1
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Fu H, Fleitas MC, Sarkes A, Wang L, Yang Y, Zahr K, Harding MW, Feindel D, Kutcher R, Feng J. Detection and Differentiation of Xanthomonas translucens Pathovars translucens and undulosa from Wheat and Barley by Duplex Quantitative PCR. PLANT DISEASE 2024; 108:270-277. [PMID: 37669171 DOI: 10.1094/pdis-05-23-0887-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Two probe-based quantitative PCR (qPCR) systems, namely P-Xtt and P-Xtu, were developed to diagnose cereal bacterial leaf streak pathogens Xanthomonas translucens pv. translucens and pv. undulosa, respectively. P-Xtt is specific to pv. translucens, and P-Xtu is specific to pv. undulosa, pv. cerealis, pv. secalis, and pv. pistaciae. P-Xtt and P-Xtu worked on all accessible strains of pv. translucens and pv. undulosa, respectively. Both systems could detect 100 copies of the target gBlock DNA. The two systems could be used in both singleplex qPCR and duplex qPCR with similar efficiencies. On genomic DNA from strains of various X. translucens pathovars, both singleplex and duplex qPCR could specifically detect and differentiate pv. translucens and pv. undulosa. The duplex qPCR could detect pv. translucens and pv. undulosa from genomic DNA of 1,000 bacterial cells. On infected barley and wheat grain samples and on one infected wheat leaf sample, the duplex qPCR showed similar efficiency compared to a previously published qPCR system but with the additional capability of pathovar differentiation. The duplex qPCR system developed in this study will be useful in studies on bacterial leaf streak and detection/differentiation of the pathogens.
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Affiliation(s)
- Heting Fu
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Irrigation (AGI), Edmonton, AB T5Y 6H3, Canada
| | | | - Alian Sarkes
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Irrigation (AGI), Edmonton, AB T5Y 6H3, Canada
| | - Lipu Wang
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Yalong Yang
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Irrigation (AGI), Edmonton, AB T5Y 6H3, Canada
| | - Kher Zahr
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Irrigation (AGI), Edmonton, AB T5Y 6H3, Canada
| | | | - David Feindel
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Irrigation (AGI), Edmonton, AB T5Y 6H3, Canada
| | - Randy Kutcher
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
| | - Jie Feng
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture and Irrigation (AGI), Edmonton, AB T5Y 6H3, Canada
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2
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Gutierrez-Castillo DE, Barrett E, Roberts R. A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates. Microb Genom 2024; 10:001177. [PMID: 38189214 PMCID: PMC10868612 DOI: 10.1099/mgen.0.001177] [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: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that is becoming increasingly destructive across the world. While BLS has caused yield losses in the past, there is anecdotal evidence that newer isolates may be more virulent. We observed that two X. translucens isolates collected from two sites in Colorado, USA, are more aggressive on current wheat and barley varieties compared to older isolates, and we hypothesize that genetic changes between recent and older isolates contribute to the differences in isolate aggressiveness. To test this, we phenotyped and genetically characterized two X. translucens isolates collected from Colorado in 2018, which we designated CO236 (from barley) and CO237 (from wheat). Using pathovar-specific phenotyping and PCR primers, we determined that CO236 belongs to pathovar translucens (Xtt) and CO237 belongs to pathovar undulosa (Xtu). We sequenced the full genomes of the isolates using Oxford Nanopore long-read sequencing, and compared their whole genomes against published X. translucens genomes. This analysis confirmed our pathovar designations for Xtt CO236 and Xtu CO237, and showed that, at the whole-genome level, there were no obvious genomic structural changes between Xtt CO236 and Xtu CO237 and other respective published pathovar genomes. Focusing on pathovar undulosa (Xtu CO237), we then compared putative type III effectors among all available Xtu isolate genomes and found that they were highly conserved. However, there were striking differences in the presence and sequence of various transcription activator-like effectors between Xtu CO237 and published undulosa genomes, which correlate with isolate virulence. Here, we explore the potential implications of the differences in these virulence factors, and provide possible explanations for the increased virulence of recently emerged isolates.
