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Jaswal R, Rajarammohan S, Dubey H, Kiran K, Rawal H, Sonah H, Deshmukh R, Sharma TR. Intrinsically Disordered Kiwellin Protein-Like Effectors Target Plant Chloroplasts and are Extensively Present in Rust Fungi. Mol Biotechnol 2024; 66:845-864. [PMID: 37000361 DOI: 10.1007/s12033-023-00717-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/08/2023] [Indexed: 04/01/2023]
Abstract
The effector proteins produced by plant pathogens are one of the essential components of host-pathogen interaction. Despite being important, most of the effector proteins remain unexplored due to the diversity in their primary sequence generated by the high selection pressure of the host immune system. However to maintain the primary function in the infection process, these effectors may tend to maintain their native protein fold to perform the corresponding biological function. In the present study, unannotated candidate secretory effector proteins of sixteen major plant fungal pathogens were analyzed to find the conserved known protein folds using homology, ab initio, and Alpha Fold/Rosetta Fold protein dimensional (3D) structure approaches. Several unannotated candidate effector proteins were found to match various known conserved protein families potentially involved in host defense manipulation in different plant pathogens. Surprisingly a large number of plant Kiwellin proteins fold like secretory proteins (> 100) were found in studied rust fungal pathogens. Many of them were predicted as potential effector proteins. Furthermore, template independent modelling using Alpha Fold/Rosetta Fold analysis and structural comparison of these candidates also predicted them to match with plant Kiwellin proteins. We also found plant Kiwellin matching proteins outside rusts including several non-pathogenic fungi suggesting the broad function of these proteins. One of the highest confidently modeled Kiwellin matching candidates effectors, Pstr_13960 (97.8%), from the Indian P. striiformis race Yr9 was characterized using overexpression, localization, and deletion studies in Nicotiana benthamiana. The Pstr_13960 suppressed the BAX-induced cell death and localized in the chloroplast. Furthermore, the expression of the Kiwellin matching region (Pst_13960_kiwi) alone suppressed the BAX-induced cell death in N. benthamiana despite the change of location to the cytoplasm and nucleus, suggesting the novel function of the Kiwellin core fold in rust fungi. Molecular docking showed that Pstr_13960 can interact with plant Chorismate mutases (CMs) using three loops conserved in plant and rust Kiwellins. Further analysis of Pstr_13960 showed to contain Intrinsically disordered regions (IDRs) in place of the N-terminal β1/β2 region found in plant Kiwellins suggesting the evolution of rust Kiwellins-like effectors (KLEs). Overall, this study reports the presence of a Kiwellin protein-like fold containing a novel effector protein family in rust fungi depicting a classical example of the evolution of effectors at the structure level as Kiwellin effectors show very low significant similarity to plant Kiwellin at the sequence level.
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Affiliation(s)
- Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | | | - Himanshu Dubey
- National Institute On Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kanti Kiran
- National Institute On Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Hukam Rawal
- National Institute On Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 140306, India.
- Division of Crop Science, Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India.
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Holden S, Bakkeren G, Hubensky J, Bamrah R, Abbasi M, Qutob D, de Graaf ML, Kim SH, Kutcher HR, McCallum BD, Randhawa HS, Iqbal M, Uloth K, Burlakoti RR, Brar GS. Uncovering the history of recombination and population structure in western Canadian stripe rust populations through mating type alleles. BMC Biol 2023; 21:233. [PMID: 37880702 PMCID: PMC10601111 DOI: 10.1186/s12915-023-01717-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The population structure of crop pathogens such as Puccinia striiformis f. sp. tritici (Pst), the cause of wheat stripe rust, is of interest to researchers looking to understand these pathogens on a molecular level as well as those with an applied focus such as disease epidemiology. Cereal rusts can reproduce sexually or asexually, and the emergence of novel lineages has the potential to cause serious epidemics such as the one caused by the 'Warrior' lineage in Europe. In a global context, Pst lineages in Canada were not well-characterized and the origin of foreign incursions was not known. Additionally, while some Pst mating type genes have been identified in published genomes, there has been no rigorous assessment of mating type diversity and distribution across the species. RESULTS We used a whole-genome/transcriptome sequencing approach for the Canadian Pst population to identify lineages in their global context and evidence tracing foreign incursions. More importantly: for the first time ever, we identified nine alleles of the homeodomain mating type locus in the worldwide Pst population and show that previously identified lineages exhibit a single pair of these alleles. Consistently with the literature, we find only two pheromone receptor mating type alleles. We show that the recent population shift from the 'PstS1' lineage to the 'PstS1-related' lineage is also associated with the introduction of a novel mating type allele (Pst-b3-HD) to the Canadian population. We also show evidence for high levels of mating type diversity in samples associated with the Himalayan center of diversity for Pst, including a single Canadian race previously identified as 'PstPr' (probable recombinant) which we identify as a foreign incursion, most closely related to isolates sampled from China circa 2015. CONCLUSIONS These data describe a recent shift in the population of Canadian Pst field isolates and characterize homeodomain-locus mating type alleles in the global Pst population which can now be utilized in testing several research questions and hypotheses around sexuality and hybridization in rust fungi.
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Affiliation(s)
- Samuel Holden
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
| | - Guus Bakkeren
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - John Hubensky
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Ramandeep Bamrah
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Mehrdad Abbasi
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada
| | - Dinah Qutob
- Kent State University, Stark Campus, North Canton, OH, USA
| | - Mei-Lan de Graaf
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Sang Hu Kim
- Agriculture and Agri-Food Canada (AAFC), Summerland Research and Development Center, Summerland, BC, Canada
| | - Hadley R Kutcher
- Department of Plant Science/Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Brent D McCallum
- Agriculture and Agri-Food Canada (AAFC), Brandon Research and Development Center, Brandon, MB, Canada
| | - Harpinder S Randhawa
- Agriculture and Agri-Food Canada (AAFC), Lethbridge Research and Development Center, Lethbridge, AB, Canada
| | - Muhammad Iqbal
- Faculty of Agricultural, Life & Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Keith Uloth
- British Columbia Pest Monitoring Network, Dawson Creek, BC, Canada
| | - Rishi R Burlakoti
- Agriculture and Agri-Food Canada (AAFC), Agassiz Research and Development Center, Agassiz, BC, Canada
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, BC, Canada.
