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Liang J, Li Y, Dodds PN, Figueroa M, Sperschneider J, Han S, Tsui CKM, Zhang K, Li L, Ma Z, Cai L. Haplotype-phased and chromosome-level genome assembly of Puccinia polysora, a giga-scale fungal pathogen causing southern corn rust. Mol Ecol Resour 2023; 23:601-620. [PMID: 36403246 DOI: 10.1111/1755-0998.13739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
Abstract
Rust fungi are characterized by large genomes with high repeat content and have two haploid nuclei in most life stages, which makes achieving high-quality genome assemblies challenging. Here, we described a pipeline using HiFi reads and Hi-C data to assemble a gigabase-sized fungal pathogen, Puccinia polysora f.sp. zeae, to haplotype-phased and chromosome-scale. The final assembled genome is 1.71 Gbp, with ~850 Mbp and 18 chromosomes in each haplotype, being currently one of the two giga-scale fungi assembled to chromosome level. Transcript-based annotation identified 47,512 genes for the dikaryotic genome with a similar number for each haplotype. A high level of interhaplotype variation was found with 10% haplotype-specific BUSCO genes, 5.8 SNPs/kbp, and structural variation accounting for 3% of the genome size. The P. polysora genome displayed over 85% repeat contents, with genome-size expansion and copy number increasing of species-specific orthogroups. Interestingly, these features did not affect overall synteny with other Puccinia species having smaller genomes. Fine-time-point transcriptomics revealed seven clusters of coexpressed secreted proteins that are conserved between two haplotypes. The fact that candidate effectors interspersed with all genes indicated the absence of a "two-speed genome" evolution in P. polysora. Genome resequencing of 79 additional isolates revealed a clonal population structure of P. polysora in China with low geographic differentiation. Nevertheless, a minor population differentiated from the major population by having mutations on secreted proteins including AvrRppC, indicating the ongoing virulence to evade recognition by RppC, a major resistance gene in Chinese corn cultivars. The high-quality assembly provides valuable genomic resources for future studies on disease management and the evolution of P. polysora.
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Affiliation(s)
- Junmin Liang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanjie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Shiling Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Clement K M Tsui
- Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore City, Singapore.,LKC School of Medicine, Nanyang Technological University, Singapore City, Singapore
| | - Keyu Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Leifu Li
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Zhanhong Ma
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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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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Maia T, Rody HVS, Bombardelli RGH, Souto TG, Camargo LEA, Monteiro-Vitorello CB. A Bacterial Type Three Secretion-Based Delivery System for Functional Characterization of Sporisorium scitamineum Plant Immune Suppressing Effector Proteins. PHYTOPATHOLOGY 2022; 112:1513-1523. [PMID: 35050679 DOI: 10.1094/phyto-08-21-0326-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The facultative biotrophic basidiomycete Sporisorium scitamineum causes smut disease in sugarcane. This study applied an assay to identify S. scitamineum candidate effectors (CEs) with plant immunity suppression activities by delivering them into Nicotiana benthamiana cells via the type-three secretion system of Pseudomonas fluorescens EtHAn. Six CEs were individually cloned into the pEDV6 vector and expressed by P. fluorescens EtHAn for translocation into the plant cells. Three CEs (g1052, g3890, and g5159) could suppress pattern-triggered immunity (PTI) responses with high reproducibility in different coinfiltration experiments with P. syringae pv. tomato DC3000. In addition, three CEs (g1052, g4549, and g5159) were also found to be AvrB-induced suppressors of effector-triggered immunity (ETI), demonstrating for the first time that S. scitamineum can defeat both PTI and ETI responses. A transcriptomic analysis at different stages of infection by the smut fungus of three sugarcane cultivars with contrasting responses to the pathogen revealed that suppressors g1052, g3890, g4549, and g5159 were induced at the early stage of infection. By contrast, the two CEs (g2666 and g6610) that did not exhibit suppression activities expressed only at the late stage of infection. Moreover, genomic structures of the CEs and searches for orthologs in other smut species suggested duplication events and further divergence in CEs evolution of S. scitamineum. Thus, the transient assay applied here demonstrated the potential of pEDV6 and P. fluorescens EtHAn as biological tools for identifying plant immune suppressors from S. scitamineum.