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Affiliation(s)
| | - Emma Barrett
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Robyn Roberts
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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3
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Ledman KE, Osdaghi E, Curland RD, Liu Z, Dill-Macky R. Epidemiology, Host Resistance, and Genomics of the Small Grain Cereals Pathogen Xanthomonas translucens: New Advances and Future Prospects. PHYTOPATHOLOGY 2023; 113:2037-2047. [PMID: 36996338 DOI: 10.1094/phyto-11-22-0403-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Bacterial leaf streak (BLS) primarily affects barley and wheat and is mainly caused by the pathogens Xanthomonas translucens pv. translucens and X. translucens pv. undulosa, respectively. BLS is distributed globally and poses a risk to food security and the supply of malting barley. X. translucens pv. cerealis can infect both wheat and barley but is rarely isolated from these hosts in natural infections. These pathogens have undergone a confusing taxonomic history, and the biology has been poorly understood, making it difficult to develop effective control measures. Recent advancements in the ability and accessibility to sequence bacterial genomes have shed light on phylogenetic relationships between strains and identified genes that may play a role in virulence, such as those that encode Type III effectors. In addition, sources of resistance to BLS have been identified in barley and wheat lines, and ongoing efforts are being made to map these genes and evaluate germplasm. Although there are still gaps in BLS research, progress has been made in recent years to further understand epidemiology, diagnostics, pathogen virulence, and host resistance.
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Affiliation(s)
- Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj, Iran
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
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4
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Osdaghi E, Taghavi SM, Aliabadi AA, Khojasteh M, Abachi H, Moallem M, Mohammadikhah S, Shah SMA, Chen G, Liu Z. Detection and Diagnosis of Bacterial Leaf Streak on Small Grain Cereals: From Laboratory to Field. PHYTOPATHOLOGY 2023; 113:2024-2036. [PMID: 37069135 DOI: 10.1094/phyto-09-22-0343-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Bacterial leaf streak of small-grain cereals is an economically important disease of wheat and barley crops. The disease occurs in many countries across the globe, with particular importance in regions characterized by high precipitation or areas in which sprinkler irrigation is used. Three genetically distinct lineages of the Gram-negative bacterium Xanthomonas translucens (X. translucens pv. undulosa, X. translucens pv. translucens, and X. translucens pv. cerealis) are responsible for most of the bacterial leaf streak infections on wheat and barley crops. Considering the seedborne nature of the pathogens, they are included in the A2 (high-risk) list of quarantine organisms for some European countries; hence, they are under strict quarantine control and zero tolerance. Due to the taxonomic complexities within X. translucens, the exact geographic distribution of each pathovar has not yet been determined. In this mini review, we provide an updated overview of the detection and diagnosis of the bacterial leaf streak pathogens. First, a short history of the leaf streak pathogens is provided, followed by the symptomology and host range of the causal agents. Then, the utility of conventional methods and high-throughput molecular approaches in the precise detection and identification of the pathogens is explained. Finally, we highlight the role of quarantine inspections and early detection of the pathogen in combating the risk of bacterial leaf streak in the 21st century's small-grains cereals' industry.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ali Alizadeh Aliabadi
- Plant Pathology Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Moein Khojasteh
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Hamid Abachi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Mahsa Moallem
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Sedighe Mohammadikhah
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
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5
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Tambong JT, Xu R, Fleitas MC, Wang L, Hubbard K, Kutcher R. Phylogenomic Insights on the Xanthomonas translucens Complex, and Development of a TaqMan Real-Time Assay for Specific Detection of pv. translucens on Barley. PHYTOPATHOLOGY 2023; 113:2091-2102. [PMID: 37097305 DOI: 10.1094/phyto-01-23-0022-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The reemergence and spread of Xanthomonas translucens, the causal agent of bacterial leaf streak in cereal crops and wilt in turfgrass and forage species, is a concern to growers in the United States and Canada. The pathogen is seedborne and listed as an A2 quarantine organism by EPPO, making it a major constraint to international trade and exchange of germplasm. The pathovar concept of the X. translucens