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Prasad P, Jain N, Chaudhary J, Thakur RK, Savadi S, Bhardwaj SC, Gangwar OP, Lata C, Adhikari S, Kumar S, Balyan HS, Gupta PK. Candidate effectors for leaf rust resistance gene Lr28 identified through transcriptome and in-silico analysis. Front Microbiol 2023; 14:1143703. [PMID: 37789861 PMCID: PMC10543267 DOI: 10.3389/fmicb.2023.1143703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/31/2023] [Indexed: 10/05/2023] Open
Abstract
Puccinia spp. causing rust diseases in wheat and other cereals secrete several specialized effector proteins into host cells. Characterization of these proteins and their interaction with host's R proteins could greatly help to limit crop losses due to diseases. Prediction of effector proteins by combining the transcriptome analysis and multiple in-silico approaches is gaining importance in revealing the pathogenic mechanism. The present study involved identification of 13 Puccinia triticina (Pt) coding sequences (CDSs), through transcriptome analysis, that were differentially expressed during wheat-leaf rust interaction; and prediction of their effector like features using different in-silico tools. NCBI-BLAST and pathogen-host interaction BLAST (PHI-BLAST) tools were used to annotate and classify these sequences based on their most closely matched counterpart in both the databases. Homology between CDSs and the annotated sequences in the NCBI database ranged from 79 to 94% and with putative effectors of other plant pathogens in PHI-BLAST from 24.46 to 54.35%. Nine of the 13 CDSs had effector-like features according to EffectorP 3.0 (≥0.546 probability of these sequences to be effector). The qRT-PCR expression analysis revealed that the relative expression of all CDSs in compatible interaction (HD2329) was maximum at 11 days post inoculation (dpi) and that in incompatible interactions (HD2329 + Lr28) was maximum at 3 dpi in seven and 9 dpi in five CDSs. These results suggest that six CDSs (>0.8 effector probability as per EffectorP 3.0) could be considered as putative Pt effectors. The molecular docking and MD simulation analysis of these six CDSs suggested that candidate Lr28 protein binds more strongly to candidate effector c14094_g1_i1 to form more stable complex than the remaining five. Further functional characterization of these six candidate effectors should prove useful for a better understanding of wheat-leaf rust interaction. In turn, this should facilitate effector-based leaf rust resistance breeding in wheat.
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Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Rajni Kant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | | | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Charu Lata
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Sneha Adhikari
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, India
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Prasad P, Thakur R, Bhardwaj SC, Savadi S, Gangwar OP, Lata C, Adhikari S, Kumar S, Kundu S, Manjul AS, Prakasha TL, Navathe S, Hegde GM, Game BC, Mishra KK, Khan H, Gupta V, Mishra CN, Kumar S, Kumar S, Singh G. Virulence and genetic analysis of Puccinia graminis tritici in the Indian sub-continent from 2016 to 2022 and evaluation of wheat varieties for stem rust resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1196808. [PMID: 37521927 PMCID: PMC10376725 DOI: 10.3389/fpls.2023.1196808] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), has re-emerged as one of the major concerns for global wheat production since the evolution of Ug99 and other virulent pathotypes of Pgt from East Africa, Europe, Central Asia, and other regions. Host resistance is the most effective, economic, and eco-friendly approach for managing stem rust. Understanding the virulence nature, genetic diversity, origin, distribution, and evolutionary pattern of Pgt pathotypes over time and space is a prerequisite for effectively managing newly emerging Pgt isolates through host resistance. In the present study, we monitored the occurrence of stem rust of wheat in India and neighboring countries from 2016 to 2022, collected 620 single-pustule isolates of Pgt from six states of India and Nepal, analyzed them on Indian stem rust differentials, and determined their virulence phenotypes and molecular genotypes. The Ug99 type of pathotypes did not occur in India. Pathotypes 11 and 40A were most predominant during these years. Virulence phenotyping of these isolates identified 14 Pgt pathotypes, which were genotyped using 37 Puccinia spp.-specific polymorphic microsatellites, followed by additional phylogenetic analyses using DARwin. These analyses identified three major molecular groups, demonstrating fewer lineages, clonality, and long-distance migration of Pgt isolates in India. Fourteen of the 40 recently released Indian wheat varieties exhibited complete resistance to all 23 Pgt pathotypes at the seedling stage. Twelve Sr genes were postulated in 39 varieties based on their seedling response to Pgt pathotypes. The values of slow rusting parameters i.e. coefficient of infection, area under disease progress curve, and infection rates, assessed at adult plant stage at five geographically different locations during two crop seasons, indicated the slow rusting behavior of several varieties. Six Sr genes (Sr2, Sr57, Sr58, Sr24, Sr31, and Sr38) were identified in 24 wheat varieties using molecular markers closely linked to these genes. These findings will guide future breeding programs toward more effective management of wheat stem rust.
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Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Rajnikant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - S. C. Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Siddanna Savadi
- Division of Crop Improvement, ICAR-Directorate of Cashew Research, Puttur, Karnataka, India
| | - O. P. Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Charu Lata
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Sneha Adhikari
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - Sonu Kundu
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - A. S. Manjul
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, India
| | - T. L. Prakasha
- ICAR-Indian Agricultural Research Institute, Indore, Regional Station, Madhya Pradesh, India
| | - Sudhir Navathe
- Genetics and Plant Breeding Group, Agharkar Research Institute, Pune, India
| | - G. M. Hegde
- All India Coordinated Research Project on Wheat & Barley, University of Agricultural Sciences, Dharwad, Karnataka, India
| | - B. C. Game
- Mahatma Phule Krishi Vidyapeeth, Rahuri, Agricultural Research Station, Niphad, Maharashtra, India
| | - K. K. Mishra
- JNKVV, Zonal Agricultural Research Station, Powarkheda, Narmadapuram, Madhya Pradesh, India
| | - Hanif Khan
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Vikas Gupta
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - C. N. Mishra
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Satish Kumar
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Sudheer Kumar
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - Gyanendra Singh
- Crop Improvement Division, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
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5
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Liu R, Lv X, Wang X, Yang L, Cao J, Dai Y, Wu W, Wu Y. Integrative analysis of the multi-omics reveals the stripe rust fungus resistance mechanism of the TaPAL in wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1174450. [PMID: 37342140 PMCID: PMC10277697 DOI: 10.3389/fpls.2023.1174450] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/05/2023] [Indexed: 06/22/2023]
Abstract
Wheat is one of the major food crops in the world. However, stripe rust fungus significantly decreases wheat yield and quality. In the present study, transcriptomic and metabolite analyses were conducted in R88 (resistant line) and CY12 (susceptible cultivar) during Pst-CYR34 infection due to the limited availability of information regarding the underlying mechanisms governing wheat-pathogen interactions. The results revealed that Pst infection promoted the genes and metabolites involved in phenylpropanoid biosynthesis. The key enzyme gene TaPAL to regulate lignin and phenolic synthesis has a positive resistance contribution to Pst in wheat, which was verified by the virus-induced gene silencing (VIGS) technique. The distinctive resistance of R88 is regulated by the selective expression of genes involved in the fine-tuning of wheat-Pst interactions. Furthermore, metabolome analysis suggested that lignin biosynthesis-related metabolite accumulation was significantly affected by Pst. These results help to elucidate the regulatory networks of wheat-Pst interactions and pave the way for durable resistance breeding in wheat, which may ease environmental and food crises around the world.
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Affiliation(s)
- Rong Liu
- Faculty of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Xue Lv
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaohua Wang
- Faculty of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Li Yang
- Wuhan Metware Biotechnology, Wuhan, Wuhan, China
| | - Jun Cao
- Faculty of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Ya Dai
- Faculty of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Wang Wu
- Faculty of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Annan EN, Huang L. Molecular Mechanisms of the Co-Evolution of Wheat and Rust Pathogens. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091809. [PMID: 37176866 PMCID: PMC10180972 DOI: 10.3390/plants12091809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
Wheat (Triticum spp.) is a cereal crop domesticated >8000 years ago and the second-most-consumed food crop nowadays. Ever since mankind has written records, cereal rust diseases have been a painful awareness in antiquity documented in the Old Testament (about 750 B.C.). The pathogen causing the wheat stem rust disease is among the first identified plant pathogens in the 1700s, suggesting that wheat and rust pathogens have co-existed for thousands of years. With advanced molecular technologies, wheat and rust genomes have been sequenced, and interactions between the host and the rust pathogens have been extensively studied at molecular levels. In this review, we summarized the research at the molecular level and organized the findings based on the pathogenesis steps of germination, penetration, haustorial formation, and colonization of the rusts to present the molecular mechanisms of the co-evolution of wheat and rust pathogens.
