9%, respectively. The genome will lay the foundation for further research on genetic variations and the evolution of rust fungi.
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Affiliation(s)
- Jierong Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiwen Xu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuxi Peng
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yiping Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jing Zhao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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2
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Kusch S, Qian J, Loos A, Kümmel F, Spanu PD, Panstruga R. Long-term and rapid evolution in powdery mildew fungi. Mol Ecol 2024; 33:e16909. [PMID: 36862075 DOI: 10.1111/mec.16909] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
The powdery mildew fungi (Erysiphaceae) are globally distributed plant pathogens with a range of more than 10,000 plant hosts. In this review, we discuss the long- and short-term evolution of these obligate biotrophic fungi and outline their diversity with respect to morphology, lifestyle, and host range. We highlight their remarkable ability to rapidly overcome plant immunity, evolve fungicide resistance, and broaden their host range, for example, through adaptation and hybridization. Recent advances in genomics and proteomics, particularly in cereal powdery mildews (genus Blumeria), provided first insights into mechanisms of genomic adaptation in these fungi. Transposable elements play key roles in shaping their genomes, where even close relatives exhibit diversified patterns of recent and ongoing transposon activity. These transposons are ubiquitously distributed in the powdery mildew genomes, resulting in a highly adaptive genome architecture lacking obvious regions of conserved gene space. Transposons can also be neofunctionalized to encode novel virulence factors, particularly candidate secreted effector proteins, which may undermine the plant immune system. In cereals like barley and wheat, some of these effectors are recognized by plant immune receptors encoded by resistance genes with numerous allelic variants. These effectors determine incompatibility ("avirulence") and evolve rapidly through sequence diversification and copy number variation. Altogether, powdery mildew fungi possess plastic genomes that enable their fast evolutionary adaptation towards overcoming plant immunity, host barriers, and chemical stress such as fungicides, foreshadowing future outbreaks, host range shifts and expansions as well as potential pandemics by these pathogens.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Jiangzhao Qian
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Anne Loos
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | - Florian Kümmel
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Pietro D Spanu
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
- Imperial College, London, UK
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
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3
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Cissé OH, Ma L, Kovacs JA. Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii. Microbiol Mol Biol Rev 2024:e0020222. [PMID: 38587383 DOI: 10.1128/mmbr.00202-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
SUMMARYEvery human being is presumed to be infected by the fungus Pneumocystis jirovecii at least once in his or her lifetime. This fungus belongs to a large group of species that appear to exclusively infect mammals, with P. jirovecii being the only one known to cause disease in humans. The mystery of P. jirovecii origin and speciation is just beginning to unravel. Here, we provide a review of the major steps of P. jirovecii evolution. The Pneumocystis genus likely originated from soil or plant-associated organisms during the period of Cretaceous ~165 million years ago and successfully shifted to mammals. The transition coincided with a substantial loss of genes, many of which are related to the synthesis of nutrients that can be scavenged from hosts or cell wall components that could be targeted by the mammalian immune system. Following the transition, the Pneumocystis genus cospeciated with mammals. Each species specialized at infecting its own host. Host specialization is presumably built at least partially upon surface glycoproteins, whose protogene was acquired prior to the genus formation. P. jirovecii appeared at ~65 million years ago, overlapping with the emergence of the first primates. P. jirovecii and its sister species P. macacae, which infects macaques nowadays, may have had overlapping host ranges in the distant past. Clues from molecular clocks suggest that P. jirovecii did not cospeciate with humans. Molecular evidence suggests that Pneumocystis speciation involved chromosomal rearrangements and the mounting of genetic barriers that inhibit gene flow among species.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Cohen AB, Cai G, Price DC, Molnar TJ, Zhang N, Hillman BI. The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut. BMC Genomics 2024; 25:347. [PMID: 38580927 PMCID: PMC10998396 DOI: 10.1186/s12864-024-10198-1] [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: 05/12/2023] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome. RESULTS The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors. CONCLUSIONS This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen's life cycle and a solid foundation for studying EFB.
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Affiliation(s)
- Alanna B Cohen
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Guohong Cai
- Crop Production and Pest Control Research Unit, USDA-ARS, West Lafayette, IN, 47907, USA.
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Dana C Price
- Department of Entomology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Center for Vector Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Thomas J Molnar
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Biochemistry and Microbiology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Bradley I Hillman
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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Wu Y, Xi Z, Liu F, Hu W, Feng H, Zhang Q. A deep semantic network-based image segmentation of soybean rust pathogens. FRONTIERS IN PLANT SCIENCE 2024; 15:1340584. [PMID: 38601300 PMCID: PMC11004377 DOI: 10.3389/fpls.2024.1340584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Introduction Asian soybean rust is a highly aggressive leaf-based disease triggered by the obligate biotrophic fungus Phakopsora pachyrhizi which can cause up to 80% yield loss in soybean. The precise image segmentation of fungus can characterize fungal phenotype transitions during growth and help to discover new medicines and agricultural biocides using large-scale phenotypic screens. Methods The improved Mask R-CNN method is proposed to accomplish the segmentation of densely distributed, overlapping and intersecting microimages. First, Res2net is utilized to layer the residual connections in a single residual block to replace the backbone of the original Mask R-CNN, which is then combined with FPG to enhance the feature extraction capability of the network model. Secondly, the loss function is optimized and the CIoU loss function is adopted as the loss function for boundary box regression prediction, which accelerates the convergence speed of the model and meets the accurate classification of high-density spore images. Results The experimental results show that the mAP for detection and segmentation, accuracy of the improved algorithm is improved by 6.4%, 12.3% and 2.2% respectively over the original Mask R-CNN algorithm. Discussion This method is more suitable for the segmentation of fungi images and provide an effective tool for large-scale phenotypic screens of plant fungal pathogens.
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Affiliation(s)
- Yalin Wu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, China
| | - Zhuobin Xi
- Mechanical Electrical Engineering School, Beijing Information Science & Technology University, Beijing, China
| | - Fen Liu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, China
| | - Weiming Hu
- Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang, China
| | - Hongjuan Feng
- Zhongzhen Kejian (ShenZhen) Holdings Co., Ltd, Shenzhen, China
| | - Qinjian Zhang
- Mechanical Electrical Engineering School, Beijing Information Science & Technology University, Beijing, China
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Lee JS, Kakishima M, Park JH, Shin HD, Choi YJ. Unraveling the Life Cycle of Nyssopsora cedrelae: A Study of Rust Diseases on Aralia elata and Toona sinensis. J Fungi (Basel) 2024; 10:239. [PMID: 38667910 PMCID: PMC11051367 DOI: 10.3390/jof10040239] [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: 12/22/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Rust disease poses a major threat to global agriculture and forestry. It is caused by types of Pucciniales, which often require alternate hosts for their life cycles. Nyssopsora cedrelae was previously identified as a rust pathogen on Toona sinensis in East and Southeast Asia. Although this species had been reported to be autoecious, completing its life cycle solely on T. sinensis, we hypothesized that it has a heteroecious life cycle, requiring an alternate host, since the spermogonial and aecial stages on Aralia elata, a plant native to East Asia, are frequently observed around the same area where N. cedrelae causes rust disease on T. sinensis. Upon collecting rust samples from both A. elata and T. sinensis, we confirmed that the rust species from both tree species exhibited matching internal transcribed spacer (ITS), large subunit (LSU) rDNA, and cytochrome oxidase subunit III (CO3) mtDNA sequences. Through cross-inoculations, we verified that aeciospores from A. elata produced a uredinial stage on T. sinensis. This study is the first report to clarify A. elata as an alternate host for N. cedrelae, thus providing initial evidence that the Nyssopsora species exhibits a heteroecious life cycle.
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Affiliation(s)
- Jae Sung Lee
- Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea;
| | - Makoto Kakishima
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
| | - Ji-Hyun Park
- Department of Forestry, Environment and Systems, Kookmin University, Seoul 02707, Republic of Korea;
| | - Hyeon-Dong Shin
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea;
| | - Young-Joon Choi
- Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea;
- Center for Convergent Agrobioengineering, Kunsan National University, Gunsan 54150, Republic of Korea
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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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Letanneur C, Brisson A, Bisaillon M, Devèze T, Plourde MB, Schattat M, Duplessis S, Germain H. Host-Specific and Homologous Pairs of Melampsora larici-populina Effectors Unveil Novel Nicotiana benthamiana Stromule Induction Factors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:277-289. [PMID: 38148279 DOI: 10.1094/mpmi-09-23-0148-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: 12/28/2023]
Abstract
The poplar rust fungus Melampsora larici-populina is part of one of the most devastating group of fungi (Pucciniales) and causes important economic losses to the poplar industry. Because M. larici-populina is a heteroecious obligate biotroph, its spread depends on its ability to carry out its reproductive cycle through larch and then poplar parasitism. Genomic approaches have identified more than 1,000 candidate secreted effector proteins (CSEPs) from the predicted secretome of M. larici-populina that are potentially implicated in the infection process. In this study, we selected CSEP pairs (and one triplet) among CSEP gene families that share high sequence homology but display specific gene expression profiles among the two distinct hosts. We determined their subcellular localization by confocal microscopy through expression in the heterologous plant system Nicotiana benthamiana. Five out of nine showed partial or complete chloroplastic localization. We also screened for potential protein interactors from larch and poplar by yeast two-hybrid assays. One pair of CSEPs and the triplet shared common interactors, whereas the members of the two other pairs did not have common targets from either host. Finally, stromule induction quantification revealed that two pairs and the triplet of CSEPs induced stromules when transiently expressed in N. benthamiana. The use of N. benthamiana eds1 and nrg1 knockout lines showed that CSEPs can induce stromules through an eds1-independent mechanism. However, CSEP homologs shared the same impact on stromule induction and contributed to discovering a new stromule induction cascade that can be partially and/or fully independent of eds1. [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)
- Claire Letanneur
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Alexandre Brisson
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Mathias Bisaillon
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Théo Devèze
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Mélodie B Plourde
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
| | - Martin Schattat
- Plant Physiology Department, Martin Luther University, 06120 Halle, Germany
| | | | - Hugo Germain
- Chemistry, Biochemistry, and Physics Department, Université du Québec à Trois-Rivières, Trois-Rivières, G8Z 4M3, Canada
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Qi M, Yu H, Bredow M, Chicowski AS, Fields LD, Whitham SA. Insights into Phakopsora pachyrhizi Effector-Effector Interactions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:227-231. [PMID: 37831963 DOI: 10.1094/mpmi-08-23-0120-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: 10/15/2023]
Abstract