group is confusing due to overlapping of plant host ranges and specificity. Here, comparative genomics, phylogenomics, and 81 up-to-date bacterial core gene set (ubcg2) were used to assign the pathovars of X. translucens into three genetically and taxonomically distinct clusters. The study also showed that whole genome-based digital DNA-DNA hybridization unambiguously can differentiate the pvs. translucens and undulosa. Orthologous gene and proteome matrix analyses suggest that the cluster consisting of graminis, poae, arrhenatheri, phlei, and phleipratensis is very divergent. Whole-genome data were exploited to develop the first pathovar-specific TaqMan real-time PCR tool for detection of pv. translucens on barley. Specificity of the TaqMan assay was validated using 62 Xanthomonas and non-Xanthomonas strains as well as growth chamber-inoculated and naturally infected barley leaves. Sensitivity levels of 0.1 pg (purified DNA) and 23 CFUs per reaction (direct culture) compared favorably with other previously reported real-time PCR assays. The phylogenomics data reported here suggest that the clusters could constitute novel taxonomic units or new species. Finally, the pathovar-specific diagnostic tool will have significant benefits to growers and facilitate international exchange of barley germplasm and trade.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Maria Constanza Fleitas
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Lipu Wang
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Randy Kutcher
- Department of Plant Sciences & Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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6
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Heiden N, Roman-Reyna V, Curland RD, Dill-Macky R, Jacobs JM. Comparative Genomics of Barley-Infecting Xanthomonas translucens Shows Overall Genetic Similarity but Globally Distributed Virulence Factor Diversity. PHYTOPATHOLOGY 2023; 113:2056-2061. [PMID: 35727947 DOI: 10.1094/phyto-04-22-0113-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Xanthomonas translucens pv. translucens (Xtt) is a global barley patho-gen and a concern for resistance breeding and regulation. Long-read whole genome sequences allow in-depth understanding of pathogen diversity. We have completed long-read PacBio sequencing of two Minnesotan Xtt strains and an in-depth analysis of available Xtt genomes. We found that average nucleotide identity (ANI)-based approaches organize Xtt strains different from the previous standard multilocus sequencing analysis approach. According to ANI, Xtt forms a separate clade from X. translucens pv. undulosa and consists of three main groups which are represented on multiple continents. Some virulence factors, such as 17 Type III-secreted effectors, are highly conserved and offer potential targets for the elicitation of broad resistance. However, there is a high degree of variation in virulence factors, meaning that germplasm should be screened for resistance with a diverse panel of Xtt.
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Affiliation(s)
- Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
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Hong E, Bankole IA, Zhao B, Shi G, Buck JW, Feng J, Curland RD, Baldwin T, Chapara V, Liu Z. DNA Markers, Pathogenicity Test, and Multilocus Sequence Analysis to Differentiate and Characterize Cereal-Specific Xanthomonas translucens Strains. PHYTOPATHOLOGY 2023; 113:2062-2072. [PMID: 37551962 DOI: 10.1094/phyto-10-22-0381-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Xanthomonas translucens contains a group of bacterial pathogens that are closely related and have been divided into several pathovars based on their host range. X. translucens pv. undulosa (Xtu) and X. translucens pv. translucens (Xtt) are two important pathovars that cause bacterial leaf streak disease on wheat and barley, respectively. In this study, DNA markers were developed to differentiate Xtu and Xtt and were then used to characterize a collection of X. translucens strains with diverse origins, followed by confirmation and characterization with pathogenicity tests and multilocus sequence analysis/typing (MLSA/MLST). We first developed cleaved amplified polymorphic sequence markers based on the single-nucleotide polymorphisms within a cereal pathovar-specific DNA sequence. In addition, two Xtt-specific markers, designated Xtt-XopM and Xtt-SP1, were developed from comparative genomics among the sequenced Xtt/Xtu genomes. Using the developed markers, a collection of X. translucens strains were successfully identified as Xtu or Xtt. Pathogenicity tests on wheat and barley plants and MLSA of four housekeeping genes validated the pathovar assignation of those strains. Furthermore, MLSA revealed distinct subclades within both Xtu and Xtt groups. Seven and three sequence types were identified from MLST for Xtu and Xtt strains, respectively. The establishment of efficient Xtt/Xtu differentiation methods and characterization of those strains will be useful in studying disease epidemiology and host-pathogen interactions and breeding programs when screening for sources of resistance for these two important bacterial pathogens.