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Affiliation(s)
- Emmanuel N Annan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
| | - Li Huang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717-3150, USA
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7
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Li S, Wang Z, Gao M, Li T, Cui X, Zu J, Sang S, Fan W, Zhang H. Intraspecific Comparative Analysis Reveals Genomic Variation of Didymella arachidicola and Pathogenicity Factors Potentially Related to Lesion Phenotype. BIOLOGY 2023; 12:biology12030476. [PMID: 36979167 PMCID: PMC10045276 DOI: 10.3390/biology12030476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Didymella arachidicola is one of the most important fungal pathogens, causing foliar disease and leading to severe yield losses of peanuts (Arachis hypogaea L.) in China. Two main lesion phenotypes of peanut web blotch have been identified as reticulation type (R type) and blotch type (B type). As no satisfactory reference genome is available, the genomic variations and pathogenicity factors of D. arachidicola remain to be revealed. In the present study, we collected 41 D. arachidicola isolates from 26 geographic locations across China (33 for R type and 8 for B type). The chromosome-scale genome of the most virulent isolate (YY187) was assembled as a reference using PacBio and Hi-C technologies. In addition, we re-sequenced 40 isolates from different sampling sites. Genome-wide alignments showed high similarity among the genomic sequences from the 40 isolates, with an average mapping rate of 97.38%. An average of 3242 SNPs and 315 InDels were identified in the genomic variation analysis, which revealed an intraspecific polymorphism in D. arachidicola. The comparative analysis of the most and least virulent isolates generated an integrated gene set containing 512 differential genes. Moreover, 225 genes individually or simultaneously harbored hits in CAZy-base, PHI-base, DFVF, etc. Compared with the R type reference, the differential gene sets from all B type isolates identified 13 shared genes potentially related to lesion phenotype. Our results reveal the intraspecific genomic variation of D. arachidicola isolates and pathogenicity factors potentially related to different lesion phenotypes. This work sets a genomic foundation for understanding the mechanisms behind genomic diversity driving different pathogenic phenotypes of D. arachidicola.
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Affiliation(s)
- Shaojian Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Meng Gao
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Tong Li
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Xiaowei Cui
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Junhuai Zu
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Suling Sang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Wanwan Fan
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
| | - Haiyan Zhang
- Institute of Plant Protection, Henan Key Laboratory of Crop Pest Control, International Joint Research Laboratory for Crop Protection of Henan, Key Laboratory of Integrated Pest Management on Crops in Southern Region of North China, Henan Academy of Agricultural Sciences, Zhengzhou 450000, China
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8
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Li Y, Dai J, Zhang T, Wang B, Zhang S, Wang C, Zhang J, Yao Q, Li M, Li C, Peng Y, Cao S, Zhan G, Tao F, Gao H, Huang W, Feng X, Bai Y, Qucuo Z, Shang H, Huang C, Liu W, Zhan J, Xu X, Chen X, Kang Z, Hu X. Genomic analysis, trajectory tracking, and field surveys reveal sources and long-distance dispersal routes of wheat stripe rust pathogen in China. PLANT COMMUNICATIONS 2023:100563. [PMID: 36809881 PMCID: PMC10363508 DOI: 10.1016/j.xplc.2023.100563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/08/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Identifying sources of phytopathogen inoculum and determining their contributions to disease outbreaks are essential for predicting disease development and establishing control strategies. Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust, is an airborne fungal pathogen with rapid virulence variation that threatens wheat production through its long-distance migration. Because of wide variation in geographic features, climatic conditions, and wheat production systems, Pst sources and related dispersal routes in China are largely unclear. In the present study, we performed genomic analyses of 154 Pst isolates from all major wheat-growing regions in China to determine Pst population structure and diversity. Through trajectory tracking, historical migration studies, genetic introgression analyses, and field surveys, we investigated Pst sources and their contributions to wheat stripe rust epidemics. We identified Longnan, the Himalayan region, and the Guizhou Plateau, which contain the highest population genetic diversities, as the Pst sources in China. Pst from Longnan disseminates mainly to eastern Liupan Mountain, the Sichuan Basin, and eastern Qinghai; that from the Himalayan region spreads mainly to the Sichuan Basin and eastern Qinghai; and that from the Guizhou Plateau migrates mainly to the Sichuan Basin and the Central Plain. These findings improve our current understanding of wheat stripe rust epidemics in China and emphasize the need for managing stripe rust on a national scale.
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Affiliation(s)
- Yuxiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Jichen Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Taixue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Siyue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Conghao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Jiguang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Qiang Yao
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province, Academy of Agriculture and Forestry Science, Qinghai University, Xining, Qinghai, China
| | - Mingju Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuelin Peng
- Department of Plant Pathology, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Shiqin Cao
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Fei Tao
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Haifeng Gao
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Weili Huang
- Xi'an Huang's Bio-technology Company Ltd, Xi'an, Shaanxi, China
| | - Xiaojun Feng
- Shaanxi Plant Protection Extension Station, Xi'an, Shaanxi, China
| | - Yingwen Bai
- Baoji Plant Protection Extension Station, Baoji, Shaanxi, China
| | - Zhuoma Qucuo
- Department of Plant Pathology, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Hongsheng Shang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Chong Huang
- National Agricultural Technology Extension and Service Center, Ministry of Agriculture, Beijing, China
| | - Wancai Liu
- National Agricultural Technology Extension and Service Center, Ministry of Agriculture, Beijing, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Xiangming Xu
- Pest & Pathogen Ecology, NIAB EMR, East Malling, West Malling, Kent, UK
| | - Xianming Chen
- Agricultural Research Service, United States Department of Agriculture and Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China.
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China.
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9
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Wu N, Ozketen AC, Cheng Y, Jiang W, Zhou X, Zhao X, Guan Y, Xiang Z, Akkaya MS. Puccinia striiformis f. sp. tritici effectors in wheat immune responses. FRONTIERS IN PLANT SCIENCE 2022; 13:1012216. [PMID: 36420019 PMCID: PMC9677129 DOI: 10.3389/fpls.2022.1012216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The obligate biotrophic fungus Puccinia striiformis f. sp. tritici, which causes yellow (stripe) rust disease, is among the leading biological agents resulting in tremendous yield losses on global wheat productions per annum. The combatting strategies include, but are not limited to, fungicide applications and the development of resistant cultivars. However, evolutionary pressure drives rapid changes, especially in its "effectorome" repertoire, thus allowing pathogens to evade and breach resistance. The extracellular and intracellular effectors, predominantly secreted proteins, are tactical arsenals aiming for many defense processes of plants. Hence, the identity of the effectors and the molecular mechanisms of the interactions between the effectors and the plant immune system have long been targeted in research. The obligate biotrophic nature of P. striiformis f. sp. tritici and the challenging nature of its host, the wheat, impede research on this topic. Next-generation sequencing and novel prediction algorithms in bioinformatics, which are accompanied by in vitro and in vivo validation approaches, offer a speedy pace for the discovery of new effectors and investigations of their biological functions. Here, we briefly review recent findings exploring the roles of P. striiformis f. sp. tritici effectors together with their cellular/subcellular localizations, host responses, and interactors. The current status and the challenges will be discussed. We hope that the overall work will provide a broader view of where we stand and a reference point to compare and evaluate new findings.