The multifaceted role of pathogen-encoded effectors in plant-pathogen interactions is complex and not fully understood. Effectors operate within intricate host environments, interacting with host proteins and other effectors to modulate virulence. The complex interplay between effectors raises the concept of metaeffectors, wherein some effectors regulate the activity of others. While previous research has demonstrated the importance of effector repertoires in pathogen virulence, only a limited number of studies have investigated the interactions between these effectors. This study explores the interactions among Phakopsora pachyrhizi effector candidates (PpECs). P. pachyrhizi haustorial transcriptome analysis identified a collection of predicted PpECs. Among these, PpEC23 was found to interact with PpEC48, prompting further exploration into their potential interaction with other effectors. Here, we utilized a yeast two-hybrid screen to explore protein-protein interactions between PpECs. A split-luciferase complementation assay also demonstrated that these interactions could occur within soybean cells. Interestingly, PpEC48 displayed the ability to interact with several small cysteine-rich proteins (SCRPs), suggesting its affinity for this specific class of effectors. We show that these interactions involve a histidine-rich domain within PpEC48, emphasizing the significance of structural motifs in mediating effector interactions. The unique nature of PpEC48, showing no sequence matches in other organisms, suggests its relatively recent evolution and potential orphan gene status. Our work reveals insights into the intricate network of interactions among P. pachyrhizi effector-effector interactions. [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)
- Mingsheng Qi
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Haiyue Yu
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, 100193, Beijing, China
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Letícia Dias Fields
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), 91501-970, Porto Alegre, RS, Brazil
| | - Steven A Whitham
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
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Schuster M, Schweizer G, Reißmann S, Happel P, Aßmann D, Rössel N, Güldener U, Mannhaupt G, Ludwig N, Winterberg S, Pellegrin C, Tanaka S, Vincon V, Presti LL, Wang L, Bender L, Gonzalez C, Vranes M, Kämper J, Seong K, Krasileva K, Kahmann R. Novel Secreted Effectors Conserved Among Smut Fungi Contribute to the Virulence of Ustilago maydis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:250-263. [PMID: 38416124 DOI: 10.1094/mpmi-09-23-0139-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: 02/29/2024]
Abstract
Fungal pathogens deploy a set of molecules (proteins, specialized metabolites, and sRNAs), so-called effectors, to aid the infection process. In comparison to other plant pathogens, smut fungi have small genomes and secretomes of 20 Mb and around 500 proteins, respectively. Previous comparative genomic studies have shown that many secreted effector proteins without known domains, i.e., novel, are conserved only in the Ustilaginaceae family. By analyzing the secretomes of 11 species within Ustilaginaceae, we identified 53 core homologous groups commonly present in this lineage. By collecting existing mutants and generating additional ones, we gathered 44 Ustilago maydis strains lacking single core effectors as well as 9 strains containing multiple deletions of core effector gene families. Pathogenicity assays revealed that 20 of these 53 mutant strains were affected in virulence. Among the 33 mutants that had no obvious phenotypic changes, 13 carried additional, sequence-divergent, structurally similar paralogs. We report a virulence contribution of seven previously uncharacterized single core effectors and of one effector family. Our results help to prioritize effectors for understanding U. maydis virulence and provide genetic resources for further characterization. [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)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Gabriel Schweizer
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Independent Data Lab UG, 80937 Munich, Germany
| | - Stefanie Reißmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Petra Happel
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Daniela Aßmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Nicole Rössel
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Ulrich Güldener
- Deutsches Herzzentrum München, Technische Universität München, 80636 München, Germany
| | - Gertrud Mannhaupt
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Nicole Ludwig
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Research & Development, Weed Control Bayer AG, Crop Science Division, 65926 Frankfurt am Main, Germany
| | - Sarah Winterberg
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Clément Pellegrin
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Shigeyuki Tanaka
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Volker Vincon
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Libera Lo Presti
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lei Wang
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lena Bender
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Department of Pharmaceutics and Biopharmaceutics, Phillips-University Marburg, 35037 Marburg, Germany
| | - Carla Gonzalez
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Miroslav Vranes
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, 76131 Karlsruhe, Germany
| | - Jörg Kämper
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Genetics, 76131 Karlsruhe, Germany
| | - Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Ksenia Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, U.S.A
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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11
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Davoudnia B, Dadkhodaie A, Moghadam A, Heidari B, Yassaie M. Transcriptome analysis in Aegilops tauschii unravels further insights into genetic control of stripe rust resistance. PLANTA 2024; 259:70. [PMID: 38345645 DOI: 10.1007/s00425-024-04347-9] [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: 10/11/2023] [Accepted: 01/14/2024] [Indexed: 02/15/2024]
Abstract
MAIN CONCLUSION The Aegilops tauschii resistant accession prevented the pathogen colonization by controlling the sugar flow and triggering the hypersensitive reaction. This study suggested that NBS-LRRs probably induce resistance through bHLH by controlling JA- and SA-dependent pathways. Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst) is one of wheat's most destructive fungal diseases that causes a severe yield reduction worldwide. The most effective and economically-friendly strategy to manage this disease is genetic resistance which can be achieved through deploying new and effective resistance genes. Aegilops tauschii, due to its small genome and co-evolution with Pst, can provide detailed information about underlying resistance mechanisms. Hence, we used RNA-sequencing approach to identify the transcriptome variations of two contrasting resistant and susceptible Ae. tauschii accessions in interaction with Pst and differentially expressed genes (DEGs) for resistance to stripe rust. Gene ontology, pathway analysis, and search for functional domains, transcription regulators, resistance genes, and protein-protein interactions were used to interpret the results. The genes encoding NBS-LRR, CC-NBS-kinase, and phenylalanine ammonia-lyase, basic helix-loop-helix (bHLH)-, basic-leucine zipper (bZIP)-, APETALA2 (AP2)-, auxin response factor (ARF)-, GATA-, and LSD-like transcription factors were up-regulated exclusively in the resistant accession. The key genes involved in response to salicylic acid, amino sugar and nucleotide sugar metabolism, and hypersensitive response contributed to plant defense against stripe rust. The activation of jasmonic acid biosynthesis and starch and sucrose metabolism pathways under Pst infection in the susceptible accession explained the colonization of the host. Overall, this study can fill the gaps in the literature on host-pathogen interaction and enrich the Ae. tauschii transcriptome sequence information. It also suggests candidate genes that could guide future breeding programs attempting to develop rust-resistant cultivars.
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Affiliation(s)
- Behnam Davoudnia
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran.
| | - Ali Moghadam
- Institute of Biotechnology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Bahram Heidari
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, 71441-65186, Iran
| | - Mohsen Yassaie
- Seed and Plant Improvement Research Department, Fars Agricultural and Natural Resources Research and Education Center, AREEO, Shiraz, Iran
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12
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Li Y, Tao S, Liang Y. Time-Course Responses of Apple Leaf Endophytes to the Infection of Gymnosporangium yamadae. J Fungi (Basel) 2024; 10:128. [PMID: 38392801 PMCID: PMC10890309 DOI: 10.3390/jof10020128] [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: 12/26/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Apple rust, caused by Gymnosporangium yamadae, poses a significant challenge to apple production. Prior studies have underscored the pivotal role played by endophytic microbial communities, intimately linked with the host, in influencing plant diseases and their pathogenic outcomes. The objective of this study is to scrutinize alternations in endophytic microbial communities within apple leaves at different stages of apple rust using high-throughput sequencing technology. The findings revealed a discernible pattern characterized by an initial increase and subsequent decrease in the alpha diversity of microbial communities in diseased leaves. A microbial co-occurrence network analysis revealed that the complexity of the bacterial community in diseased leaves diminished initially and then rebounded during the progression of the disease. Additionally, employing the PICRUSt2 platform, this study provided preliminary insights into the functions of microbial communities at specific disease timepoints. During the spermogonial stage, endophytic bacteria particularly exhibited heightened activity in genetic information processing, metabolism, and environmental information processing pathways. Endophytic fungi also significantly enriched a large number of metabolic pathways during the spermogonial stage and aecial stage, exhibiting abnormally active life activities. These findings establish a foundation for comprehending the role of host endophytes in the interaction between pathogens and hosts. Furthermore, they offer valuable insights for the development and exploitation of plant endophytic resources, thereby contributing to enhanced strategies for managing apple rust.
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Affiliation(s)
- Yunfan Li
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan 518000, China
| | - Yingmei Liang
- Museum of Beijing Forestry University, Beijing Forestry University, Beijing 100083, China
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13
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Chicowski AS, Bredow M, Utiyama AS, Marcelino‐Guimarães FC, Whitham SA. Soybean-Phakopsora pachyrhizi interactions: towards the development of next-generation disease-resistant plants. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:296-315. [PMID: 37883664 PMCID: PMC10826999 DOI: 10.1111/pbi.14206] [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: 07/06/2023] [Revised: 09/19/2023] [Accepted: 10/08/2023] [Indexed: 10/28/2023]
Abstract
Soybean rust (SBR), caused by the obligate biotrophic fungus Phakopsora pachyrhizi, is a devastating foliar disease threatening soybean production. To date, no commercial cultivars conferring durable resistance to SBR are available. The development of long-lasting SBR resistance has been hindered by the lack of understanding of this complex pathosystem, encompassing challenges posed by intricate genetic structures in both the host and pathogen, leading to a gap in the knowledge of gene-for-gene interactions between soybean and P. pachyrhizi. In this review, we focus on recent advancements and emerging technologies that can be used to improve our understanding of the P. pachyrhizi-soybean molecular interactions. We further explore approaches used to combat SBR, including conventional breeding, transgenic approaches and RNA interference, and how advances in our understanding of plant immune networks, the availability of new molecular tools, and the recent sequencing of the P. pachyrhizi genome could be used to aid in the development of better genetic resistance against SBR. Lastly, we discuss the research gaps of this pathosystem and how new technologies can be used to shed light on these questions and to develop durable next-generation SBR-resistant soybean plants.
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Affiliation(s)
- Aline Sartor Chicowski
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Melissa Bredow
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
| | - Alice Satiko Utiyama
- Brazilian Agricultural Research Corporation – National Soybean Research Center (Embrapa Soja)LondrinaParanáBrazil
- Department of AgronomyFederal University of ViçosaViçosaMinas GeraisBrazil
| | | | - Steven A. Whitham
- Department of Plant Pathology, Entomology and MicrobiologyIowa State UniversityAmesIowaUSA
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14
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Rahman Bhuiyan MZ, Solanki S, Del Rio Mendoza LE, Borowicz P, Lakshman DK, Qi A, Ameen G, Khan MFR. Histopathological Investigation of Varietal Responses to Cercospora beticola Infection Process on Sugar Beet Leaves. PLANT DISEASE 2023; 107:3906-3912. [PMID: 37330633 DOI: 10.1094/pdis-03-23-0562-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cercospora leaf spot (CLS) is the most destructive foliar disease in sugar beet (Beta vulgaris). It is caused by Cercospora beticola Sacc., a fungal pathogen that produces toxins and enzymes which affect membrane permeability and cause cell death during infection. In spite of its importance, little is known about the initial stages of leaf infection by C. beticola. Therefore, we investigated the progression of C. beticola on leaf tissues of susceptible and resistant sugar beet varieties at 12-h intervals during the first 5 days after inoculation using confocal microscopy. Inoculated leaf samples were collected and stored in DAB (3,3'-diaminobenzidine) solution until processed. Samples were stained with Alexa Fluor-488-WGA dye to visualize fungal structures. Fungal biomass accumulation, reactive oxygen species (ROS) production, and the area under the disease progress curve were evaluated and compared. ROS production was not detected on any variety before 36 h postinoculation (hpi). C. beticola biomass accumulation, percentage leaf cell death, and disease severity were all significantly greater in the susceptible variety compared with the resistant variety (P < 0.05). Conidia penetrated directly through stomata between 48 to 60 hpi and produced appressoria on stomatal guard cells at 60 to 72 hpi in susceptible and resistant varieties, respectively. Penetration of hyphae inside the parenchymatous tissues varied in accordance with time postinoculation and varietal genotypes. Overall, this study provides a detailed account to date of events leading to CLS disease development in two contrasting varieties.