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Affiliation(s)
- Eunhye Hong
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Ibukunoluwa A Bankole
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Bin Zhao
- Department of Statistics, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - James W Buck
- Department of Plant Pathology, University of Georgia, Griffin, GA 30223, U.S.A
| | - Jie Feng
- Alberta Plant Health Lab, Crop Diversification Centre North, AAFRED, Edmonton, AB, T5Y 6H3, Canada
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Thomas Baldwin
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Venkata Chapara
- Langdon Research Extension Center, ND Agricultural Experimental Station, Langdon, ND 58249, U.S.A
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
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8
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Román-Reyna V, Curland RD, Velez-Negron Y, Ledman KE, Gutierrez-Castillo DE, Beutler J, Butchacas J, Brar GS, Roberts R, Dill-Macky R, Jacobs JM. Development of Genome-Driven, Lifestyle-Informed Markers for Identification of the Cereal-Infecting Pathogens Xanthomonas translucens Pathovars undulosa and translucens. PHYTOPATHOLOGY 2023; 113:2110-2118. [PMID: 36224751 DOI: 10.1094/phyto-07-22-0262-sa] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacterial leaf streak, bacterial blight, and black chaff caused by Xanthomonas translucens pathovars are major diseases affecting small grains. Xanthomonas translucens pv. translucens and X. translucens pv. undulosa are seedborne pathogens that cause similar symptoms on barley, but only X. translucens pv. undulosa causes bacterial leaf streak of wheat. Recent outbreaks of X. translucens have been a concern for wheat and barley growers in the Northern Great Plains; however, there are limited diagnostic tools for pathovar differentiation. We developed a multiplex PCR based on whole-genome differences to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. We validated the primers across different Xanthomonas and non-Xanthomonas strains. To our knowledge, this is the first multiplex PCR to distinguish X. translucens pv. translucens and X. translucens pv. undulosa. These molecular tools will support disease management strategies enabling detection and pathovar incidence analysis of X. translucens. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Verónica Román-Reyna
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Yesenia Velez-Negron
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | | | - Jonathan Beutler
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Jules Butchacas
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Gurcharn Singh Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Robyn Roberts
- Agricultural Biology, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Jonathan M Jacobs
- Plant Pathology Department, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
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Liu Z, Friskop A, Jacobs JM, Dill-Macky R. Bacterial Leaf Streak: A Persistent and Increasingly Important Disease Problem for Cereal Crops. PHYTOPATHOLOGY 2023; 113:2020-2023. [PMID: 38015599 DOI: 10.1094/phyto-11-23-0423-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Affiliation(s)
- Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108
| | - Andrew Friskop
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Alvandi H, Taghavi SM, Khojasteh M, Rahimi T, Dutrieux C, Taghouti G, Jacques MA, Portier P, Osdaghi E. Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa. PLANT DISEASE 2023; 107:2279-2287. [PMID: 36611242 DOI: 10.1094/pdis-11-22-2677-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Bacterial leaf streak disease caused by Xanthomonas translucens pv. undulosa is an economically important disease threatening wheat and barley crops around the globe. Thus far, specific PCR-based detection and identification tests for X. translucens pathovars are not available. In this study, we used comparative genomics approach to design a pathovar-specific primer pair for detection of X. translucens pv. undulosa in naturally infected seeds and its differentiation from other pathovars of the species. For this aim, complete genome sequences of strains of different X. translucens pathovars were compared and the specific PCR primer pair XtuF/XtuR was designed. These primers were strictly specific to X. translucens pv. undulosa because the expected 229-bp DNA fragment was not amplified in the closely related pathovars or in other xanthomonads, wheat-pathogenic bacteria, and other plant-pathogenic bacteria. High sensitivity of the primer pair XtuF/XtuR allowed detection of pure DNA of the pathogen in a concentration as low as 4.5 pg/μl. The pathogen was also detected in water suspension at a concentration of 8.6 × 102 CFU/ml. The PCR test was capable of detecting the pathogen in extracts of naturally infected wheat seeds at a concentration of 3.5 × 104 CFU/g while a culture-plate method was able to detect the pathogen at a concentration of 50 × 105 CFU/g of the same seeds. The PCR test developed in this study is a step forward for precise detection and identification of X. translucens pv. undulosa to prevent outbreaks of the bacterial leaf streak disease.