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Affiliation(s)
- Nan Wu
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | | | - Yu Cheng
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Wanqing Jiang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xuan Zhou
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xinran Zhao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Yaorong Guan
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Zhaoxia Xiang
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Mahinur S. Akkaya
- School of Bioengineering, Dalian University of Technology, Dalian, China
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10
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Yadav IS, Bhardwaj SC, Kaur J, Singla D, Kaur S, Kaur H, Rawat N, Tiwari VK, Saunders D, Uauy C, Chhuneja P. Whole genome resequencing and comparative genome analysis of three Puccinia striiformis f. sp. tritici pathotypes prevalent in India. PLoS One 2022; 17:e0261697. [PMID: 36327308 PMCID: PMC9632834 DOI: 10.1371/journal.pone.0261697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Stripe rust disease of wheat, caused by Puccinia striiformis f. sp. tritici, (Pst) is one of the most serious diseases of wheat worldwide. In India, virulent stripe rust races have been constantly evolving in the North-Western Plains Zone leading to the failure of some of the most widely grown resistant varieties in the region. With the goal of studying the recent evolution of virulent races in this region, we conducted whole-genome re-sequencing of three prevalent Indian Pst pathotypes Pst46S119, Pst78S84 and Pst110S119. We assembled 58.62, 58.33 and 55.78 Mb of Pst110S119, Pst46S119 and Pst78S84 genome, respectively and found that pathotypes were highly heterozygous. Comparative phylogenetic analysis indicated the recent evolution of pathotypes Pst110S119 and Pst78S84 from Pst46S119. Pathogenicity-related genes classes (CAZyme, proteases, effectors, and secretome proteins) were identified and found to be under positive selection. Higher rate of gene families expansion were also observed in the three pathotypes. A strong association between the effector genes and transposable elements may be the source of the rapid evolution of these strains. Phylogenetic analysis differentiated the Indian races in this study from other known United States, European, African, and Asian races. Diagnostic markers developed for the identification of three Pst pathotypes will help tracking of yellow rust at farmers field and strategizing resistance gene deployment.
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Affiliation(s)
- Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - S. C. Bhardwaj
- Regional Station, Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, India
| | - Jaspal Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Harmandeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland College Park, College Park, Maryland, United States of America
| | - Vijay Kumar Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland College Park, College Park, Maryland, United States of America
| | - Diane Saunders
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- * E-mail:
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11
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Xia C, Qiu A, Wang M, Liu T, Chen W, Chen X. Current Status and Future Perspectives of Genomics Research in the Rust Fungi. Int J Mol Sci 2022; 23:ijms23179629. [PMID: 36077025 PMCID: PMC9456177 DOI: 10.3390/ijms23179629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Rust fungi in Pucciniales have caused destructive plant epidemics, have become more aggressive with new virulence, rapidly adapt to new environments, and continually threaten global agriculture. With the rapid advancement of genome sequencing technologies and data analysis tools, genomics research on many of the devastating rust fungi has generated unprecedented insights into various aspects of rust biology. In this review, we first present a summary of the main findings in the genomics of rust fungi related to variations in genome size and gene composition between and within species. Then we show how the genomics of rust fungi has promoted our understanding of the pathogen virulence and population dynamics. Even with great progress, many questions still need to be answered. Therefore, we introduce important perspectives with emphasis on the genome evolution and host adaptation of rust fungi. We believe that the comparative genomics and population genomics of rust fungi will provide a further understanding of the rapid evolution of virulence and will contribute to monitoring the population dynamics for disease management.
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Affiliation(s)
- Chongjing Xia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
| | - Age Qiu
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Taiguo Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430, USA
- Correspondence: (C.X.); (X.C.); Tel.: +86-13880134318 (C.X.); +1-509-335-8086 (X.C.)
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12
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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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13
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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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Prasad P, Thakur RK, Savadi S, Bhardwaj SC, Gangwar OP, Lata C, Adhikari S, Kumar S. Genetic Diversity and Population Structure Reveal Cryptic Genetic Variation and Long Distance Migration of Puccinia graminis f. sp. tritici in the Indian Subcontinent. Front Microbiol 2022; 13:842106. [PMID: 35495673 PMCID: PMC9044083 DOI: 10.3389/fmicb.2022.842106] [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: 12/23/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022] Open
Abstract
Stem rust caused by Puccinia graminis f. sp. tritici (Pgt) is a devastating disease of wheat worldwide since time immemorial. Several wheat stem rust outbreaks have been reported worldwide including India. Approximately 7 mha wheat area in central and peninsular India is highly vulnerable to stem rust epidemics. In this study, a repository of 29 single genotype uredospore pathotypes, representing five geographical regions, was characterized by investigating their virulence phenotype and simple sequence repeat (SSR) genotypes using 37 reproducible polymorphic SSR markers, 32 of which had ≥ 0.50 polymorphic information content (PIC) value. Virulence phenotypes were used to evaluate the virulence frequency (VF) and construct a hypothetical evolutionary hierarchy of these pathotypes. We projected seven lineages to explain the evolutionary pattern of the Pgt population. The VF of these pathotypes ranged between 0% and 100%. The virulence-based neighbor-joining (NJ) cluster analysis grouped Pgt pathotypes into five virulence groups. Likewise, five molecular groups were categorized using molecular genotypes. The molecular grouping was supported by principal coordinate analysis (PCoA), which revealed 25% of the cumulative variance contributed by the first two axes. Analysis of molecular variance (AMOVA) revealed 8 and 92% of the variation among and within the populations, respectively. The Mantel test confirmed a positive but weak correlation (R 2 = 0.15) between virulence phenotypes and SSR genotypes. The highest and lowest values of different genetic diversity parameters (Na, Ne, I, He, uHe, and %P) revealed maximum and minimum variability in the Pgt population from Maharashtra and Uttar Pradesh, respectively. The population structure analysis clustered 29 Pgt pathotypes into two subpopulations and an admixture. Our results demonstrated that there was significant genetic diversity among Pgt pathotypes resulting from their long-distance dispersal ability complemented by gene flow. These findings provide insights into the virulence patterns, genetic variations, and possible evolution of Pgt pathotypes, which would support strategic stem rust resistance breeding.