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Affiliation(s)
| | - Shyam Solanki
- South Dakota State University, Brookings, SD 57007, U.S.A
| | | | - Pawel Borowicz
- Department of Animal Sciences, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Dilip K Lakshman
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A
| | - Aiming Qi
- Centre for Agriculture, Food, and Environmental Management Research, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, U.K
| | - Gazala Ameen
- South Dakota State University, Brookings, SD 57007, U.S.A
| | - Mohamed F R Khan
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
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15
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Santiago-Santiago M, Sánchez-Viveros G, Hernández-Adame L, Chiquito-Contreras CJ, Salinas-Castro A, Chiquito-Contreras RG, Hernández-Montiel LG. Essential Oils and Antagonistic Microorganisms as Eco-Friendly Alternatives for Coffee Leaf Rust Control. PLANTS (BASEL, SWITZERLAND) 2023; 12:3519. [PMID: 37895983 PMCID: PMC10609872 DOI: 10.3390/plants12203519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
Abstract
Coffee leaf rust (CLR) is caused by the biotrophic fungus Hemileia vastatrix Berk. & Br., a disease of economic importance, reducing coffee yield up to 60%. Currently, CLR epidemics have negatively impacted food security. Therefore, the objective of the present research study is to show a current framework of this disease and its effects on diverse areas, as well as the biological systems used for its control, mode of action, and effectiveness. The use of essential plant oils and antagonistic microorganisms to H. vastatrix are highlighted. Terpenes, terpenoids, and aromatic compounds are the main constituents of these oils, which alter the cell wall and membrane composition and modify the basic cell functions. Beneficial microorganisms inhibit urediniospore germination and reduce disease incidence and severity. The antagonistic microorganisms and essential oils of some aromatic plants have great potential in agriculture. These biological systems may have more than one mechanism of action, which reduces the possibility of the emergence of resistant strains of H. vastatrix.
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Affiliation(s)
| | - Gabriela Sánchez-Viveros
- Facultad de Ciencias Agrícolas, Universidad Veracruzana, Xalapa 91090, Mexico; (G.S.-V.); (C.J.C.-C.)
| | - Luis Hernández-Adame
- CONAHCYT-Centro de Investigaciones Biológicas del Noroeste, La Paz 23096, Mexico;
- Nanotechnology & Microbial Biocontrol Group, Centro de Investigaciones Biológicas del Noroeste, La Paz 23096, Mexico
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16
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Dracatos PM, Lu J, Sánchez‐Martín J, Wulff BB. Resistance that stacks up: engineering rust and mildew disease control in the cereal crops wheat and barley. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1938-1951. [PMID: 37494504 PMCID: PMC10502761 DOI: 10.1111/pbi.14106] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 07/28/2023]
Abstract
Staying ahead of the arms race against rust and mildew diseases in cereal crops is essential to maintain and preserve food security. The methodological challenges associated with conventional resistance breeding are major bottlenecks for deploying resistance (R) genes in high-yielding crop varieties. Advancements in our knowledge of plant genomes, structural mechanisms, innovations in bioinformatics, and improved plant transformation techniques have alleviated this bottleneck by permitting rapid gene isolation, functional studies, directed engineering of synthetic resistance and precise genome manipulation in elite crop cultivars. Most cloned cereal R genes encode canonical immune receptors which, on their own, are prone to being overcome through selection for resistance-evading pathogenic strains. However, the increasingly large repertoire of cloned R genes permits multi-gene stacking that, in principle, should provide longer-lasting resistance. This review discusses how these genomics-enabled developments are leading to new breeding and biotechnological opportunities to achieve durable rust and powdery mildew control in cereals.
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Affiliation(s)
- Peter M. Dracatos
- La Trobe Institute for Sustainable Agriculture & Food (LISAF)Department of Animal, Plant and Soil SciencesLa Trobe UniversityVIC 3086Australia
| | - Jing Lu
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Center for Desert AgricultureKAUSTThuwalSaudi Arabia
- College of Life SciencesSichuan UniversityChengduChina
- Chengdu Institute of Biology, Chinese Academy of SciencesChengduChina
| | - Javier Sánchez‐Martín
- Department of Microbiology and Genetics, Spanish‐Portuguese Agricultural Research Center (CIALE)University of SalamancaSalamancaSpain
| | - Brande B.H. Wulff
- Plant Science Program, Biological and Environmental Science and Engineering Division (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
- Center for Desert AgricultureKAUSTThuwalSaudi Arabia
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17
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Jost M, Outram MA, Dibley K, Zhang J, Luo M, Ayliffe M. Plant and pathogen genomics: essential approaches for stem rust resistance gene stacks in wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1223504. [PMID: 37727853 PMCID: PMC10505659 DOI: 10.3389/fpls.2023.1223504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/27/2023] [Indexed: 09/21/2023]
Abstract
The deployment of disease resistance genes is currently the most economical and environmentally sustainable method of crop protection. However, disease resistance genes can rapidly break down because of constant pathogen evolution, particularly when they are deployed singularly. Polygenic resistance is, therefore, considered the most durable, but combining and maintaining these genes by breeding is a laborious process as effective genes are usually unlinked. The deployment of polygenic resistance with single-locus inheritance is a promising innovation that overcomes these difficulties while enhancing resistance durability. Because of major advances in genomic technologies, increasing numbers of plant resistance genes have been cloned, enabling the development of resistance transgene stacks (RTGSs) that encode multiple genes all located at a single genetic locus. Gene stacks encoding five stem rust resistance genes have now been developed in transgenic wheat and offer both breeding simplicity and potential resistance durability. The development of similar genomic resources in phytopathogens has advanced effector gene isolation and, in some instances, enabled functional validation of individual resistance genes in RTGS. Here, the wheat stem rust pathosystem is used as an illustrative example of how host and pathogen genomic advances have been instrumental in the development of RTGS, which is a strategy applicable to many other agricultural crop species.
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Affiliation(s)
| | | | | | | | | | - Michael Ayliffe
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
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18
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Advances in molecular interactions on the Rhizoctonia solani-sugar beet pathosystem. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Padilla-Roji I, Ruiz-Jiménez L, Bakhat N, Vielba-Fernández A, Pérez-García A, Fernández-Ortuño D. RNAi Technology: A New Path for the Research and Management of Obligate Biotrophic Phytopathogenic Fungi. Int J Mol Sci 2023; 24:ijms24109082. [PMID: 37240427 DOI: 10.3390/ijms24109082] [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: 04/05/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Powdery mildew and rust fungi are major agricultural problems affecting many economically important crops and causing significant yield losses. These fungi are obligate biotrophic parasites that are completely dependent on their hosts for growth and reproduction. Biotrophy in these fungi is determined by the presence of haustoria, specialized fungal cells that are responsible for nutrient uptake and molecular dialogue with the host, a fact that undoubtedly complicates their study under laboratory conditions, especially in terms of genetic manipulation. RNA interference (RNAi) is the biological process of suppressing the expression of a target gene through double-stranded RNA that induces mRNA degradation. RNAi technology has revolutionized the study of these obligate biotrophic fungi by enabling the analysis of gene function in these fungal. More importantly, RNAi technology has opened new perspectives for the management of powdery mildew and rust diseases, first through the stable expression of RNAi constructs in transgenic plants and, more recently, through the non-transgenic approach called spray-induced gene silencing (SIGS). In this review, the impact of RNAi technology on the research and management of powdery mildew and rust fungi will be addressed.
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Affiliation(s)
- Isabel Padilla-Roji
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Laura Ruiz-Jiménez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Nisrine Bakhat
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Alejandra Vielba-Fernández
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29071 Málaga, Spain
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20
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Gupta YK, Marcelino-Guimarães FC, Lorrain C, Farmer A, Haridas S, Ferreira EGC, Lopes-Caitar VS, Oliveira LS, Morin E, Widdison S, Cameron C, Inoue Y, Thor K, Robinson K, Drula E, Henrissat B, LaButti K, Bini AMR, Paget E, Singan V, Daum C, Dorme C, van Hoek M, Janssen A, Chandat L, Tarriotte Y, Richardson J, Melo BDVA, Wittenberg AHJ, Schneiders H, Peyrard S, Zanardo LG, Holtman VC, Coulombier-Chauvel F, Link TI, Balmer D, Müller AN, Kind S, Bohnert S, Wirtz L, Chen C, Yan M, Ng V, Gautier P, Meyer MC, Voegele RT, Liu Q, Grigoriev IV, Conrath U, Brommonschenkel SH, Loehrer M, Schaffrath U, Sirven C, Scalliet G, Duplessis S, van Esse HP. Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi. Nat Commun 2023; 14:1835. [PMID: 37005409 PMCID: PMC10067951 DOI: 10.1038/s41467-023-37551-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/22/2023] [Indexed: 04/04/2023] Open
Abstract
With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world's most economically damaging agricultural diseases. Despite P. pachyrhizi's impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.
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Affiliation(s)
- Yogesh K Gupta
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | | | - Cécile Lorrain
- Pathogen Evolutionary Ecology, ETH Zürich, Zürich, Switzerland
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Everton Geraldo Capote Ferreira
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Valéria S Lopes-Caitar
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | - Liliane Santana Oliveira
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | | | | | - Connor Cameron
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | - Yoshihiro Inoue
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kathrin Thor
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Kelly Robinson
- 2Blades, Evanston, Illinois, USA
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK
| | - Elodie Drula
- AFMB, Aix-Marseille Univ., INRAE, Marseille, France
- Biodiversité et Biotechnologie Fongiques, INRAE, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- DTU Bioengineering, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aline Mara Rudsit Bini
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
- Department of Computer Science, Federal University of Technology of Paraná (UTFPR), Paraná, Brazil
| | - Eric Paget
- Bayer SAS, Crop Science Division, Lyon, France
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher Daum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tobias I Link
- Institute of Phytomedicine, University of Hohenheim, Stuttgart, Germany
| | - Dirk Balmer
- Syngenta Crop Protection AG, Stein, Switzerland
| | - André N Müller
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Sabine Kind
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Stefan Bohnert
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Louisa Wirtz
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mi Yan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vivian Ng
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Maurício Conrado Meyer
- Brazilian Agricultural Research Corporation - National Soybean Research Center (Embrapa Soja), Paraná, Brazil
| | | | - Qingli Liu
- Syngenta Crop Protection, LLC, Research Triangle Park, Durham, NC, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Uwe Conrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | - Marco Loehrer
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schaffrath
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | | | | | | | - H Peter van Esse
- 2Blades, Evanston, Illinois, USA.