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Affiliation(s)
- Hosna Alvandi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Moein Khojasteh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Touraj Rahimi
- Department of Plant Production and Genetics, Agriculture Faculty, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Cecile Dutrieux
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Geraldine Taghouti
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marie-Agnes Jacques
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
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Sarkes A, Yang Y, Dijanovic S, Fu H, Zahr K, Harding MW, Feindel D, Feng J. Detection of Xanthomonas translucens pv. undulosa, pv. translucens, and pv. secalis by Quantitative PCR. PLANT DISEASE 2022; 106:2876-2883. [PMID: 35442047 DOI: 10.1094/pdis-03-22-0574-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A probe-based quantitative PCR (qPCR) protocol was developed for detection and evaluation of the wheat bacterial leaf streak pathogen Xanthomonas translucens pathovar (pv.) undulosa. The protocol can also detect X. translucens pv. translucens and X. translucens pv. secalis but can't differentiate the three pathovars. When tested on nontarget DNA (i.e., from plant; bacteria other than X. translucens pv. undulosa, X. translucens pv. translucens, and X. translucens pv. secalis; and culture of microorganisms from wheat grains), the qPCR showed a high specificity. On purified X. translucens pv. undulosa DNA, the qPCR was more sensitive than a loop-mediated isothermal amplification assay. When DNA samples from a set of serial dilutions of X. translucens pv. undulosa cells were tested, the qPCR method could repeatedly generate quantification cycle (Cq) values from the dilutions containing ≥1,000 cells. Since 2 µl of the total 50 µl of DNA was used in one reaction, one qPCR reaction could detect the presence of the bacteria in samples containing as few as 40 bacterial cells. The qPCR could detect the bacteria from both infected grain and leaf tissues. For seed testing, a protocol for template preparation was standardized, which allowed one qPCR reaction to test DNA from the surface of one wheat grain. Thus, the qPCR system could detect X. translucens pv. undulosa, X. translucens pv. translucens, and/or X. translucens pv. secalis in samples where the bacteria had an average concentration of ≥40 cells per grain.
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Affiliation(s)
- Alian Sarkes
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture, Forestry and Rural Economic Development (AAFRED), Edmonton, AB, T5Y 6H3, Canada
| | - Yalong Yang
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture, Forestry and Rural Economic Development (AAFRED), Edmonton, AB, T5Y 6H3, Canada
| | - Snezana Dijanovic
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture, Forestry and Rural Economic Development (AAFRED), Edmonton, AB, T5Y 6H3, Canada
| | - Heting Fu
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture, Forestry and Rural Economic Development (AAFRED), Edmonton, AB, T5Y 6H3, Canada
| | - Kher Zahr
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture, Forestry and Rural Economic Development (AAFRED), Edmonton, AB, T5Y 6H3, Canada
| | - Michael W Harding
- Crop Diversification Centre South, AAFRED, Brooks, AB, T1R 1E6, Canada
| | - David Feindel
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture, Forestry and Rural Economic Development (AAFRED), Edmonton, AB, T5Y 6H3, Canada
| | - Jie Feng
- Alberta Plant Health Lab, Crop Diversification Centre North, Alberta Agriculture, Forestry and Rural Economic Development (AAFRED), Edmonton, AB, T5Y 6H3, Canada
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12
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Goettelmann F, Roman-Reyna V, Cunnac S, Jacobs JM, Bragard C, Studer B, Koebnik R, Kölliker R. Complete Genome Assemblies of All Xanthomonas translucens Pathotype Strains Reveal Three Genetically Distinct Clades. Front Microbiol 2022; 12:817815. [PMID: 35310401 PMCID: PMC8924669 DOI: 10.3389/fmicb.2021.817815] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
The Xanthomonas translucens species comprises phytopathogenic bacteria that can cause serious damage to cereals and to forage grasses. So far, the genomic resources for X. translucens were limited, which hindered further understanding of the host–pathogen interactions at the molecular level and the development of disease-resistant cultivars. To this end, we complemented the available complete genome sequence of the X. translucens pv. translucens pathotype strain DSM 18974 by sequencing the genomes of all the other 10 X. translucens pathotype strains using PacBio long-read technology and assembled complete genome sequences. Phylogeny based on average nucleotide identity (ANI) revealed three distinct clades within the species, which we propose to classify as clades Xt-I, Xt-II, and Xt-III. In addition to 2,181 core X. translucens genes, a total of 190, 588, and 168 genes were found to be exclusive to each clade, respectively. Moreover, 29 non-transcription activator-like effector (TALE) and 21 TALE type III effector classes were found, and clade- or strain-specific effectors were identified. Further investigation of these genes could help to identify genes that are critically involved in pathogenicity and/or host adaptation, setting the grounds for the development of new resistant cultivars.