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Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Rajni Kant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | | | | | - Om Prakash Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Charu Lata
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Sneha Adhikari
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, India
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15
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Kiran K, Rawal HC, Dubey H, Jaswal R, Bhardwaj SC, Deshmukh R, Sharma TR. Genome-Wide Analysis of Four Pathotypes of Wheat Rust Pathogen ( Puccinia graminis) Reveals Structural Variations and Diversifying Selection. J Fungi (Basel) 2021; 7:701. [PMID: 34575739 PMCID: PMC8468629 DOI: 10.3390/jof7090701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/19/2021] [Accepted: 08/21/2021] [Indexed: 12/28/2022] Open
Abstract
Diseases caused by Puccinia graminis are some of the most devastating diseases of wheat. Extensive genomic understanding of the pathogen has proven helpful not only in understanding host- pathogen interaction but also in finding appropriate control measures. In the present study, whole-genome sequencing of four diverse P. graminis pathotypes was performed to understand the genetic variation and evolution. An average of 63.5 Gb of data per pathotype with about 100× average genomic coverage was achieved with 100-base paired-end sequencing performed with Illumina Hiseq 1000. Genome structural annotations collectively predicted 9273 functional proteins including ~583 extracellular secreted proteins. Approximately 7.4% of the genes showed similarity with the PHI database which is suggestive of their significance in pathogenesis. Genome-wide analysis demonstrated pathotype 117-6 as likely distinct and descended through a different lineage. The 3-6% more SNPs in the regulatory regions and 154 genes under positive selection with their orthologs and under negative selection in the other three pathotypes further supported pathotype 117-6 to be highly diverse in nature. The genomic information generated in the present study could serve as an important source for comparative genomic studies across the genus Puccinia and lead to better rust management in wheat.
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Affiliation(s)
- Kanti Kiran
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; (K.K.); (H.C.R.); (H.D.); (R.J.)
| | - Hukam C. Rawal
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; (K.K.); (H.C.R.); (H.D.); (R.J.)
| | - Himanshu Dubey
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; (K.K.); (H.C.R.); (H.D.); (R.J.)
| | - Rajdeep Jaswal
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; (K.K.); (H.C.R.); (H.D.); (R.J.)
| | - Subhash C. Bhardwaj
- Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Shimla 171002, India;
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute, Punjab 140306, India;
| | - Tilak Raj Sharma
- Pusa Campus, ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; (K.K.); (H.C.R.); (H.D.); (R.J.)
- Division of Crop Science, ICAR-Indian Council of Agricultural Research, New Delhi 110001, India
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16
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Wyka SA, Mondo SJ, Liu M, Dettman J, Nalam V, Broders KD. Whole-Genome Comparisons of Ergot Fungi Reveals the Divergence and Evolution of Species within the Genus Claviceps Are the Result of Varying Mechanisms Driving Genome Evolution and Host Range Expansion. Genome Biol Evol 2021; 13:evaa267. [PMID: 33512490 PMCID: PMC7883665 DOI: 10.1093/gbe/evaa267] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 12/26/2022] Open
Abstract
The genus Claviceps has been known for centuries as an economically important fungal genus for pharmacology and agricultural research. Only recently have researchers begun to unravel the evolutionary history of the genus, with origins in South America and classification of four distinct sections through ecological, morphological, and metabolic features (Claviceps sects. Citrinae, Paspalorum, Pusillae, and Claviceps). The first three sections are additionally characterized by narrow host range, whereas section Claviceps is considered evolutionarily more successful and adaptable as it has the largest host range and biogeographical distribution. However, the reasons for this success and adaptability remain unclear. Our study elucidates factors influencing adaptability by sequencing and annotating 50 Claviceps genomes, representing 21 species, for a comprehensive comparison of genome architecture and plasticity in relation to host range potential. Our results show the trajectory from specialized genomes (sects. Citrinae and Paspalorum) toward adaptive genomes (sects. Pusillae and Claviceps) through colocalization of transposable elements around predicted effectors and a putative loss of repeat-induced point mutation resulting in unconstrained tandem gene duplication coinciding with increased host range potential and speciation. Alterations of genomic architecture and plasticity can substantially influence and shape the evolutionary trajectory of fungal pathogens and their adaptability. Furthermore, our study provides a large increase in available genomic resources to propel future studies of Claviceps in pharmacology and agricultural research, as well as, research into deeper understanding of the evolution of adaptable plant pathogens.
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Affiliation(s)
- Stephen A Wyka
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Stephen J Mondo
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
- U.S. Department of Energy Joint Genome Institute, Berkeley, California, USA
| | - Miao Liu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jeremy Dettman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Vamsi Nalam
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Kirk D Broders
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
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17
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Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina. Genes (Basel) 2020; 11:genes11091107. [PMID: 32967372 PMCID: PMC7564353 DOI: 10.3390/genes11091107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/18/2020] [Indexed: 11/17/2022] Open
Abstract
The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and identify candidate avirulence genes. Using a long-read based de novo genome assembly of an isolate of Pt ('Pt104') as the reference, whole-genome resequencing data of 12 Pt pathotypes derived from three lineages Pt104, Pt53, and Pt76 were analyzed. Candidate avirulence genes were identified by correlating virulence profiles with small variants (SNP and InDel) and CNV, and RNA-seq data of an additional three Pt isolates to validate expression of genes encoding secreted proteins (SPs). Out of the annotated 29,043 genes, 2392 genes were selected as SP genes with detectable expression levels. Small variant comparisons between the isolates identified 27-40 candidates and CNV analysis identified 14-31 candidates for each Avr gene, which when combined, yielded the final 40, 64, and 69 candidates for AvrLr1, AvrLr15, and AvrLr24, respectively. Taken together, our results will facilitate future work on experimental validation and cloning of Avr genes. In addition, the integrated framework of data analysis that we have developed and reported provides a more comprehensive approach for Avr gene mining than is currently available.
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18
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Jaswal R, Rajarammohan S, Dubey H, Sharma TR. Smut fungi as a stratagem to characterize rust effectors: opportunities and challenges. World J Microbiol Biotechnol 2020; 36:150. [PMID: 32924088 DOI: 10.1007/s11274-020-02927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/05/2020] [Indexed: 11/30/2022]
Abstract
The rust pathogens are one of the most complex fungi in the Basidiomycetes. The development of genomic resources for rust and other plant pathogens has opened the opportunities for functional genomics of fungal genes. Despite significant progress in the field of fungal genomics, functional characterization of the genome components has lacked, especially for the rust pathogens. Their obligate nature and lack of standard stable transformation protocol are the primary reasons for rusts to be one of the least explored genera despite its significance. In the recently sequenced rust genomes, a vast catalogue of predicted effectors and pathogenicity genes have been reported. However, most of these candidate genes remained unexplored due to the lack of suitable characterization methods. The heterologous expression of putative effectors in Nicotiana benthamiana and Arabidopsis thaliana has proved to be a rapid screening method for identifying the role of these effectors in virulence. However, no fungal system has been used for the functional validation of these candidate genes. The smuts, from the evolutionary point of view, are closely related to the rust pathogens. Moreover, they have been widely studied and hence could be a suitable model system for expressing rust fungal genes heterologously. The genetic manipulation methods for smuts are also well standardized. Complementation assays can be used for functional validation of the homologous genes present in rust and smut fungal pathogens, while the species-specific proteins can be expressed in the mutant strains of smut pathogens having reduced or no virulence for virulence analysis. We propose that smuts, especially Ustilago maydis, may prove to be a good model system to characterize rust effector proteins in the absence of methods to manipulate the rust genomes directly.
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Affiliation(s)
- Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), PO Manauli, S.A.S. Nagar, Mohali, Punjab, 140306, India
| | - Sivasubramanian Rajarammohan
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), PO Manauli, S.A.S. Nagar, Mohali, Punjab, 140306, India
| | - Himanshu Dubey
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - T R Sharma
- National Agri-Food Biotechnology Institute (NABI), Sector-81 (Knowledge City), PO Manauli, S.A.S. Nagar, Mohali, Punjab, 140306, India.