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Affiliation(s)
- Thiago Maia
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Piracicaba, SP, Brazil
- Departamento de Genética, USP, ESALQ, Piracicaba, SP, Brazil
| | - Hugo V S Rody
- Departamento de Genética, USP, ESALQ, Piracicaba, SP, Brazil
| | | | - Tiarla Graciane Souto
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Piracicaba, SP, Brazil
- Departamento de Genética, USP, ESALQ, Piracicaba, SP, Brazil
| | - Luis Eduardo Aranha Camargo
- Departamento de Fitopatologia e Nematologia, Universidade de São Paulo (USP), Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Piracicaba, SP, Brazil
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Figueroa M, Ortiz D, Henningsen EC. Tactics of host manipulation by intracellular effectors from plant pathogenic fungi. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102054. [PMID: 33992840 DOI: 10.1016/j.pbi.2021.102054] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Fungal pathogens can secrete hundreds of effectors, some of which are known to promote host susceptibility. This biological complexity, together with the lack of genetic tools in some fungi, presents a substantial challenge to develop a broad picture of the mechanisms these pathogens use for host manipulation. Nevertheless, recent advances in understanding individual effector functions are beginning to flesh out our view of fungal pathogenesis. This review discusses some of the latest findings that illustrate how effectors from diverse species use similar strategies to modulate plant physiology to their advantage. We also summarize recent breakthroughs in the identification of effectors from challenging systems, like obligate biotrophs, and emerging concepts such as the 'iceberg model' to explain how the activation of plant immunity can be turned off by effectors with suppressive activity.
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Affiliation(s)
- Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Diana Ortiz
- National Research Institute for Agriculture, Food and Environment, Unit of Genetics and Breeding of Fruit and Vegetables, Domaine St Maurice, CS 60094, F-84143 Montfavet, France
| | - Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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Leaping into the Unknown World of Sporisorium scitamineum Candidate Effectors. J Fungi (Basel) 2020; 6:jof6040339. [PMID: 33291820 PMCID: PMC7762069 DOI: 10.3390/jof6040339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/28/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Sporisorium scitamineum is a biotrophic fungus causing sugarcane smut disease. In this study, we set up a pipeline and used genomic and dual transcriptomic data previously obtained by our group to identify candidate effectors of S. scitamineum and their expression profiles in infected smut-resistant and susceptible sugarcane plants. The expression profile of different genes after infection in contrasting sugarcane genotypes assessed by RT-qPCR depended on the plant genotypes and disease progression. Three candidate effector genes expressed earlier only in resistant plants, four expressed in both genotypes, and three later in susceptible plants. Ten genes were cloned and transiently expressed in N. benthamiana leaves to determine their subcellular location, while four localized in more than one compartment. Two candidates, g3890 having a nucleoplasmic and mitochondrial location and g5159 targeting the plant cell wall, were selected to obtain their possible corresponding host targets using co-immunoprecipitation (CoIP) experiments and mass spectrometry. Various potential interactors were identified, including subunits of the protein phosphatase 2A and an endochitinase. We investigated the presence of orthologs in sugarcane and using transcriptome data present their expression profiles. Orthologs of sugarcane shared around 70% similarity. Identifying a set of putative fungal effectors and their plant targets provides a valuable resource for functional characterization of the molecular events leading to smut resistance in sugarcane plants and uncovers further opportunities for investigation.
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Figueroa M, Dodds PN, Henningsen EC. Evolution of virulence in rust fungi - multiple solutions to one problem. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:20-27. [PMID: 32244171 DOI: 10.1016/j.pbi.2020.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 05/18/2023]
Abstract
Rust fungi are major pathogens that negatively affect crops and ecosystems. Recent rust disease epidemics driven by the emergence of strains with novel virulence profiles demand a better understanding of the evolutionary mechanisms of these organisms. Here, we review research advances in genome-scale analysis coupled with functional validation of effector candidate genes that have been instrumental to elucidate processes that contribute to changes in virulence phenotypes. We highlight how haplotype-phased genome references have paved the road to link these processes to the reproductive phases of rust fungi and have provided evidence for somatic exchange between strains as an important mechanism for generating diversity in asexual populations. With increasing data availability, we envision the future development of molecular virulence diagnostic tools.