- The Sainsbury Laboratory, University of East Anglia, Norwich, UK.
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21
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Ren X, Zhang G, Jin M, Wan F, Day MD, Qian W, Liu B. Metabolomics and Transcriptomics Reveal the Response Mechanisms of Mikania micrantha to Puccinia spegazzinii Infection. Microorganisms 2023; 11:microorganisms11030678. [PMID: 36985252 PMCID: PMC10057677 DOI: 10.3390/microorganisms11030678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/18/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Mikania micrantha is one of the 100 worst invasive species globally and can cause significant negative impacts on agricultural and forestry economics, particularly in Asia and the Pacific region. The rust Puccinia spegazzinii has been used successfully as a biological control agent in several countries to help manage M. micrantha. However, the response mechanisms of M. micrantha to P. spegazzinii infection have never been studied. To investigate the response of M. micrantha to infection by P. spegazzinii, an integrated analysis of metabolomics and transcriptomics was performed. The levels of 74 metabolites, including organic acids, amino acids, and secondary metabolites in M. micrantha infected with P. spegazzinii, were significantly different compared to those in plants that were not infected. After P. spegazzinii infection, the expression of the TCA cycle gene was significantly induced to participate in energy biosynthesis and produce more ATP. The content of most amino acids, such as L-isoleucine, L-tryptophan and L-citrulline, increased. In addition, phytoalexins, such as maackiain, nobiletin, vasicin, arachidonic acid, and JA-Ile, accumulated in M. micrantha. A total of 4978 differentially expressed genes were identified in M. micrantha infected by P. spegazzinii. Many key genes of M. micrantha in the PTI (pattern-triggered immunity) and ETI (effector-triggered immunity) pathways showed significantly higher expression under P. spegazzinii infection. Through these reactions, M. micrantha is able to resist the infection of P. spegazzinii and maintain its growth. These results are helpful for us to understand the changes in metabolites and gene expression in M. micrantha after being infected by P. spegazzinii. Our results can provide a theoretical basis for weakening the defense response of M. micrantha to P. spegazzinii, and for P. spegazzinii as a long-term biological control agent of M. micrantha.
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Affiliation(s)
- Xinghai Ren
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Guangzhong Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Mengjiao Jin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Fanghao Wan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Michael D. Day
- Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD 4001, Australia
| | - Wanqiang Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Correspondence: (W.Q.); (B.L.)
| | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Correspondence: (W.Q.); (B.L.)
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22
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Siddique AB, Menke L, Dinedurga M, Albrectsen BR. Molecular studies of rust on European aspen suggest an autochthonous relationship shaped by genotype. FRONTIERS IN PLANT SCIENCE 2023; 14:1111001. [PMID: 36890907 PMCID: PMC9986475 DOI: 10.3389/fpls.2023.1111001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Forests are at increasing risk from pathogen outbreak. Climate change for example enhance the risk of local disease outbreaks, and naturalization of exotic pathogens may follow human activities, warranting robust pest surveillance routines to support forest management. Melampsora pinitorqua (pine twisting rust) is of concern in Swedish forestry, and here we evaluate the use of visible rust scores (VRS) on its obligate summer host, European aspen (Populus tremula) as a tool for quantification of the pathogen. With use of species-specific primers, we could detect the native rust, but we failed to detect two exotic rusts (M. medusae and M. larici-populina). We found that aspen genotype determined the presence of fungal genetic markers (amplifying the ITS2 region of the fungal rDNA sequence) as well as DNA sequences specific to M. pinitorqua. We correlated VRS with the amount of fungal DNA in the same leaf, and we related the findings to aspen genotype-specific parameters such as the ability to synthesize and store leaf condensed tannins (CT). At the genotype level both positive and negative relationships were observed between CTs, fungal markers, and rust infestations. However, at the population level, foliar CT concentrations correlated negatively with general fungal- and rust-specific marker abundances. Our results, therefore, do not support the use of VRS to assess Melampsora infestation in Aspen. They do, however, suggest that the relationship between European aspen and rust infestation may be characterized as autochthonous in northern Sweden.
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23
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Li C, Qiao L, Lu Y, Xing G, Wang X, Zhang G, Qian H, Shen Y, Zhang Y, Yao W, Cheng K, Ma Z, Liu N, Wang D, Zheng W. Gapless Genome Assembly of Puccinia triticina Provides Insights into Chromosome Evolution in Pucciniales. Microbiol Spectr 2023; 11:e0282822. [PMID: 36688678 PMCID: PMC9927501 DOI: 10.1128/spectrum.02828-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023] Open
Abstract
Chromosome evolution drives species evolution, speciation, and adaptive radiation. Accurate genome assembly is crucial to understanding chromosome evolution of species, such as dikaryotic fungi. Rust fungi (Pucciniales) in dikaryons represent the largest group of plant pathogens, but the evolutionary process of adaptive radiation in Pucciniales remains poorly understood. Here, we report a gapless genome for the wheat leaf rust fungus Puccinia triticina determined using PacBio high-fidelity (HiFi) sequencing. This gapless assembly contains two sets of chromosomes, showing that one contig represents one chromosome. Comparisons of homologous chromosomes between the phased haplotypes revealed that highly frequent small-scale sequence divergence shapes haplotypic variation. Genome analyses of Puccinia triticina along with other rusts revealed that recent transposable element bursts and extensive segmental gene duplications synergistically highlight the evolution of chromosome structures. Comparative analysis of chromosomes indicated that frequent chromosomal rearrangements may act as a major contributor to rapid radiation of Pucciniales. This study presents the first gapless, phased assembly for a dikaryotic rust fungus and provides insights into adaptive evolution and species radiation in Pucciniales. IMPORTANCE Rust fungi (Pucciniales) are the largest group of plant pathogens. Adaptive radiation is a predominant feature in Pucciniales evolution. Chromosome evolution plays an important role in adaptive evolution. Accurate chromosome-scale assembly is required to understand the role of chromosome evolution in Pucciniales. We took advantage of HiFi sequencing to construct a gapless, phased genome for Puccinia triticina. Further analyses revealed that the evolution of chromosome structures in rust lineage is shaped by the combination of transposable element bursts and segmental gene duplications. Chromosome comparisons of Puccinia triticina and other rusts suggested that frequent chromosomal arrangements may make remarkable contributions to high species diversity of rust fungi. Our results present the first gapless genome for Pucciniales and shed light on the feature of chromosome evolution in Pucciniales.
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Affiliation(s)
- Chuang Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Liuhui Qiao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Yanan Lu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Guozhen Xing
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, Baoding, China
| | | | - Huimin Qian
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yilin Shen
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yibo Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Kun Cheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhenling Ma
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Na Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Daowen Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Wenming Zheng
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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24
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Guerillot P, Salamov A, Louet C, Morin E, Frey P, Grigoriev IV, Duplessis S. A Remarkable Expansion of Oligopeptide Transporter Genes in Rust Fungi (Pucciniales) Suggests a Specialization in Nutrient Acquisition for Obligate Biotrophy. PHYTOPATHOLOGY 2023; 113:252-264. [PMID: 36044359 DOI: 10.1094/phyto-04-22-0128-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: 06/15/2023]
Abstract
Nutrient acquisition by rust fungi during their biotrophic growth has been assigned to a few transporters expressed in haustorial infection structures. We performed a comparative genomic analysis of all transporter genes (hereafter termed transportome) classified according to the Transporter Classification Database, focusing specifically on rust fungi (order Pucciniales) versus other species in the Dikarya. We also surveyed expression of transporter genes in the poplar rust fungus for which transcriptomics data are available across the whole life cycle. Despite a significant increase in gene number, rust fungi presented a reduced transportome compared with most fungi in the Dikarya. However, a few transporter families in the subclass Porters showed significant expansions. Notably, three metal transport-related families involved in the import, export, and sequestration of metals were expanded in Pucciniales and expressed at various stages of the rust life cycle, suggesting a tight regulation of metal homeostasis. The most remarkable gene expansion in the Pucciniales was observed for the oligopeptide transporter (OPT) family, with 25 genes on average compared with seven to 14 genes in the other surveyed taxonomical ranks. A phylogenetic analysis showed several specific expansion events at the root of the order Pucciniales with subsequent expansions in rust taxonomical families. The OPT genes showed dynamic expression patterns along the rust life cycle and more particularly during infection of the poplar host tree, suggesting a possible specialization for the acquisition of nitrogen and sulfur through the transport of oligopeptides from the host during biotrophic growth.
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Affiliation(s)
- Pamela Guerillot
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Clémentine Louet
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Emmanuelle Morin
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
| | - Pascal Frey
- Université de Lorraine, INRAE, UMR 1136 IAM, 54000 Nancy, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, U.S.A
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25
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Magnaporthe oryzae pathotype Triticum (MoT) can act as a heterologous expression system for fungal effectors with high transcript abundance in wheat. Sci Rep 2023; 13:108. [PMID: 36596834 PMCID: PMC9810704 DOI: 10.1038/s41598-022-27030-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 12/23/2022] [Indexed: 01/04/2023] Open
Abstract
Plant pathogens deliver effector proteins to reprogramme a host plants circuitry, supporting their own growth and development, whilst thwarting defence responses. A subset of these effectors are termed avirulence factors (Avr) and can be recognised by corresponding host resistance (R) proteins, creating a strong evolutionary pressure on pathogen Avr effectors that favours their modification/deletion to evade the immune response. Hence, identifying Avr effectors and tracking their allele frequencies in a population is critical for understanding the loss of host recognition. However, the current systems available to confirm Avr effector function, particularly for obligate biotrophic fungi, remain limited and challenging. Here, we explored the utility of the genetically tractable wheat blast pathogen Magnaporthe oryzae pathotype Triticum (MoT) as a suitable heterologous expression system in wheat. Using the recently confirmed wheat stem rust pathogen (Puccina graminis f. sp. tritici) avirulence effector AvrSr50 as a proof-of-concept, we found that delivery of AvrSr50 via MoT could elicit a visible Sr50-dependant cell death phenotype. However, activation of Sr50-mediated cell death correlated with a high transgene copy number and transcript abundance in MoT transformants. This illustrates that MoT can act as an effective heterologous delivery system for fungal effectors from distantly related fungal species, but only when enough transgene copies and/or transcript abundance is achieved.