- Crop Science Division, Indian Council of Agricultural Research, New Delhi, 110001, India.
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Carmona M, Sautua F, Pérez-Hérnandez O, Reis EM. Role of Fungicide Applications on the Integrated Management of Wheat Stripe Rust. FRONTIERS IN PLANT SCIENCE 2020; 11:733. [PMID: 32582257 PMCID: PMC7296138 DOI: 10.3389/fpls.2020.00733] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/07/2020] [Indexed: 05/14/2023]
Abstract
First described in Europe in 1777, stripe rust (SR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss (Pst) is one of the most important and destructive diseases of wheat worldwide. Until 2000, SR was mainly endemic to cooler regions, but since then, new aggressive strains have emerged, spread intercontinentally, and caused severe epidemics in warmer regions across the world. This has put SR as a disease that poses a threat to the world food security. At present, the preferred strategy for control of SR is the access to wheat cultivars with adequate levels of SR resistance. However, wheat breeding programs are not sufficiently advanced to cope with the recently emerged Pst strains. Under this scenario, foliar fungicide applications have become an important component of SR management, but information on the effects of fungicide applications on SR control and wheat cultivar yield response is scarce. This review seeks to provide an overview of the impact and role of fungicides on SR management. With focus on wheat management in the major wheat-growing regions of the world, the review addresses: (a) the efficacy of different fungicide active ingredients, optimal fungicide timing and number of applications in controlling SR, and (b) the impact of fungicide on wheat grain yield response. Inclusion of fungicides in an integrated crop management approach is discussed.
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Affiliation(s)
- Marcelo Carmona
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Francisco Sautua
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Oscar Pérez-Hérnandez
- School of Agricultural Sciences, Northwest Missouri State University, Maryville, MO, United States
| | - Erlei M. Reis
- Escuela Para Graduados “Alberto Soriano”, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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20
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Wu JQ, Dong C, Song L, Park RF. Long-Read-Based de novo Genome Assembly and Comparative Genomics of the Wheat Leaf Rust Pathogen Puccinia triticina Identifies Candidates for Three Avirulence Genes. Front Genet 2020; 11:521. [PMID: 32582280 PMCID: PMC7287177 DOI: 10.3389/fgene.2020.00521] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/29/2020] [Indexed: 11/18/2022] Open
Abstract
Leaf rust, caused by Puccinia triticina (Pt), is one of the most devastating diseases of wheat, affecting production in nearly all wheat-growing regions worldwide. Despite its economic importance, genomic resources for Pt are very limited. In the present study, we have used long-read sequencing (LRS) and the pipeline of FALCON and FALCON-Unzip (v4.1.0) to carry out the first LRS-based de novo genome assembly for Pt. Using 22.4-Gb data with an average read length of 11.6 kb and average coverage of 150-fold, we generated a genome assembly for Pt104 [strain 104-2,3,(6),(7),11; isolate S423], considered to be the founding isolate of a clonal lineage of Pt in Australia. The Pt104 genome contains 162 contigs with a total length of 140.5 Mb and N50 of 2 Mb, with the associated haplotigs providing haplotype information for 91% of the genome. This represents the best quality of Pt genome assembly to date, which reduces the contig number by 91-fold and improves the N50 by 4-fold as compared to the previous Pt race1 assembly. An annotation pipeline that combined multiple lines of evidence including the transcriptome assemblies derived from RNA-Seq, previously identified expressed sequence tags and Pt race 1 protein sequences predicted 29,043 genes for Pt104 genome. Based on the presence of a signal peptide, no transmembrane segment, and no target location to mitochondria, 2,178 genes were identified as secreted proteins (SPs). Whole-genome sequencing (Illumina paired-end) was performed for Pt104 and six additional strains with differential virulence profile on the wheat leaf rust resistance genes Lr26, Lr2a, and Lr3ka. To identify candidates for the corresponding avirulence genes AvrLr26, AvrLr2a, and AvrLr3ka, genetic variation within each strain was first identified by mapping to the Pt104 genome. Variants within predicted SP genes between the strains were then correlated to the virulence profiles, identifying 38, 31, and 37 candidates for AvrLr26, AvrLr2a, and AvrLr3ka, respectively. The identification of these candidate genes lays a good foundation for future studies on isolating these avirulence genes, investigating the molecular mechanisms underlying host-pathogen interactions, and the development of new diagnostic tools for pathogen monitoring.
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Affiliation(s)
| | | | | | - Robert F. Park
- Plant Breeding Institute, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
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21
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Parisi M, Alioto D, Tripodi P. Overview of Biotic Stresses in Pepper ( Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics. Int J Mol Sci 2020; 21:E2587. [PMID: 32276403 PMCID: PMC7177692 DOI: 10.3390/ijms21072587] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 12/16/2022] Open
Abstract
Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers' demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.
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Affiliation(s)
- Mario Parisi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, Italy;
| | - Daniela Alioto
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici, Naples, Italy;
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano Faiano, Italy;
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22
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Li Y, Xia C, Wang M, Yin C, Chen X. Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates. BMC Genomics 2020; 21:247. [PMID: 32197579 PMCID: PMC7085141 DOI: 10.1186/s12864-020-6677-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 03/13/2020] [Indexed: 12/30/2022] Open
Abstract
Background The stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), threats world wheat production. Resistance to Pst is often overcome by pathogen virulence changes, but the mechanisms of variation are not clearly understood. To determine the role of mutation in Pst virulence changes, in previous studies 30 mutant isolates were developed from a least virulent isolate using ethyl methanesulfonate (EMS) mutagenesis and phenotyped for virulence changes. The progenitor isolate was sequenced, assembled and annotated for establishing a high-quality reference genome. In the present study, the 30 mutant isolates were sequenced and compared to the wide-type isolate to determine the genomic variation and identify candidates for avirulence (Avr) genes. Results The sequence reads of the 30 mutant isolates were mapped to the wild-type reference genome to identify genomic changes. After selecting EMS preferred mutations, 264,630 and 118,913 single nucleotide polymorphism (SNP) sites and 89,078 and 72,513 Indels (Insertion/deletion) were detected among the 30 mutant isolates compared to the primary scaffolds and haplotigs of the wild-type isolate, respectively. Deleterious variants including SNPs and Indels occurred in 1866 genes. Genome wide association analysis identified 754 genes associated with avirulence phenotypes. A total of 62 genes were found significantly associated to 16 avirulence genes after selection through six criteria for putative effectors and degree of association, including 48 genes encoding secreted proteins (SPs) and 14 non-SP genes but with high levels of association (P ≤ 0.001) to avirulence phenotypes. Eight of the SP genes were identified as avirulence-associated effectors with high-confidence as they met five or six criteria used to determine effectors. Conclusions Genome sequence comparison of the mutant isolates with the progenitor isolate unraveled a large number of mutation sites along the genome and identified high-confidence effector genes as candidates for avirulence genes in Pst. Since the avirulence gene candidates were identified from associated SNPs and Indels caused by artificial mutagenesis, these avirulence gene candidates are valuable resources for elucidating the mechanisms of the pathogen pathogenicity, and will be studied to determine their functions in the interactions between the wheat host and the Pst pathogen.
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Affiliation(s)
- Yuxiang Li
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Chongjing Xia
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA. .,USDA-ARS, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA, 99164-6430, USA.