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Affiliation(s)
- Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
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Abstract
Among the thousands of rust species described, many are known for their devastating effects on their hosts, which include major agriculture crops and trees. Hence, for over a century, these basidiomycete pathogenic fungi have been researched and experimented with. However, due to their biotrophic nature, they are challenging organisms to work with and, needing their hosts for propagation, represent pathosystems that are not easily experimentally accessible. Indeed, efforts to perform genetics have been few and far apart for the rust fungi, though one study performed in the 1940s was famously instrumental in formulating the gene-for-gene hypothesis describing pathogen-host interactions. By taking full advantage of the molecular genetic tools developed in the 1980s, research on many plant pathogenic microbes thrived, yet similar work on the rusts remained very challenging though not without some successes. However, the genomics era brought real breakthrough research for the biotrophic fungi and with innovative experimentation and the use of heterologous systems, molecular genetic analyses over the last 2 decades have significantly advanced our insight into the function of many rust fungus genes and their role in the interaction with their hosts. This has allowed optimizing efforts for resistance breeding and the design and testing of various novel strategies to reduce the devastating diseases they cause.
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Affiliation(s)
- Guus Bakkeren
- Agriculture and Agri-Food Canada, Summerland Research & Development Centre, 4200 Hwy 97, Summerland, BC, Canada V0H 1Z0
| | - Les J Szabo
- U.S. Department of Agriculture-Agriculture Research Service, Cereal Disease Laboratory and University of Minnesota, 1551 Lindig Street, St. Paul, MN 55108, U.S.A
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Lorrain C, Gonçalves Dos Santos KC, Germain H, Hecker A, Duplessis S. Advances in understanding obligate biotrophy in rust fungi. THE NEW PHYTOLOGIST 2019; 222:1190-1206. [PMID: 30554421 DOI: 10.1111/nph.15641] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/13/2018] [Indexed: 05/18/2023]
Abstract
Contents Summary 1190 I. Introduction 1190 II. Rust fungi: a diverse and serious threat to agriculture 1191 III. The different facets of rust life cycles and unresolved questions about their evolution 1191 IV. The biology of rust infection 1192 V. Rusts in the genomics era: the ever-expanding list of candidate effector genes 1195 VI. Functional characterization of rust effectors 1197 VII. Putting rusts to sleep: Pucciniales research outlooks 1201 Acknowledgements 1202 References 1202 SUMMARY: Rust fungi (Pucciniales) are the largest group of plant pathogens and represent one of the most devastating threats to agricultural crops worldwide. Despite the economic importance of these highly specialized pathogens, many aspects of their biology remain obscure, largely because rust fungi are obligate biotrophs. The rise of genomics and advances in high-throughput sequencing technology have presented new options for identifying candidate effector genes involved in pathogenicity mechanisms of rust fungi. Transcriptome analysis and integrated bioinformatics tools have led to the identification of key genetic determinants of host susceptibility to infection by rusts. Thousands of genes encoding secreted proteins highly expressed during host infection have been reported for different rust species, which represents significant potential towards understanding rust effector function. Recent high-throughput in planta expression screen approaches (effectoromics) have pushed the field ahead even further towards predicting high-priority effectors and identifying avirulence genes. These new insights into rust effector biology promise to inform future research and spur the development of effective and sustainable strategies for managing rust diseases.
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Affiliation(s)
- Cécile Lorrain
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
| | | | - Hugo Germain
- Department of Chemistry, Biochemistry and Physics, Université du Quebec à Trois-Rivières, Trois-Rivières, QC, G9A 5H7, Canada
| | - Arnaud Hecker
- Université de Lorraine, UMR 1136 Université de Lorraine/INRA Interactions Arbres/Microorganismes, Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- INRA Centre Grand Est - Nancy, UMR 1136 INRA/Université de Lorraine Interactions Arbres/Microorganismes, Champenoux, 54280, France
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Porto BN, Caixeta ET, Mathioni SM, Vidigal PMP, Zambolim L, Zambolim EM, Donofrio N, Polson SW, Maia TA, Chen C, Adetunji M, Kingham B, Dalio RJD, de Resende MLV. Genome sequencing and transcript analysis of Hemileia vastatrix reveal expression dynamics of candidate effectors dependent on host compatibility. PLoS One 2019; 14:e0215598. [PMID: 30998802 PMCID: PMC6472787 DOI: 10.1371/journal.pone.0215598] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 04/04/2019] [Indexed: 12/17/2022] Open
Abstract
Coffee leaf rust caused by the fungus Hemileia vastatrix is one of the most important leaf diseases of coffee plantations worldwide. Current knowledge of the H. vastatrix genome is limited and only a small fraction of the total fungal secretome has been identified. In order to obtain a more comprehensive understanding of its secretome, we aimed to sequence and assemble the entire H. vastatrix genome using two next-generation sequencing platforms and a hybrid assembly strategy. This resulted in a 547 Mb genome of H. vastatrix race XXXIII (Hv33), with 13,364 predicted genes that encode 13,034 putative proteins with transcriptomic support. Based on this proteome, 615 proteins contain putative secretion peptides, and lack transmembrane domains. From this putative secretome, 111 proteins were identified as candidate effectors (EHv33) unique to H. vastatrix, and a subset consisting of 17 EHv33 genes was selected for a temporal gene expression analysis during infection. Five genes were significantly induced early during an incompatible interaction, indicating their potential role as pre-haustorial effectors possibly recognized by the resistant coffee genotype. Another nine genes were significantly induced after haustorium formation in the compatible interaction. Overall, we suggest that this fungus is able to selectively mount its survival strategy with effectors that depend on the host genotype involved in the infection process.