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Affiliation(s)
- Florian Goettelmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Sébastien Cunnac
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Claude Bragard
- Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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13
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Clavijo F, Curland RD, Croce V, Lapaz MI, Dill-Macky R, Pereyra S, Siri MI. Genetic and Phenotypic Characterization of Xanthomonas Species Pathogenic in Wheat in Uruguay. PHYTOPATHOLOGY 2022; 112:511-520. [PMID: 34384244 DOI: 10.1094/phyto-06-21-0231-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacterial diseases affecting wheat production in Uruguay are an issue of growing concern yet remain largely uninvestigated in the region. Surveys of 61 wheat fields carried out from 2017 to 2019 yielded a regional collection of 63 strains identified by 16S rRNA gene analysis as Xanthomonas spp. A real-time PCR protocol with species-specific primers previously reported allowed the identification of 44 strains as X. translucens, the causal agent of bacterial leaf streak (BLS) in wheat and other cereal crops. Multilocus sequence analysis of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD) revealed that these strains were most closely related to X. translucens pv. undulosa, the pathovar that is most commonly associated with BLS of wheat. Multilocus sequence typing was applied to examine the genetic diversity of X. translucens strains. Strains were assigned to four different sequence types, three of which were previously reported globally. Additionally, 17 Xanthomonas strains not belonging to X. translucens were obtained from diseased wheat leaves. Phylogenetic analysis showed that these strains are closely related to X. prunicola and clustered together with previously uncharacterized Xanthomonas strains isolated from wheat in Minnesota. In planta pathogenicity assays carried out on a BLS-susceptible wheat cultivar showed that X. translucens pv. undulosa strains caused brown necrosis symptoms typical of BLS, whereas non-translucens Xanthomonas sp. strains elicited an atypical symptom of dry necrosis. These findings suggest that local wheat fields are affected by X. translucens pv. undulosa and by a new wheat pathogen within the Xanthomonas genus.
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Affiliation(s)
- Felipe Clavijo
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Udelar, 11800, Montevideo, Uruguay
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Valentina Croce
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Udelar, 11800, Montevideo, Uruguay
| | - María I Lapaz
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Udelar, 11800, Montevideo, Uruguay
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Silvia Pereyra
- Instituto Nacional de Investigación Agropecuaria, La Estanzuela, 70006, Colonia, Uruguay
| | - María I Siri
- Laboratorio de Microbiología Molecular, Departamento de Biociencias, Facultad de Química, Udelar, 11800, Montevideo, Uruguay
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14
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Yang L, Zhang L, Cao J, Wang L, Shi H, Zhu F, Ji Z. Rapid Detection of Peach Shoot Blight Caused by Phomopsis amygdali Utilizing a New Target Gene Identified from Genome Sequences Within Loop-Mediated Isothermal Amplification. PLANT DISEASE 2022; 106:669-675. [PMID: 34597154 DOI: 10.1094/pdis-08-21-1645-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Peach shoot blight (PSB), caused by Phomopsis amygdali, is a serious threat to the healthy development of the peach industry and leads to 30 to 50% damage to peach production in southern China. In this study, loop-mediated isothermal amplification (LAMP) technology was used to detect the P. amygdali target of a gene of GME6801 that was unique in the whole genome of the pathogen compared with that of Diaporthe (Phomopsis) longicolla TWH P74, Fusarium graminearum PH-1, Colletotrichum gloeosporioides SMCG1 and Magnaporthe oryzae 70-15. Blast comparison of this gene sequence in NCBI database showed that no homologous sequences were found. Therefore, the gene sequence of GME6801 was used to design two pairs of LAMP primers and one pair of PCR primers. The results showed that both primer sets were specific to the 15 strains of P. amygdali, and the other 15 fungal strains presented negative reactions, similar to the control. In addition, 50 pg of genomic DNA of P. amygdali in a 25-μl reaction system could be detected by LAMP assay, which was 100 times more sensitive than PCR. Furthermore, the GME6801 LAMP assay was used to detect artificially inoculated twigs of the pathogen, disease twigs within significantly symptomatic PSB in the fields, and healthy twigs in the same orchard, with detection rates of 100, 75, and 20.8%, respectively. However, detection rates of conventional PCR were separately 100, 62.5, and 16.7%. The results indicated that GME6801-based LAMP could be used for P. amygdali detection as its specificity, sensitivity, and simplicity. This study provides a rapid experimental basis for the identification and prediction of P. amygdali that causes PSB and is beneficial for precise prevention and control of the disease.