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Prasad P, Savadi S, Bhardwaj SC, Gupta PK. The progress of leaf rust research in wheat. Fungal Biol 2020; 124:537-550. [PMID: 32448445 DOI: 10.1016/j.funbio.2020.02.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/25/2023]
Abstract
Leaf rust (also called brown rust) in wheat, caused by fungal pathogen Puccinia triticina Erikss. (Pt) is one of the major constraints in wheat production worldwide. Pt is widespread with diverse population structure and undergoes rapid evolution to produce new virulent races against resistant cultivars that are regularly developed to provide resistance against the prevailing races of the pathogen. Occasionally, the disease may also take the shape of an epidemic in some wheat-growing areas causing major economic losses. In the recent past, substantial progress has been made in characterizing the sources of leaf rust resistance including non-host resistance (NHR). Progress has also been made in elucidating the population biology of Pt and the mechanisms of wheat-Pt interaction. So far, ∼80 leaf rust resistance genes (Lr genes) have been identified and characterized; some of them have also been used for the development of resistant wheat cultivars. It has also been shown that a gene-for-gene relationship exists between individual wheat Lr genes and the corresponding Pt Avr genes so that no Lr gene can provide resistance unless the prevailing race of the pathogen carries the corresponding Avr gene. Several Lr genes have also been cloned and their products characterized, although no Avr gene corresponding a specific Lr gene has so far been identified. However, several candidate effectors for Pt have been identified and functionally characterized using genome-wide analyses, transcriptomics, RNA sequencing, bimolecular fluorescence complementation (BiFC), virus-induced gene silencing (VIGS), transient expression and other approaches. This review summarizes available information on different aspects of the pathogen Pt, genetics/genomics of leaf rust resistance in wheat including cloning and characterization of Lr genes and epigenetic regulation of disease resistance.
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Affiliation(s)
- Pramod Prasad
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Siddanna Savadi
- ICAR-Directorate of Cashew Research, Puttur, Karnataka, 574202, India
| | - S C Bhardwaj
- Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India.
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24
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Abstract
It is challenging to sequence and assemble genomes of obligate plant pathogens and microorganisms because of limited amounts of DNA, comparatively large genomes and high numbers of repeat regions. We sequenced the 1.2 gigabase genome of an obligate rust fungus, Austropuccinia psidii, the cause of rust on Myrtaceae, with a Chromium 10X library. This technology has mostly been applied for single-cell sequencing in immunological studies of mammals. We compared scaffolds of a genome assembled from the Chromium library with one assembled from combined paired-end and mate-pair libraries, sequenced with Illumina HiSeq. Chromium 10X provided a superior assembly, in terms of number of scaffolds, N50 and number of genes recovered. It required less DNA than other methods and was sequenced and assembled at a lower cost. Chromium sequencing could provide a solution to sequence and assemble genomes of obligate plant pathogens where the amount of available DNA is a limiting factor.
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25
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Roy A, van Staden J. Insights into the riddles of codon usage patterns and codon context signatures in fungal genus
Puccinia
, a persistent threat to global agriculture. J Cell Biochem 2019; 120:19555-19566. [DOI: 10.1002/jcb.29263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/06/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Ayan Roy
- Research Centre for Plant Growth and Development School of Life Sciences, University of KwaZulu‐Natal Pietermaritzburg South Africa
| | - Johannes van Staden
- Research Centre for Plant Growth and Development School of Life Sciences, University of KwaZulu‐Natal Pietermaritzburg South Africa
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26
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Prasad P, Savadi S, Bhardwaj SC, Gangwar OP, Kumar S. Rust pathogen effectors: perspectives in resistance breeding. PLANTA 2019; 250:1-22. [PMID: 30980247 DOI: 10.1007/s00425-019-03167-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Identification and functional characterization of plant pathogen effectors promise to ameliorate future research and develop effective and sustainable strategies for controlling or containing crop diseases. Wheat is the second most important food crop of the world after rice. Rust pathogens, one of the major biotic stresses in wheat production, are capable of threatening the world food security. Understanding the molecular basis of plant-pathogen interactions is essential for devising novel strategies for resistance breeding and disease management. Now, it has been established that effectors, the proteins secreted by pathogens, play a key role in plant-pathogen interactions. Therefore, effector biology has emerged as one of the most important research fields in plant biology. Recent advances in genomics and bioinformatics have allowed identification of a large repertoire of candidate effectors, while the evolving high-throughput tools have continued to assist in their functional characterization. The repertoires of effectors have become an important resource for better understanding of effector biology of pathosystems and resistance breeding of crop plants. In recent years, a significant progress has been made in the field of rust effector biology. This review describes the recent advances in effector biology of obligate fungal pathogens, identification and functional analysis of wheat rust pathogens effectors and the potential applications of effectors in molecular plant biology and rust resistance breeding in wheat.
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Affiliation(s)
- Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Siddanna Savadi
- ICAR-Directorate of Cashew Research, Puttur, Karnataka, 574202, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India.
| | - O P Gangwar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
| | - Subodh Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla, Himachal Pradesh, 171002, India
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27
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Dubey H, Kiran K, Jaswal R, Jain P, Kayastha AM, Bhardwaj SC, Mondal TK, Sharma TR. Discovery and profiling of small RNAs from Puccinia triticina by deep sequencing and identification of their potential targets in wheat. Funct Integr Genomics 2019; 19:391-407. [PMID: 30618015 DOI: 10.1007/s10142-018-00652-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/30/2018] [Accepted: 12/18/2018] [Indexed: 12/18/2022]
Abstract
Cross-kingdom RNAi is a well-documented phenomenon where sRNAs generated by host and pathogens may govern resistance or susceptible phenotypes during host-pathogen interaction. With the first example of the direct involvement of fungal generated sRNAs in virulence of plant pathogenic fungi Botrytis cinerea and recently from Puccinia striiformis f. sp. tritici, we attempted to identify sRNAs in Puccinia triticina (P. triticina). Four sRNA libraries were prepared and sequenced using Illumina sequencing technology and a total of ~ 1-1.28 million potential sRNAs and two microRNA-like small RNA (mil-RNAs) candidates were identified. Computational prediction of targets using a common set of sRNAs and P. triticina mil-RNAs (pt-mil-RNAs) within P. triticina and wheat revealed the majority of the targets as repetitive elements in P. triticina whereas in wheat, the target genes were identified to be involved in many biological processes including defense-related pathways. We found 9 receptor-like kinases (RLKs) and 14 target genes of each related to reactive oxygen species (ROS) pathway and transcription factors respectively, including significant numbers of target genes from various other categories. Expression analysis of twenty selected sRNAs, targeting host genes pertaining to ROS related, disease resistance, metabolic processes, transporter, apoptotic inhibitor, and transcription factors along with two pt-mil-RNAs by qRT-PCR showed distinct patterns of expression of the sRNAs in urediniospore-specific libraries. In this study, for the first time, we report identification of novel sRNAs identified in P. triticina including two pt-mil-RNAs that may play an important role in biotrophic growth and pathogenicity.
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Affiliation(s)
- Himanshu Dubey
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.,School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Kanti Kiran
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 160071, India
| | - Priyanka Jain
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Subhash C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, 171009, India
| | - Tapan Kumar Mondal
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India. .,National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, 160071, India.