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Affiliation(s)
- Brenda Neves Porto
- Programa de Pós-graduação em Biotecnologia Vegetal, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | - Sandra Marisa Mathioni
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | | | - Laércio Zambolim
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Eunize Maciel Zambolim
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Nicole Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Shawn W. Polson
- Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, Newark, Delaware, United States of America
| | - Thiago Andrade Maia
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Chuming Chen
- Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, Newark, Delaware, United States of America
| | - Modupe Adetunji
- Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, Newark, Delaware, United States of America
| | - Brewster Kingham
- Sequencing and Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Ronaldo José Durigan Dalio
- Instituto Agronômico de Campinas, Centro de Citricultura “Sylvio Moreira”, Cordeirópolis, São Paulo, Brazil
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Qi M, Mei Y, Grayczyk JP, Darben LM, Rieker MEG, Seitz JM, Voegele RT, Whitham SA, Link TI. Candidate Effectors From Uromyces appendiculatus, the Causal Agent of Rust on Common Bean, Can Be Discriminated Based on Suppression of Immune Responses. FRONTIERS IN PLANT SCIENCE 2019; 10:1182. [PMID: 31636645 PMCID: PMC6787271 DOI: 10.3389/fpls.2019.01182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/29/2019] [Indexed: 05/07/2023]
Abstract
Rust fungi are devastating pathogens for several important crop plants. The biotrophic lifestyle of rust fungi requires that they influence their host plants to create a favorable environment for growth and reproduction. Rust fungi secrete a variety of effector proteins that manipulate host target proteins to alter plant metabolism and suppress defense responses. Because of the obligate biotrophic lifestyle of rust fungi, direct evidence for effector function is difficult to obtain, and so suites of experiments utilizing expression in heterologous systems are necessary. Here, we present results from a yeast cell death suppression assay and assays for suppression of PAMP-triggered immunity (PTI) and effector triggered immunity (ETI) based on delivery of effectors through the bacterial type III secretion system. In addition, subcellular localization was tested using transient expression of GFP fusion proteins in Nicotiana benthamiana through Agrobacterium infiltration. We tested 31 representative effector candidates from the devastating common bean rust pathogen Uromyces appendiculatus. These effector candidates were selected based on features of their gene families, most important lineage specificity. We show that several of our effector candidates suppress plant defense. Some of them also belong to families of effector candidates that are present in multiple rust species where their homologs probably also have effector functions. In our analysis of candidate effector mRNA expression, some of those effector candidates that gave positive results in the other assays were not up-regulated during plant infection, indicating that either these proteins have functions at multiple life stages or that strong up-regulation of RNA level in planta may not be as important a criterion for identifying effectors as previously thought. Overall, our pipeline for selecting effector candidates based on sequence features followed by screening assays using heterologous expression systems was successful in discriminating effector candidates. This work lays the foundation for functional characterization of U. appendiculatus effectors, the identification of effector targets, and identification of novel sources for resistance in common bean.