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Affiliation(s)
- Lina Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Liang Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jun Cao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lingyun Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hengsong Shi
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Feng Zhu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhaolin Ji
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
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15
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Ledman KE, Curland RD, Ishimaru CA, Dill-Macky R. Xanthomonas translucens pv. undulosa Identified on Common Weedy Grasses in Naturally Infected Wheat Fields in Minnesota. PHYTOPATHOLOGY 2021; 111:1114-1121. [PMID: 33225830 DOI: 10.1094/phyto-08-20-0337-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bacterial leaf streak (BLS) of wheat, caused by Xanthomonas translucens pv. undulosa, has been a notable disease in Minnesota wheat fields over the past decade. Potential sources of the pathogen include infested seed and crop debris. Perennial weeds are also considered a possible inoculum source, but no surveys have been conducted to evaluate which X. translucens pathovars are present on weedy grasses that are common in Minnesota wheat fields. Multilocus sequence analysis (MLSA) of four housekeeping genes (rpoD, dnaK, fyuA, and gyrB) was used to identify 77 strains isolated from six weedy grass species, wheat, and barley in and around naturally infected wheat fields in Minnesota. The MLSA phylogeny identified all strains originating from weedy grass species, except smooth brome, as X. translucens pv. undulosa, whereas strains isolated from smooth brome were determined to be X. translucens pv. cerealis. In planta character states corroborated these identifications on a subset of 41 strains, as all strains from weedy grasses caused water-soaking on wheat and barley in greenhouse assays. Multilocus sequence typing was used to evaluate genetic diversity and revealed that sequence types of X. translucens pv. undulosa originating from weedy grass hosts are similar to those found on wheat. This study identifies both annual and perennial poaceous weeds common in Minnesota that harbor X. translucens pv. undulosa and expands our understanding of the diversity of the pathogen population.
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Affiliation(s)
- Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Carol A Ishimaru
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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16
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Tambong JT, Xu R, Gerdis S, Daniels GC, Chabot D, Hubbard K, Harding MW. Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov. Front Microbiol 2021; 12:666689. [PMID: 34093484 PMCID: PMC8170138 DOI: 10.3389/fmicb.2021.666689] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Xanthomonas translucens is the etiological agent of the wheat bacterial leaf streak (BLS) disease. The isolation of this pathogen is usually based on the Wilbrink's-boric acid-cephalexin semi-selective medium which eliminates 90% of other bacteria, some of which might be novel species. In our study, a general purpose nutrient agar was used to isolate 49 bacterial strains including X. translucens from necrotic wheat leaf tissues. Maximum likelihood cluster analysis of 16S rRNA sequences grouped the strains into 10 distinct genera. Pseudomonas (32.7%) and Pantoea (28.6%) were the dominant genera while Xanthomonas, Clavibacter and Curtobacterium had 8.2%, each. Erwinia and Sphingomonas had two strains, each. BLAST and phylogenetic analyses of multilocus sequence analysis (MLSA) of specific housekeeping genes taxonomically assigned all the strains to validly described bacterial species, except three strains (10L4B, 12L4D and 32L3A) of Pseudomonas and two (23L3C and 15L3B) of Sphingomonas. Strains 10L4B and12L4D had Pseudomonas caspiana as their closest known type strain while strain 32L3A was closest to Pseudomonas asturiensis. Sphingomonas sp. strains 23L3C and 15L3B were closest to S. faeni based on MLSA analysis. Our data on MLSA, whole genome-based cluster analysis, DNA-DNA hybridization and average nucleotide identity, matrix-assisted laser desorption/ionization-time-of-flight, chemotaxonomy and phenotype affirmed that these 5 strains constitute three novel lineages and are taxonomically described in this study. We propose the names, Sphingomonas albertensis sp. nov. (type strain 23L3CT = DOAB 1063T = CECT 30248T = LMG 32139T), Pseudomonas triticumensis sp. nov. (type strain 32L3AT = DOAB 1067T = CECT 30249T = LMG 32140T) and Pseudomonas foliumensis sp. nov. (type strain 10L4BT = DOAB 1069T = CECT 30250T = LMG 32142T). Comparative genomics of these novel species, relative to their closest type strains, revealed unique repertoires of core secretion systems and secondary metabolites/antibiotics. Also, the detection of CRISPR-Cas systems in the genomes of these novel species suggests an acquired mechanism for resistance against foreign mobile genetic elements. The results presented here revealed a cohabitation, within the BLS lesions, of diverse bacterial species, including novel lineages.