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26
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Tao S, Yin H, Fang Y, Zhang Y, Zhang N, Qu L. Elevated O 3 concentrations alter the compartment-specific microbial communities inhabiting rust-infected poplars. Environ Microbiol 2022; 25:990-1006. [PMID: 36582119 DOI: 10.1111/1462-2920.16332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Elevated ozone (O3 ) can affect the susceptivity of plants to rust pathogens. However, the collective role of microbiomes involved in such interaction remains largely elusive. We exposed two cultivated poplar clones exhibiting differential O3 sensitivities, to non-filtered ambient air (NF), NF + 40 ppb or NF + 60 ppb O3 -enriched air in field open-top chambers and then inoculated Melampsora larici-populina urediniospores to study their response to rust infection and to investigate how microbiomes inhabiting four compartments (phyllosphere, rhizosphere, root endosphere, bulk soil) are involved in this response. We found that hosts with higher O3 sensitivity had significantly lower rust severity than hosts with lower sensitivity. Furthermore, the effect of increased O3 on the diversity and composition of microbial communities was highly dependent on poplar compartments, with the microbial network complexity patterns being completely opposite between the two clones. Notably, microbial source analysis estimated that phyllosphere fungal communities predominately derived from root endosphere and vice versa, suggesting a potential transmission mechanism between plant above- and below-ground systems. These promising results suggest that further investigations are needed to better understand the interactions of abiotic and biotic stresses on plant performance and the role of the microbiome in driving these changes.
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Affiliation(s)
- Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China.,Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People's Republic of China
| | - Haiyue Yin
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yue Fang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, China.,Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People's Republic of China
| | - Laiye Qu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing, China
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27
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Si B, Wang H, Bai J, Zhang Y, Cao Y. Evaluating the Utility of Simplicillium lanosoniveum, a Hyperparasitic Fungus of Puccinia graminis f. sp. tritici, as a Biological Control Agent against Wheat Stem Rust. Pathogens 2022; 12:pathogens12010022. [PMID: 36678370 PMCID: PMC9862854 DOI: 10.3390/pathogens12010022] [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: 11/18/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Wheat stem rust is one of the wheat diseases caused by Puccinia graminis Pers. f. sp. tritici (Pgt). This disease has been responsible for major losses to wheat production worldwide. Currently used methods for controlling this disease include fungicides, the breeding of stem rust-resistant cultivars, and preventive agricultural measures. However, the excessive use of fungicides can have various deleterious effects on the environment. A hyperparasitic fungus with white mycelia and oval conidia, Simplicillium lanosoniveum, was isolated from the urediniospores of Pgt. When Pgt-infected wheat leaves were inoculation with isolates of S. lanosoniveum, it was found that S. lanosoniveum inoculation inhibited the production and germination of urediniospores, suggesting that S. lanosoniveum could inhibit the growth and spread of Pgt. Scanning electron microscopy revealed that S. lanosoniveum could inactivate the urediniospores by inducing structural damage. Overall, findings indicate that S. lanosoniveum might provide an effective biological agent for the control of Pgt.
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Affiliation(s)
- Binbin Si
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- College of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Hui Wang
- College of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Jiaming Bai
- College of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Yuzhen Zhang
- College of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China
| | - Yuanyin Cao
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence: ; Tel.: +86-136-0400-0358
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28
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Jensen C, Korolev A, Corredor-Moreno P, Minter F, Dodds PN, Saunders DGO. Caveats of Using Bacterial Type Three Secretion Assays for Validating Fungal Avirulence Effectors in Wheat. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:1061-1066. [PMID: 36445162 DOI: 10.1094/mpmi-08-22-0167-sc] [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: 06/16/2023]
Abstract
Functional characterization of effector proteins of fungal obligate biotrophic pathogens, especially confirmation of avirulence (Avr) properties, has been notoriously difficult, due to the experimental intractability of many of these organisms. Previous studies in wheat have shown promising data suggesting the type III secretion system (T3SS) of bacteria may be a suitable surrogate for delivery and detection of Avr properties of fungal effectors. However, these delivery systems were tested in the absence of confirmed Avr effectors. Here, we tested two previously described T3SS-mediated delivery systems for their suitability when delivering two confirmed Avr effectors from two fungal pathogens of wheat, Puccinia graminis f. sp. tritici and Magnaporthe oryzae pathotype tritici. We showed that both effectors (AvrSr50 and AvrRmg8) were unable to elicit a hypersensitive response on wheat seedlings with the corresponding resistance gene when expressed by the Pseudomonas fluorescens "Effector to Host Analyser" (EtHAn) system. Furthermore, we found the utility of Burkholderia glumae for screening Avr phenotypes is severely limited, as the wild-type strain elicits nonhost cell death in multiple wheat accessions. These results provide valuable insight into the suitability of these systems for screening fungal effectors for Avr properties that may help guide further development of surrogate bacterial delivery systems in wheat. [Formula: see text] Copyright © 2022 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)
- Cassandra Jensen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Andrey Korolev
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | | | - Francesca Minter
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Peter N Dodds
- CSIRO Agriculture and Food Australia, GPO Box 1700, Clunies Ross Street, Canberra ACT 2601, Australia
| | - Diane G O Saunders
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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29
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Petre B, Duplessis S. A decade after the first Pucciniales genomes: A bibliometric snapshot of (post) genomics studies in three model rust fungi. Front Microbiol 2022; 13:989580. [PMID: 36187960 PMCID: PMC9515648 DOI: 10.3389/fmicb.2022.989580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pucciniales (rust fungi) are one of the largest fungal order of plant pathogens. They collectively infect key crops such as wheat and soybean, and threaten global food security. In the early 2010s, the genome sequences of three rust fungi were released: Melampsora larici-populina (the poplar leaf rust fungus), Puccinia graminis f. sp. tritici (the wheat stem rust fungus), and Puccinia striiformis f. sp. triciti (the wheat stripe rust or wheat yellow rust fungus). The availability of those genomes has forwarded rust biology into the post-genomic era, sparking a series of genomics, transcriptomics, in silico, and functional studies. Here, we snapshot the last 10 years of post-genomics studies addressing M. larici-populina, P. graminis f. sp. tritici, and/or P. striiformis f. sp. tritici. This mini-review notably reveals the model species-centered structure of the research community, and highlights the drastic increase of the number of functional studies focused on effectors since 2014, which notably revealed chloroplasts as a central host compartment targeted by rust fungi. This mini-review also discusses genomics-facilitated studies in other rust species, and emerging post-genomic research trends related to fully-phased rust genomes.
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30
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RoyChowdhury M, Sternhagen J, Xin Y, Lou B, Li X, Li C. Evolution of pathogenicity in obligate fungal pathogens and allied genera. PeerJ 2022; 10:e13794. [PMID: 36042858 PMCID: PMC9420410 DOI: 10.7717/peerj.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 07/06/2022] [Indexed: 01/17/2023] Open
Abstract
Obligate fungal pathogens (ascomycetes and basidiomycetes) and oomycetes are known to cause diseases in cereal crop plants. They feed on living cells and most of them have learned to bypass the host immune machinery. This paper discusses some of the factors that are associated with pathogenicity drawing examples from ascomycetes, basidiomycetes and oomycetes, with respect to their manifestation in crop plants. The comparisons have revealed a striking similarity in the three groups suggesting convergent pathways that have arisen from three lineages independently leading to an obligate lifestyle. This review has been written with the intent, that new information on adaptation strategies of biotrophs, modifications in pathogenicity strategies and population dynamics will improve current strategies for breeding with stable resistance.
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Affiliation(s)
- Moytri RoyChowdhury
- Infectious Diseases Program, California Department of Public Health, Richmond, California, United States of America
| | - Jake Sternhagen
- Riverside School of Medicine, University of California, Riverside, Riverside, CA, United States of America
| | - Ya Xin
- Hangzhou Academy of Agricultural Sciences, Hangzhou, P.R. China
| | - Binghai Lou
- Guangxi Academy of Specialty Crops, Guilin, Guangxi, P.R. China
| | - Xiaobai Li
- Zhejiang Academy of Agricultural Sciences, Hangzhou, P.R. China
| | - Chunnan Li
- Hangzhou Academy of Agricultural Sciences, Hangzhou, P.R. China
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31
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Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses. PLANTS 2022; 11:plants11151962. [PMID: 35956440 PMCID: PMC9370660 DOI: 10.3390/plants11151962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
Switchgrass rust caused by Puccinia novopanici (P. novopanici) has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of P. novopanici with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between P. novopanici and P. sorghi; P. graminis tritici 21–0 (Pgt 21) and P. graminis tritici Ug99 (Pgt Ug99) and between Pgt 21 and P. triticina (Pt). Repeat element analysis indicated a strong presence of retro elements among different Puccinia genomes, contributing to the genome size variation between ~1 and 3%. A comparative look at the enriched protein families of Puccinia spp. revealed a predominant role of restriction of telomere capping proteins (RTC), disulfide isomerases, polysaccharide deacetylases, glycoside hydrolases, superoxide dismutases and multi-copper oxidases (MCOs). All the proteomes of Puccinia spp. share in common a repertoire of 75 secretory and 24 effector proteins, including glycoside hydrolases cellobiohydrolases, peptidyl-propyl isomerases, polysaccharide deacetylases and protein disulfide-isomerases, that remain central to their pathogenicity. Comparison of the predicted effector proteins from Puccinia spp. genomes to the validated proteins from the Pathogen–Host Interactions database (PHI-base) resulted in the identification of validated effector proteins PgtSR1 (PGTG_09586) from P. graminis and Mlp124478 from Melampsora laricis across all the rust pathogen genomes.
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Mapuranga J, Zhang N, Zhang L, Chang J, Yang W. Infection Strategies and Pathogenicity of Biotrophic Plant Fungal Pathogens. Front Microbiol 2022; 13:799396. [PMID: 35722337 PMCID: PMC9201565 DOI: 10.3389/fmicb.2022.799396] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 04/19/2022] [Indexed: 01/01/2023] Open
Abstract
Biotrophic plant pathogenic fungi are widely distributed and are among the most damaging pathogenic organisms of agriculturally important crops responsible for significant losses in quality and yield. However, the pathogenesis of obligate parasitic pathogenic microorganisms is still under investigation because they cannot reproduce and complete their life cycle on an artificial medium. The successful lifestyle of biotrophic fungal pathogens depends on their ability to secrete effector proteins to manipulate or evade plant defense response. By integrating genomics, transcriptomics, and effectoromics, insights into how the adaptation of biotrophic plant fungal pathogens adapt to their host populations can be gained. Efficient tools to decipher the precise molecular mechanisms of rust–plant interactions, and standardized routines in genomics and functional pipelines have been established and will pave the way for comparative studies. Deciphering fungal pathogenesis not only allows us to better understand how fungal pathogens infect host plants but also provides valuable information for plant diseases control, including new strategies to prevent, delay, or inhibit fungal development. Our review provides a comprehensive overview of the efforts that have been made to decipher the effector proteins of biotrophic fungal pathogens and demonstrates how rapidly research in the field of obligate biotrophy has progressed.