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Affiliation(s)
- Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Yu Mei
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - James P. Grayczyk
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | | | | | - Janina M. Seitz
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Ralf T. Voegele
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Steven A. Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Tobias I. Link
- Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
- *Correspondence: Tobias Link,
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Omidvar V, Dugyala S, Li F, Rottschaefer SM, Miller ME, Ayliffe M, Moscou MJ, Kianian SF, Figueroa M. Detection of Race-Specific Resistance Against Puccinia coronata f. sp. avenae in Brachypodium Species. PHYTOPATHOLOGY 2018; 108:1443-1454. [PMID: 29923800 DOI: 10.1094/phyto-03-18-0084-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in nonhost species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine whether effector-triggered immunity contributes to nonhost resistance to P. coronata f. sp. avenae in Brachypodium spp.
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Affiliation(s)
- Vahid Omidvar
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Sheshanka Dugyala
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Feng Li
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Susan M Rottschaefer
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Marisa E Miller
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Mick Ayliffe
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Matthew J Moscou
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Shahryar F Kianian
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
| | - Melania Figueroa
- First, second, third, fourth, fifth, eighth, and ninth authors: Plant Pathology, University of Minnesota, St. Paul; sixth author: CSIRO Agriculture and Food, ACT, Australia; seventh author: The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, U.K.; eighth author: Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, MN, USA; and ninth author: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul
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Nazareno ES, Li F, Smith M, Park RF, Kianian SF, Figueroa M. Puccinia coronata f. sp. avenae: a threat to global oat production. MOLECULAR PLANT PATHOLOGY 2018; 19:1047-1060. [PMID: 28846186 PMCID: PMC6638059 DOI: 10.1111/mpp.12608] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 05/20/2023]
Abstract
UNLABELLED Puccinia coronata f. sp. avenae (Pca) causes crown rust disease in cultivated and wild oat (Avena spp.). The significant yield losses inflicted by this pathogen make crown rust the most devastating disease in the oat industry. Pca is a basidiomycete fungus with an obligate biotrophic lifestyle, and is classified as a typical macrocyclic and heteroecious fungus. The asexual phase in the life cycle of Pca occurs in oat, whereas the sexual phase takes place primarily in Rhamnus species as the alternative host. Epidemics of crown rust happens in areas with warm temperatures (20-25 °C) and high humidity. Infection by the pathogen leads to plant lodging and shrivelled grain of poor quality. Disease symptoms: Infection of susceptible oat varieties gives rise to orange-yellow round to oblong uredinia (pustules) containing newly formed urediniospores. Pustules vary in size and can be larger than 5 mm in length. Infection occurs primarily on the surfaces of leaves, although occasional symptoms develop in the oat leaf sheaths and/or floral structures, such as awns. Symptoms in resistant oat varieties vary from flecks to small pustules, typically accompanied by chlorotic halos and/or necrosis. The pycnial and aecial stages are mostly present in the leaves of Rhamnus species, but occasionally symptoms can also be observed in petioles, young stems and floral structures. Aecial structures display a characteristic hypertrophy and can differ in size, occasionally reaching more than 5 mm in diameter. Taxonomy: Pca belongs to the kingdom Fungi, phylum Basidiomycota, class Pucciniomycetes, order Pucciniales and family Pucciniaceae. Host range: Puccinia coronata sensu lato can infect 290 species of grass hosts. Pca is prevalent in all oat-growing regions and, compared with other cereal rusts, displays a broad telial host range. The most common grass hosts of Pca include cultivated hexaploid oat (Avena sativa) and wild relatives, such as bluejoint grass, perennial ryegrass and fescue. Alternative hosts include several species of Rhamnus, with R. cathartica (common buckthorn) as the most important alternative host in Europe and North America. CONTROL Most crown rust management strategies involve the use of rust-resistant crop varieties and the application of fungicides. The attainment of the durability of resistance against Pca is difficult as it is a highly variable pathogen with a great propensity to overcome the genetic resistance of varieties. Thus, adult plant resistance is often exploited in oat breeding programmes to develop new crown rust-resistant varieties. Useful website: https://www.ars.usda.gov/midwest-area/st-paul-mn/cereal-disease-lab/docs/cereal-rusts/race-surveys/.