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28
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Xia C, Wang M, Yin C, Cornejo OE, Hulbert SH, Chen X. Genome Sequence Resources for the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) and the Barley Stripe Rust Pathogen (Puccinia striiformis f. sp. hordei). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1117-1120. [PMID: 29792772 DOI: 10.1094/mpmi-04-18-0107-a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interactions.
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Affiliation(s)
- Chongjing Xia
- 1 Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Meinan Wang
- 1 Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Chuntao Yin
- 1 Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Omar E Cornejo
- 2 School of Biological Sciences, Washington State University; and
| | - Scot H Hulbert
- 1 Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Xianming Chen
- 1 Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
- 3 Wheat Health, Genetics, and Quality Research Unit, Agriculture Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430, U.S.A
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Aggarwal R, Kulshreshtha D, Sharma S, Singh VK, Manjunatha C, Bhardwaj SC, Saharan MS. Molecular characterization of Indian pathotypes of Puccinia striiformis f. sp. tritici and multigene phylogenetic analysis to establish inter- and intraspecific relationships. Genet Mol Biol 2018; 41:834-842. [PMID: 30281059 PMCID: PMC6415613 DOI: 10.1590/1678-4685-gmb-2017-0171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/12/2017] [Indexed: 11/30/2022] Open
Abstract
Stripe rust caused by Puccinia striiformis f. sp.
tritici (Pst) is one of the most devastating diseases of
wheat (Triticum spp.) worldwide. Indian isolates were
characterised based on their phenotypic reaction on differential hosts carrying
different Yr genes. Based on virulence/avirulence structure,
isolates were characterised into ten different pathotypes viz.
70S0-2, 67S64, 70S4, 66S0, 70S64, 66S64-1, 38S102, 47S102, 46S119, and 78S84.
These Indian pathotypes of P. striiformis f. sp.
tritici and 38 pathotypes of other rust species (P.
graminis tritici and P. triticina) were used in
this study to analyze their molecular phylogenetic relationship. The nucleotides
of rDNA-ITS, partial β-tubulin and ketopantoate
reductase genes of all the pathotypes were sequenced directly after
PCR. Based on sequence data of rDNA-ITS and β-tubulin, three
phylogenetic groups corresponding to three different species of
Puccinia were obtained. Asian isolates formed a distinct
evolutionary lineage than from those derived from USA. The sequence similarity
of Indian pathotypes with other Asian (China and Iran) isolates indicated the
same origin of pathotypes. The results will allow rapid identification of Indian
P.striiformis f. sp. tritici pathotypes
causing stripe rust in wheat, assist in making predictions regarding potential
rust pathotypes, and identifying sources of resistance to the disease in
advance.
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Affiliation(s)
- Rashmi Aggarwal
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Deepika Kulshreshtha
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Sapna Sharma
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Vaibhav K Singh
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
| | - Channappa Manjunatha
- ICAR- Indian Agricultural Research Institute, Regional Station Wellington, Tamilnadu, India
| | - Subhash C Bhardwaj
- Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, Himachal Pradesh, India
| | - Mahender S Saharan
- Fungal Molecular Biology Laboratory, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, India
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30
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Xia C, Wang M, Yin C, Cornejo OE, Hulbert SH, Chen X. Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei). BMC Genomics 2018; 19:664. [PMID: 30208837 PMCID: PMC6134786 DOI: 10.1186/s12864-018-5041-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plant fungal pathogens can rapidly evolve and adapt to new environmental conditions in response to sudden changes of host populations in agro-ecosystems. However, the genomic basis of their host adaptation, especially at the forma specialis level, remains unclear. RESULTS We sequenced two isolates each representing Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), different formae speciales of the stripe rust fungus P. striiformis highly adapted to wheat and barley, respectively. The divergence of Pst and Psh, estimated to start 8.12 million years ago, has been driven by high nucleotide mutation rates. The high genomic variation within dikaryotic urediniospores of P. striiformis has provided raw genetic materials for genome evolution. No specific gene families have enriched in either isolate, but extensive gene loss events have occurred in both Pst and Psh after the divergence from their most recent common ancestor. A large number of isolate-specific genes were identified, with unique genomic features compared to the conserved genes, including 1) significantly shorter in length; 2) significantly less expressed; 3) significantly closer to transposable elements; and 4) redundant in pathways. The presence of specific genes in one isolate (or forma specialis) was resulted from the loss of the homologues in the other isolate (or forma specialis) by the replacements of transposable elements or losses of genomic fragments. In addition, different patterns and numbers of telomeric repeats were observed between the isolates. CONCLUSIONS Host adaptation of P. striiformis at the forma specialis level is a complex pathogenic trait, involving not only virulence-related genes but also other genes. Gene loss, which might be adaptive and driven by transposable element activities, provides genomic basis for host adaptation of different formae speciales of P. striiformis.
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Affiliation(s)
- Chongjing Xia
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA 99164-7520 USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
- Wheat Health, Genetics, and Quality Research Unit, Agriculture Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430 USA
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Xia C, Wang M, Cornejo OE, Jiwan DA, See DR, Chen X. Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici. Front Microbiol 2017; 8:2394. [PMID: 29312156 PMCID: PMC5732408 DOI: 10.3389/fmicb.2017.02394] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/20/2017] [Indexed: 12/30/2022] Open
Abstract
Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat worldwide. Planting resistant cultivars is an effective way to control this disease, but race-specific resistance can be overcome quickly due to the rapid evolving Pst population. Studying the pathogenicity mechanisms is critical for understanding how Pst virulence changes and how to develop wheat cultivars with durable resistance to stripe rust. We re-sequenced 7 Pst isolates and included additional 7 previously sequenced isolates to represent balanced virulence/avirulence profiles for several avirulence loci in seretome analyses. We observed an uneven distribution of heterozygosity among the isolates. Secretome comparison of Pst with other rust fungi identified a large portion of species-specific secreted proteins, suggesting that they may have specific roles when interacting with the wheat host. Thirty-two effectors of Pst were identified from its secretome. We identified candidates for Avr genes corresponding to six Yr genes by correlating polymorphisms for effector genes to the virulence/avirulence profiles of the 14 Pst isolates. The putative AvYr76 was present in the avirulent isolates, but absent in the virulent isolates, suggesting that deleting the coding region of the candidate avirulence gene has produced races virulent to resistance gene Yr76. We conclude that incorporating avirulence/virulence phenotypes into correlation analysis with variations in genomic structure and secretome, particularly presence/absence polymorphisms of effectors, is an efficient way to identify candidate Avr genes in Pst. The candidate effector genes provide a rich resource for further studies to determine the evolutionary history of Pst populations and the co-evolutionary arms race between Pst and wheat. The Avr candidates identified in this study will lead to cloning avirulence genes in Pst, which will enable us to understand molecular mechanisms underlying Pst-wheat interactions, to determine the effectiveness of resistance genes and further to develop durable resistance to stripe rust.
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Affiliation(s)
- Chongjing Xia
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Derick A. Jiwan
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
| | - Deven R. See
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
- Wheat Health, Genetics, and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Pullman, WA, United States
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Phylogenetics and Phylogenomics of Rust Fungi. FUNGAL PHYLOGENETICS AND PHYLOGENOMICS 2017; 100:267-307. [DOI: 10.1016/bs.adgen.2017.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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