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Louet C, Blot C, Shelest E, Guerillot P, Zannini F, Pétrowski J, Frey P, Duplessis S. Annotation survey and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) identify a possible role for cold shock proteins in dormancy exit. Fungal Genet Biol 2022; 161:103698. [PMID: 35483517 DOI: 10.1016/j.fgb.2022.103698] [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: 10/19/2021] [Revised: 03/03/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster -two of the most represented TF families in fungi- indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The regulatory gene family encoding cold shock protein (CSP) showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, suggesting a probable regulatory function when the poplar rust fungus exits dormancy. This study addresses for the first time TF and regulatory genes involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.
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Affiliation(s)
| | - Carla Blot
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | - Ekaterina Shelest
- School of biological Sciences, University of Portsmouth, King Henry 1 Street, PO1 D2Y, Portsmouth, United Kingdom
| | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
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Zhou X, Yu D, Cao Z. Convergence Analysis of Rust Fungi and Anther Smuts Reveals Their Common Molecular Adaptation to a Phytoparasitic Lifestyle. Front Genet 2022; 13:863617. [PMID: 35464858 PMCID: PMC9023891 DOI: 10.3389/fgene.2022.863617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 11/28/2022] Open
Abstract
Convergent evolution between distantly related taxa often mirrors adaptation to similar environments. Rust fungi and anther smuts, which belong to different classes in Pucciniomycotina, have independently evolved a phytoparasitic lifestyle, representing an example of convergent evolution in the fungal kingdom. To investigate their adaptations and the genetic bases underlying their phytoparasitic lifestyles, we performed genome-wide convergence analysis of amino acid substitutions, evolutionary rates, and gene gains and losses. Convergent substitutions were detected in ATPeV0D and RP-S27Ae, two genes important for the generation of turgor pressure and ribosomal biosynthesis, respectively. A total of 51 positively selected genes were identified, including eight genes associated with translation and three genes related to the secretion pathway. In addition, rust fungi and anther smuts contained more proteins associated with oligopeptide transporters and vacuolar proteases than did other fungi. For rust fungi and anther smuts, these forms of convergence suggest four adaptive mechanisms for a phytoparasitic lifestyle: 1) reducing the metabolic demand for hyphal growth and penetration at the pre-penetration stage, 2) maintaining the efficiency of protein synthesis during colonization, 3) ensuring the normal secretion of rapidly evolving secreted proteins, and 4) improving the capacity for oligopeptide metabolism. Our results are the first to shed light on the genetic convergence mechanisms and molecular adaptation underlying phytoparasitic lifestyles in fungi.
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35
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Austropuccinia psidii uses tetrapolar mating and produces meiotic spores in older infections on Eucalyptus grandis. Fungal Genet Biol 2022; 160:103692. [DOI: 10.1016/j.fgb.2022.103692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/27/2022] [Accepted: 04/03/2022] [Indexed: 12/30/2022]
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Duan H, Jones AW, Hewitt T, Mackenzie A, Hu Y, Sharp A, Lewis D, Mago R, Upadhyaya NM, Rathjen JP, Stone EA, Schwessinger B, Figueroa M, Dodds PN, Periyannan S, Sperschneider J. Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data. Genome Biol 2022; 23:84. [PMID: 35337367 PMCID: PMC8957140 DOI: 10.1186/s13059-022-02658-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 03/21/2022] [Indexed: 12/21/2022] Open
Abstract
Background Most animals and plants have more than one set of chromosomes and package these haplotypes into a single nucleus within each cell. In contrast, many fungal species carry multiple haploid nuclei per cell. Rust fungi are such species with two nuclei (karyons) that contain a full set of haploid chromosomes each. The physical separation of haplotypes in dikaryons means that, unlike in diploids, Hi-C chromatin contacts between haplotypes are false-positive signals. Results We generate the first chromosome-scale, fully-phased assembly for the dikaryotic leaf rust fungus Puccinia triticina and compare Nanopore MinION and PacBio HiFi sequence-based assemblies. We show that false-positive Hi-C contacts between haplotypes are predominantly caused by phase switches rather than by collapsed regions or Hi-C read mis-mappings. We introduce a method for phasing of dikaryotic genomes into the two haplotypes using Hi-C contact graphs, including a phase switch correction step. In the HiFi assembly, relatively few phase switches occur, and these are predominantly located at haplotig boundaries and can be readily corrected. In contrast, phase switches are widespread throughout the Nanopore assembly. We show that haploid genome read coverage of 30–40 times using HiFi sequencing is required for phasing of the leaf rust genome, with 0.7% heterozygosity, and that HiFi sequencing resolves genomic regions with low heterozygosity that are otherwise collapsed in the Nanopore assembly. Conclusions This first Hi-C based phasing pipeline for dikaryons and comparison of long-read sequencing technologies will inform future genome assembly and haplotype phasing projects in other non-haploid organisms. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02658-2.
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Affiliation(s)
- Hongyu Duan
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | - Ashley W Jones
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Tim Hewitt
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Amy Mackenzie
- Research School of Biology, The Australian National University, Canberra, Australia.,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Yiheng Hu
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Anna Sharp
- Research School of Biology, The Australian National University, Canberra, Australia.,Current Address: John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - David Lewis
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Rohit Mago
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Narayana M Upadhyaya
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - John P Rathjen
- Research School of Biology, The Australian National University, Canberra, Australia
| | - Eric A Stone
- Biological Data Science Institute, The Australian National University, Canberra, Australia
| | | | - Melania Figueroa
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Peter N Dodds
- Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Sambasivam Periyannan
- Research School of Biology, The Australian National University, Canberra, Australia.,Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, Australia. .,Current Address: Black Mountain Science and Innovation Park, CSIRO Agriculture and Food, Canberra, Australia.
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Kortei NK, Tetteh RA, Wiafe-Kwagyan M, Amon DNK, Odamtten GT. Mycobiota profile, phenology, and potential toxicogenic and pathogenic species associated with stored groundnuts ( Arachis hypogaea L.) from the Volta Region, Ghana. Food Sci Nutr 2022; 10:888-902. [PMID: 35311164 PMCID: PMC8907750 DOI: 10.1002/fsn3.2719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/02/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022] Open
Abstract
This study updates the mycobiota resident in groundnut seeds, their phenology during storage with the view to ascertain their occurrence, potential toxigenic species, and pathologically important species in the stored samples. The moisture content of the seeds ranged from 5.7% to 6.5% within the stipulated safe moisture content of 8% for extension of shelf life. Culturing the seeds on mycological media (Sabouraud's Dextrose Agar SDA; Oxytetracycline Glucose Yeast Extract OGYE, Potato Dextrose Agar, PDA) caused a de novo growth of the quiescent spores at 28-30°C for 7-14 days. Fungal population counts on the three media ranged from 2.01 to 2.16 log10 CFU/g samples to a final 6-month count of 1.67-2.60 log10 CFU/g. Eighteen different fungal species belonging to ten genera were encountered on the media, namely Aspergillus, Cladosporium, Curvularia, Fusarium, Penicillium, Trichoderma, Rhizopus, Rhodotorula, Sporendonema, and Paecilomyces. Aspergillus spp. (A. niger, A. flavus, A. fumigatus, and A. terreus) were the most frequently isolated, followed by Fusarium species (F. oxysporum, F. solani, and F. verticillioides), Trichoderma (T. harzianum and T. viride), Rhizopus spp (R. oligosporus and R. stolonifer), and Penicillium verrucosum. The species which were seed borne (A. niger, A. flavus, A. terreus, A. fumigatus, F. solani, F. verticillioides, T. viride, C. herbarum, and Curvularia lunata) were isolated on both surface sterilized and non-surface sterilized seeds. The phenology of the encountered fungal species generally followed five patterns. The most frequently isolated Aspergillus niger, A. flavus, and A. fumigatus predominated throughout the 6 months sampling period, while A. ustus and A. terreus appeared sporadically and disappeared. The early colonizers (R. oligosporus, R. stolonifer, and Paecilomyces) could not be isolated after 2-3 months owing presumably to stronger antibiosis competition from the Aspergillus species. The most predominant Aspergillus species initially constituted 36%-48% of the total population but declined to 10%-36% in 6 months. Mycobiota encountered with mycotoxigenic potential and human health importance were A. niger, A. flavus, A. fumigatus, F. verticillioides, and Penicillium verrucosum. Other species of pathological importance to plants were Curvularia lunata and Fusarium oxysporum. The practical implications of these findings are discussed.
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Affiliation(s)
- Nii Korley Kortei
- Department of Nutrition and Dietetics School of Allied Health Sciences University of Health and Allied Sciences Ho Ghana
| | - Rachel Adinorkie Tetteh
- Department of Nutrition and Dietetics School of Allied Health Sciences University of Health and Allied Sciences Ho Ghana
| | - Michael Wiafe-Kwagyan
- Department of Plant and Environmental Biology College of Basic and Applied Sciences University of Ghana Legon Ghana
| | - Denick Nii Kotey Amon
- Department of Plant and Environmental Biology College of Basic and Applied Sciences University of Ghana Legon Ghana
| | - George Tawia Odamtten
- Department of Plant and Environmental Biology College of Basic and Applied Sciences University of Ghana Legon Ghana
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38
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Chen W, Radford D, Hambleton S. Towards Improved Detection and Identification of Rust Fungal Pathogens in Environmental Samples Using a Metabarcoding Approach. PHYTOPATHOLOGY 2022; 112:535-548. [PMID: 34384241 DOI: 10.1094/phyto-01-21-0020-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The dispersion of fungal inocula such as the airborne spores of rust fungi (Pucciniales) can be monitored through metabarcoding of the internal transcribed spacer 2 (ITS2) of the rRNA gene in environmental DNAs. This method is largely dependent on a high-quality reference database (refDB) and primers with proper taxonomic coverage and specificity. For this study, a curated ITS2 reference database (named CR-ITS2-refDB) comprising representatives of the major cereal rust fungi and phylogenetically related species was compiled. Interspecific and intraspecific variation analyses suggested that the ITS2 region had reasonable discriminating power for the majority of the Puccinia species or species complexes in the database. In silico evaluation of nine forward and seven reverse ITS2 primers, including three newly designed, revealed marked variation in DNA amplification efficiency for the rusts. We validated the theoretical assessment of rust-enhanced (Rust2inv/ITS4var_H) and universal fungal (ITS9F/ITS4) ITS2 primer pairs by profiling the airborne rust fungal communities from environmental samples via a metabarcoding approach. Species- or subspecies-level identification of the rusts was improved by use of CR-ITS2-refDB and the Automated Oligonucleotide Design Pipeline (AODP), which identified all mutations distinguishing highly conserved DNA markers between close relatives. A generic bioinformatics pipeline was developed, including all steps used in this study from in silico evaluation of primers to accurate identification of short metabarcodes at the level of interest for defining phytopathogens. The results highlight the importance of primer selection, refDBs that are resolved to reflect phylogenetic relationships, and the use of AODP for improving the reliability of metabarcoding in phytopathogen biosurveillance.