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Affiliation(s)
- Eric S. Nazareno
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Feng Li
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
| | - Madeleine Smith
- Department of Plant PathologyUniversity of Minnesota‐Northwest Research and Outreach CenterCrookstonMN 56716USA
| | - Robert F. Park
- Plant Breeding InstituteThe University of SydneyNarellanNSW2567Australia
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, US Department of Agriculture‐Agricultural Research ServiceSt. PaulMN 55108USA
| | - Melania Figueroa
- Department of Plant PathologyUniversity of MinnesotaSt. PaulMN 55108USA
- Stakman‐Borlaug Center for Sustainable Plant HealthUniversity of MinnesotaSt. PaulMN 55108USA
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Miller ME, Zhang Y, Omidvar V, Sperschneider J, Schwessinger B, Raley C, Palmer JM, Garnica D, Upadhyaya N, Rathjen J, Taylor JM, Park RF, Dodds PN, Hirsch CD, Kianian SF, Figueroa M. De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust. mBio 2018; 9:e01650-17. [PMID: 29463655 PMCID: PMC5821079 DOI: 10.1128/mbio.01650-17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/09/2018] [Indexed: 01/18/2023] Open
Abstract
Oat crown rust, caused by the fungus Pucinnia coronata f. sp. avenae, is a devastating disease that impacts worldwide oat production. For much of its life cycle, P. coronata f. sp. avenae is dikaryotic, with two separate haploid nuclei that may vary in virulence genotype, highlighting the importance of understanding haplotype diversity in this species. We generated highly contiguous de novo genome assemblies of two P. coronata f. sp. avenae isolates, 12SD80 and 12NC29, from long-read sequences. In total, we assembled 603 primary contigs for 12SD80, for a total assembly length of 99.16 Mbp, and 777 primary contigs for 12NC29, for a total length of 105.25 Mbp; approximately 52% of each genome was assembled into alternate haplotypes. This revealed structural variation between haplotypes in each isolate equivalent to more than 2% of the genome size, in addition to about 260,000 and 380,000 heterozygous single-nucleotide polymorphisms in 12SD80 and 12NC29, respectively. Transcript-based annotation identified 26,796 and 28,801 coding sequences for isolates 12SD80 and 12NC29, respectively, including about 7,000 allele pairs in haplotype-phased regions. Furthermore, expression profiling revealed clusters of coexpressed secreted effector candidates, and the majority of orthologous effectors between isolates showed conservation of expression patterns. However, a small subset of orthologs showed divergence in expression, which may contribute to differences in virulence between 12SD80 and 12NC29. This study provides the first haplotype-phased reference genome for a dikaryotic rust fungus as a foundation for future studies into virulence mechanisms in P. coronata f. sp. avenaeIMPORTANCE Disease management strategies for oat crown rust are challenged by the rapid evolution of Puccinia coronata f. sp. avenae, which renders resistance genes in oat varieties ineffective. Despite the economic importance of understanding P. coronata f. sp. avenae, resources to study the molecular mechanisms underpinning pathogenicity and the emergence of new virulence traits are lacking. Such limitations are partly due to the obligate biotrophic lifestyle of P. coronata f. sp. avenae as well as the dikaryotic nature of the genome, features that are also shared with other important rust pathogens. This study reports the first release of a haplotype-phased genome assembly for a dikaryotic fungal species and demonstrates the amenability of using emerging technologies to investigate genetic diversity in populations of P. coronata f. sp. avenae.
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Affiliation(s)
- Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Ying Zhang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Vahid Omidvar
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organization, Agriculture and Food, Perth, WA, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Castle Raley
- Leidos Biomedical Research, Frederick, Maryland, USA
| | - Jonathan M Palmer
- Center for Forest Mycology Research, Northern Research Station, USDA Forest Service, Madison, Wisconsin, USA
| | - Diana Garnica
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Narayana Upadhyaya
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - John Rathjen
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jennifer M Taylor
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - Peter N Dodds
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, Australia
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, USA
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
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14
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Periyannan S, Milne RJ, Figueroa M, Lagudah ES, Dodds PN. An overview of genetic rust resistance: From broad to specific mechanisms. PLoS Pathog 2017; 13:e1006380. [PMID: 28704545 PMCID: PMC5509339 DOI: 10.1371/journal.ppat.1006380] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Sambasivam Periyannan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
- Research School of Biology, The Australian National University, Canberra Australian Capital Territory, Australia
| | - Ricky J. Milne
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Melania Figueroa
- Department of Plant Pathology and The Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Evans S. Lagudah
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Peter N. Dodds
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra, Australian Capital Territory, Australia
- * E-mail:
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