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Affiliation(s)
- Wen Chen
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Devon Radford
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
| | - Sarah Hambleton
- Biodiversity and Bioresources, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, K1A 0C6, Canada
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Rocher F, Alouane T, Philippe G, Martin ML, Label P, Langin T, Bonhomme L. Fusarium graminearum Infection Strategy in Wheat Involves a Highly Conserved Genetic Program That Controls the Expression of a Core Effectome. Int J Mol Sci 2022; 23:ijms23031914. [PMID: 35163834 PMCID: PMC8836836 DOI: 10.3390/ijms23031914] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
Fusarium graminearum, the main causal agent of Fusarium Head Blight (FHB), is one of the most damaging pathogens in wheat. Because of the complex organization of wheat resistance to FHB, this pathosystem represents a relevant model to elucidate the molecular mechanisms underlying plant susceptibility and to identify their main drivers, the pathogen’s effectors. Although the F. graminearum catalog of effectors has been well characterized at the genome scale, in planta studies are needed to confirm their effective accumulation in host tissues and to identify their role during the infection process. Taking advantage of the genetic variability from both species, a RNAseq-based profiling of gene expression was performed during an infection time course using an aggressive F. graminearum strain facing five wheat cultivars of contrasting susceptibility as well as using three strains of contrasting aggressiveness infecting a single susceptible host. Genes coding for secreted proteins and exhibiting significant expression changes along infection progress were selected to identify the effector gene candidates. During its interaction with the five wheat cultivars, 476 effector genes were expressed by the aggressive strain, among which 91% were found in all the infected hosts. Considering three different strains infecting a single susceptible host, 761 effector genes were identified, among which 90% were systematically expressed in the three strains. We revealed a robust F. graminearum core effectome of 357 genes expressed in all the hosts and by all the strains that exhibited conserved expression patterns over time. Several wheat compartments were predicted to be targeted by these putative effectors including apoplast, nucleus, chloroplast and mitochondria. Taken together, our results shed light on a highly conserved parasite strategy. They led to the identification of reliable key fungal genes putatively involved in wheat susceptibility to F. graminearum, and provided valuable information about their putative targets.
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Affiliation(s)
- Florian Rocher
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
| | - Tarek Alouane
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
| | - Géraldine Philippe
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
| | - Marie-Laure Martin
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université Paris-Saclay, Université Evry, 91190 Gif sur Yvette, France;
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, 91190 Gif sur Yvette, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France
| | - Philippe Label
- UMR 547 Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant, INRAE, Université Clermont Auvergne, 63178 Aubière, France;
| | - Thierry Langin
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
| | - Ludovic Bonhomme
- UMR 1095 Génétique Diversité Ecophysiologie des Céréales, INRAE, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (F.R.); (T.A.); (G.P.); (T.L.)
- Correspondence:
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40
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Mapuranga J, Zhang L, Zhang N, Yang W. The haustorium: The root of biotrophic fungal pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:963705. [PMID: 36105706 PMCID: PMC9465030 DOI: 10.3389/fpls.2022.963705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/15/2022] [Indexed: 05/02/2023]
Abstract
Biotrophic plant pathogenic fungi are among the dreadful pathogens that continuously threaten the production of economically important crops. The interaction of biotrophic fungal pathogens with their hosts necessitates the development of unique infection mechanisms and involvement of various virulence-associated components. Biotrophic plant pathogenic fungi have an exceptional lifestyle that supports nutrient acquisition from cells of a living host and are fully dependent on the host for successful completion of their life cycle. The haustorium, a specialized infection structure, is the key organ for biotrophic fungal pathogens. The haustorium is not only essential in the uptake of nutrients without killing the host, but also in the secretion and delivery of effectors into the host cells to manipulate host immune system and defense responses and reprogram the metabolic flow of the host. Although there is a number of unanswered questions in this area yet, results from various studies indicate that the haustorium is the root of biotrophic fungal pathogens. This review provides an overview of current knowledge of the haustorium, its structure, composition, and functions, which includes the most recent haustorial transcriptome studies.
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Persoons A, Maupetit A, Louet C, Andrieux A, Lipzen A, Barry KW, Na H, Adam C, Grigoriev IV, Segura V, Duplessis S, Frey P, Halkett F, De Mita S. Genomic signatures of a major adaptive event in the pathogenic fungus Melampsora larici-populina. Genome Biol Evol 2021; 14:6468622. [PMID: 34919678 PMCID: PMC8755504 DOI: 10.1093/gbe/evab279] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/14/2022] Open
Abstract
The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in nonmodel organisms. Host–pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected the poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar. Based on 76 virulent and avirulent isolates framing narrowly the estimated date of the adaptive event, we examined the molecular signatures of selection. Using an array of genome scan methods based on different features of nucleotide diversity, we detected a single locus exhibiting a consistent pattern suggestive of a selective sweep in virulent individuals (excess of differentiation between virulent and avirulent samples, linkage disequilibrium, genotype–phenotype statistical association, and long-range haplotypes). Our study pinpoints a single gene and further a single amino acid replacement which may have allowed the adaptive event. Although our samples are nearly contemporary to the selective sweep, it does not seem to have affected genome diversity further than the immediate vicinity of the causal locus, which can be explained by a soft selective sweep (where selection acts on standing variation) and by the impact of recombination in mitigating the impact of selection. Therefore, it seems that properties of the life cycle of M. larici-populina, which entails both high genetic diversity and outbreeding, has facilitated its adaptation.
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Affiliation(s)
| | - Agathe Maupetit
- Université de Lorraine,INRAE, IAM, Nancy, France.,Physiology and Biotechnology of Algae Laboratory,IFREMER, Nantes, France
| | | | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kerrie W Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Catherine Adam
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, USA
| | - Vincent Segura
- BioForA,INRAE, ONF, Orléans, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398 Montpellier, France
| | | | - Pascal Frey
- Université de Lorraine,INRAE, IAM, Nancy, France
| | | | - Stéphane De Mita
- Université de Lorraine,INRAE, IAM, Nancy, France.,PHIM, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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Louet C, Saubin M, Andrieux A, Persoons A, Gorse M, Pétrowski J, Fabre B, De Mita S, Duplessis S, Frey P, Halkett F. A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown. Mol Ecol 2021; 32:2472-2483. [PMID: 34843142 DOI: 10.1111/mec.16294] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 01/29/2023]
Abstract
The deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R-mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici-populina is a damaging pathogen of poplars in Europe. It underwent a major adaptive event in 1994, with the breakdown of the poplar RMlp7 resistance gene. Population genomics studies identified a locus in the genome of M. larici-populina that probably corresponds to the candidate avirulence gene AvrMlp7. Here, to further characterize this effector, we used a population genetics approach on a comprehensive set of 281 individuals recovered throughout a 28-year period encompassing the resistance breakdown event. Using two dedicated molecular tools, genotyping at the candidate locus highlighted two different alterations of a predominant allele found mainly before the resistance breakdown: a nonsynonymous mutation and a complete deletion of this locus. This results in six diploid genotypes: three genotypes related to the avirulent phenotype and three related to the virulent phenotype. The temporal survey of the candidate locus revealed that both alterations were found in association during the resistance breakdown event. They pre-existed before the breakdown in a heterozygous state with the predominant allele cited above. Altogether, these results suggest that the association of both alterations at the candidate locus AvrMlp7 drove the poplar rust adaptation to RMlp7-mediated immunity. This study demonstrates for the first time a case of adaptation from standing genetic variation in rust fungi during a qualitative resistance breakdown.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
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Cardenas DE, Cheema J, Oppelaar TS, Hincapie M, Sood S, Zheng Q, Carrillo-Tarazona Y, Huguet-Tapia J, Saunders DGO, Comstock JC, Rott PC, Cano LM. Draft Genome Sequence Resource for the Orange Rust Pathogen of Sugarcane Puccinia kuehnii. PHYTOPATHOLOGY 2021; 111:1893-1896. [PMID: 33734870 DOI: 10.1094/phyto-01-21-0008-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: 06/12/2023]
Abstract
Puccinia kuehnii is an obligate biotrophic fungal pathogen that causes orange rust of sugarcane, which is prevalent in many countries around the globe. In the United States, orange rust was first detected in sugarcane in Florida in 2007 and poses a persistent and economically damaging threat to the sugarcane industry in this region. Here, we generated the first genome assemblies for two isolates of P. kuehnii (1040 and 2143) collected in Florida in 2017 from two sugarcane cultivars, CL85-1040 and CP89-2143, respectively. These two rust genome resources will be of immense value for future genomic studies, particularly further exploration of the predicted secretomes that may help define key pathogenicity determinants for this economically important pathogen.
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Affiliation(s)
- Daniela E Cardenas
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Indian River Research and Education Center, Fort Pierce, FL, 34945, U.S.A
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Everglades Research and Education Center, Belle Glade, FL, 33430, U.S.A
| | | | - Theodora S Oppelaar
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Indian River Research and Education Center, Fort Pierce, FL, 34945, U.S.A
| | - Martha Hincapie
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Everglades Research and Education Center, Belle Glade, FL, 33430, U.S.A
| | - Sushma Sood
- U.S. Department of Agriculture, Agriculture Research Services, Sugarcane Field Station, Canal Point, FL 33438, U.S.A
| | - Qiaolin Zheng
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Indian River Research and Education Center, Fort Pierce, FL, 34945, U.S.A
| | - Yisel Carrillo-Tarazona
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Indian River Research and Education Center, Fort Pierce, FL, 34945, U.S.A
| | - Jose Huguet-Tapia
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Gainesville, FL 32611, U.S.A
| | | | - Jack C Comstock
- U.S. Department of Agriculture, Agriculture Research Services, Sugarcane Field Station, Canal Point, FL 33438, U.S.A
| | - Philippe C Rott
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Everglades Research and Education Center, Belle Glade, FL, 33430, U.S.A
- CIRAD, UMR PHIM, 34090 Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Liliana M Cano
- University of Florida, Institute of Food and Agricultural Sciences, Plant Pathology Department, Indian River Research and Education Center, Fort Pierce, FL, 34945, U.S.A
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Ding Y, Cuddy WS, Wellings CR, Zhang P, Thach T, Hovmøller MS, Qutob D, Brar GS, Kutcher HR, Park RF. Incursions of divergent genotypes, evolution of virulence and host jumps shape a continental clonal population of the stripe rust pathogen Puccinia striiformis. Mol Ecol 2021; 30:6566-6584. [PMID: 34543497 DOI: 10.1111/mec.16182] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/22/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
Long-distance migration and host adaptation by transboundary plant pathogens often brings detrimental effects to important agroecosystems. Efficient surveillance as a basis for responding to the dynamics of such pathogens is often hampered by a lack of information on incursion origin, evolutionary pathways and the genetic basis of rapidly evolving virulence across larger timescales. Here, we studied these genetic features by using historical isolates of the obligate biotrophic pathogen Puccinia striiformis f. sp. tritici (Pst), which causes one of the most widespread and devastating diseases, stripe (yellow) rust, of wheat. Through a combination of genotypic, phenotypic and genomic analyses, we assigned eight Pst isolates representing putative exotic Pst incursions into Australia to four previously defined genetic groups, PstS0, PstS1, PstS10 and PstS13. We showed that isolates of an additional incursion of P. striiformis, known locally as P. striiformis f. sp. pseudo-hordei, had a new and unique multilocus SSR genotype (MLG). We provide results of overall genomic variation of representative Pst isolates from each genetic group by comparative genomic analyses. We showed that isolates within the PstS1 and PstS13 genetic groups are most distinct at the whole-genome variant level from isolates belonging to genetic group PstS0, whereas the isolate from the PstS10 genetic group is intermediate. We further explored variable gene content, including putative effectors, representing both shared but also unique genetic changes that have occurred following introduction, some of which may additionally account for local adaptation of these isolates to triticale. Our genotypic and genomic data revealed new genetic insights into the evolution of diverse phenotypes of rust pathogens following incursion into a geographically isolated continental region.
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Affiliation(s)
- Yi Ding
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Will S Cuddy
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Colin R Wellings
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia.,NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Peng Zhang
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
| | - Tine Thach
- Department of Agroecology, Global Rust Reference Center, Aarhus University, Slagelse, Denmark
| | - Mogens S Hovmøller
- Department of Agroecology, Global Rust Reference Center, Aarhus University, Slagelse, Denmark
| | - Dinah Qutob
- Department of Biological Sciences, Kent State University at Stark, North Canton, ON, USA
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Hadley R Kutcher
- College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
| | - Robert F Park
- School of Life and Environmental Sciences, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, Australia
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Duplessis S, Lorrain C, Petre B, Figueroa M, Dodds PN, Aime MC. Host Adaptation and Virulence in Heteroecious Rust Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:403-422. [PMID: 34077239 DOI: 10.1146/annurev-phyto-020620-121149] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rust fungi (Pucciniales, Basidiomycota) are obligate biotrophic pathogens that cause rust diseases in plants, inflicting severe damage to agricultural crops. Pucciniales possess the most complex life cycles known in fungi. These include an alternation of generations, the development of up to five different sporulating stages, and, for many species, the requirement of infecting two unrelated host plants during different parts of their life cycle, termed heteroecism. These fungi have been extensively studied in the past century through microscopy and inoculation studies, providing precise descriptions of their infection processes, although the molecular mechanisms underlying their unique biology are poorly understood. In this review, we cover recent genomic and life cycle transcriptomic studies in several heteroecious rust species, which provide insights into the genetic tool kits associated with host adaptation and virulence, opening new avenues for unraveling their unique evolution.
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Affiliation(s)
- Sebastien Duplessis
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Cecile Lorrain
- Plant Pathology Group, ETH Zurich, 8092 Zurich, Switzerland;
| | - Benjamin Petre
- Université de Lorraine, INRAE, UMR 1136 IAM, Interactions Arbres-Microorganismes, 54000 Nancy, France; ,
| | - Melania Figueroa
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT 2601, Australia; ,
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA;
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Zheng W, Peng Z, Peng S, Yu Z, Cao Z. Multinuclei Occurred Under Cryopreservation and Enhanced the Pathogenicity of Melampsora larici-populina. Front Microbiol 2021; 12:650902. [PMID: 34248868 PMCID: PMC8270653 DOI: 10.3389/fmicb.2021.650902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
Melampsora larici-populina is a macrocyclic rust, and the haploid stage with two nuclei and the diploid of mononuclear sequentially occur annually. During the preservation of dry urediniospores at −80°C, we found that one isolate, ΔTs06, was different from the usual wild-type isolate Ts06 at −20°C because it has mixed polykaryotic urediniospores. However, the other spores, including the 0, I, III, and IV stages of a life cycle, were the same as Ts06. After five generations of successive inoculation and harvest of urediniospores from the compatible host Populus purdomii, the isolate ΔTs06 steadily maintained more than 20% multiple nucleus spores. To test the pathogenesis variation of ΔTs06, an assay of host poplars was applied to evaluate the differences between ΔTs06 and Ts06. After ΔTs06 and Ts06 inoculation, leaves of P. purdomii were used to detect the expression of small secreted proteins (SSPs) and fungal biomasses using quantitative real-time PCR (qRT-PCR) and trypan blue staining. ΔTs06 displayed stronger expression of five SSPs and had a shorter latent period, a higher density of uredinia, and higher DNA mass. A transcriptomic comparison between ΔTs06 and Ts06 revealed that 3,224 were differentially expressed genes (DEGs), 55 of which were related to reactive oxygen species metabolism, the Mitogen-activated protein kinase (MAPK) signaling pathway, and the meiosis pathway. Ten genes in the mitotic and meiotic pathways and another two genes associated with the “response to DNA damage stimulus” all had an upward expression, which were detected by qRT-PCR in ΔTs06 during cryopreservation. Gas chromatography–mass spectrometry (GC-MS) confirmed that the amounts of hexadecanoic acid and octadecadienoic acid were much more in ΔTs06 than in Ts06. In addition, using spectrophotometry, hydrogen peroxide (H2O2) was also present in greater quantities in ΔTs06 compared with those found in Ts06. Increased fatty acids metabolism could prevent damage to urediniospores in super-low temperatures, but oxidant species that involved H2O2 may destroy tube proteins of mitosis and meiosis, which could cause abnormal nuclear division and lead to multinucleation, which has a different genotype. Therefore, the multinuclear isolate is different from the wild-type isolate in terms of phenotype and genotype; this multinucleation phenomenon in urediniospores improves the pathogenesis and environmental fitness of M. larici-populina.
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Affiliation(s)
- Wei Zheng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zijia Peng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Shaobing Peng
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zhongdong Yu
- College of Forestry, Northwest A&F University, Yangling, China
| | - Zhimin Cao
- College of Forestry, Northwest A&F University, Yangling, China
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Cushion MT, Tisdale-Macioce N, Sayson SG, Porollo A. The Persistent Challenge of Pneumocystis Growth Outside the Mammalian Lung: Past and Future Approaches. Front Microbiol 2021; 12:681474. [PMID: 34093506 PMCID: PMC8174303 DOI: 10.3389/fmicb.2021.681474] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022] Open
Abstract
The pathogenic fungi in the genus, Pneumocystis, have eluded attempts to continuously grow them in an ex vivo cultivation system. New data from transcriptomic and genomic sequencing studies have identified a myriad of absent metabolic pathways, helping to define their host obligate nature. These nutrients, factors, and co-factors are acquired from their mammalian host and provide clues to further supplementation of existing media formulations. Likewise, a new appreciation of the pivotal role for the sexual cycle in the survival and dissemination of the infection suggests that Pneumocystis species are obligated to undergo mating and sexual reproduction in their life cycle with a questionable role for an asexual cycle. The lack of ascus formation in any previous cultivation attempts may explain the failure to identify a sustainable system. Many characteristics of these ascomycetes suggest a biotrophic existence within the lungs of the mammalian hosts. In the present review, previous attempts at growing these fungi ex vivo are summarized. The significance of their life cycle is considered, and a list of potential supplements based on the genomic and transcriptomic studies is presented. State of the art technologies such as metabolomics, organoids, lung-on-a chip, and air lift cultures are discussed as potential growth systems.
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Affiliation(s)
- Melanie T Cushion
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Nikeya Tisdale-Macioce
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Steven G Sayson
- Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Medical Research Service, Cincinnati Veterans Affairs Medical Center, Cincinnati, OH, United States
| | - Aleksey Porollo
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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Singh Y, Nair AM, Verma PK. Surviving the odds: From perception to survival of fungal phytopathogens under host-generated oxidative burst. PLANT COMMUNICATIONS 2021; 2:100142. [PMID: 34027389 PMCID: PMC8132124 DOI: 10.1016/j.xplc.2021.100142] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/04/2020] [Accepted: 01/01/2021] [Indexed: 05/04/2023]
Abstract
Fungal phytopathogens pose a serious threat to global crop production. Only a handful of strategies are available to combat these fungal infections, and the increasing incidence of fungicide resistance is making the situation worse. Hence, the molecular understanding of plant-fungus interactions remains a primary focus of plant pathology. One of the hallmarks of host-pathogen interactions is the overproduction of reactive oxygen species (ROS) as a plant defense mechanism, collectively termed the oxidative burst. In general, high accumulation of ROS restricts the growth of pathogenic organisms by causing localized cell death around the site of infection. To survive the oxidative burst and achieve successful host colonization, fungal phytopathogens employ intricate mechanisms for ROS perception, ROS neutralization, and protection from ROS-mediated damage. Together, these countermeasures maintain the physiological redox homeostasis that is essential for cell viability. In addition to intracellular antioxidant systems, phytopathogenic fungi also deploy interesting effector-mediated mechanisms for extracellular ROS modulation. This aspect of plant-pathogen interactions is significantly under-studied and provides enormous scope for future research. These adaptive responses, broadly categorized into "escape" and "exploitation" mechanisms, are poorly understood. In this review, we discuss the oxidative stress response of filamentous fungi, their perception signaling, and recent insights that provide a comprehensive understanding of the distinct survival mechanisms of fungal pathogens in response to the host-generated oxidative burst.
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Affiliation(s)
- Yeshveer Singh
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Athira Mohandas Nair
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
- Corresponding author
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Effectors of Puccinia striiformis f. sp. tritici Suppressing the Pathogenic-Associated Molecular Pattern-Triggered Immune Response Were Screened by Transient Expression of Wheat Protoplasts. Int J Mol Sci 2021; 22:ijms22094985. [PMID: 34067160 PMCID: PMC8125866 DOI: 10.3390/ijms22094985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/29/2021] [Accepted: 05/03/2021] [Indexed: 11/17/2022] Open
Abstract
Puccinia striiformis f. sp. tritici (Pst) is an important pathogen of wheat (Triticum aestivum L.) stripe rust, and the effector protein secreted by haustoria is a very important component involved in the pathogenic process. Although the candidate effector proteins secreted by Pst haustoria have been predicted to be abundant, few have been functionally validated. Our study confirmed that chitin and flg22 could be used as elicitors of the pathogenic-associated molecular pattern-triggered immune (PTI) reaction in wheat leaves and that TaPr-1-14 could be used as a marker gene to detect the PTI reaction. In addition, the experimental results were consistent in wheat protoplasts. A rapid and efficient method for screening and identifying the effector proteins of Pst was established by using the wheat protoplast transient expression system. Thirty-nine Pst haustorial effector genes were successfully cloned and screened for expression in the protoplast. We identified three haustorial effector proteins, PSEC2, PSEC17, and PSEC45, that may inhibit the response of wheat to PTI. These proteins are localized in the somatic cytoplasm and nucleus of wheat protoplasts and are highly expressed during the infection and parasitism of wheat.
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