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Affiliation(s)
- James T Tambong
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Renlin Xu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Suzanne Gerdis
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Greg C Daniels
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada
| | - Denise Chabot
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Keith Hubbard
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Michael W Harding
- Crop Diversification Centre South, Alberta Agriculture and Forestry, Brooks, AB, Canada
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17
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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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18
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Xu L, Wang Y, Zhu S, Li J, Chang Y, Huang L. Development and Application of a LAMP Assay for the Detection of the Latent Apple Tree Pathogen Valsa mali. PLANT DISEASE 2021; 105:1065-1071. [PMID: 32910734 DOI: 10.1094/pdis-07-20-1449-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Valsa mali, the causal agent of apple Valsa canker, produces cankers, resulting in the death of infected tissues and eventually the entire tree. Because of the long latent period of the disease, it is necessary to develop a rapid, sensitive, and reliable field-based assay to effectively diagnose apple Valsa canker when the plant is still symptomless. Loop-mediated isothermal amplification (LAMP) is a novel detection method that synthesizes a large amount of DNA and produces the visible byproduct (magnesium pyrophosphate) without conventional thermal cycling. Six LAMP primers were designed to target a species-specific region of the elongation factor-1α sequence, which can be completed at 61°C in 60 min. A positive result is indicated by color change after the intercalating dye SYBR Green I is added. The specificity of the LAMP was validated with DNA from 45 representative isolates of V. mali and closely related species V. malicola, V. leucostoma, and V. sordida. The sensitivity of the LAMP was determined to be 1 ng of DNA or as few as 10 spores. Because the assay does not require expensive equipment or specialized techniques, the LAMP-based diagnostic method can be applied under field conditions to more precisely and efficiently access disease pressure in apple orchards.
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Affiliation(s)
- Liangsheng Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yibo Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shan Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jianyu Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yali Chang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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19
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Ramachandran S, Dobhal S, Alvarez AM, Arif M. Improved multiplex TaqMan qPCR assay with universal internal control offers reliable and accurate detection of Clavibacter michiganensis. J Appl Microbiol 2021; 131:1405-1416. [PMID: 33484618 DOI: 10.1111/jam.15017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/16/2020] [Accepted: 01/21/2021] [Indexed: 11/27/2022]
Abstract
AIM Clavibacter michiganensis (Cm) is a seed-borne plant pathogen that significantly reduces tomato production worldwide. Due to repeated outbreaks and rapid spread of the disease, seeds/transplants need to be certified free of the pathogen before planting. To this end, we developed a multiplex TaqMan qPCR assay that can accurately detect Cm in infected samples. METHODS AND RESULTS A specific region of Cm (clvG gene) was selected for primer design using comparative genomics approach. A fully synthetic universal internal control (UIC) was also designed to detect PCR inhibitors and false-negative results in qPCRs. The Cm primers can be used alone or in a triplex TaqMan qPCR assay with UIC and previously described Clavibacter primers. The assay was specific for Cm and detected up to 10 fg of Cm DNA in sensitivity and spiked assays. Addition of the UIC did not change the specificity or sensitivity of the multiplex TaqMan qPCR assay. CONCLUSION The triplex TaqMan qPCR provides a specific and sensitive diagnostic assay for Cm. SIGNIFICANCE AND IMPACT OF THE STUDY This assay can be used for biosecurity surveillance, routine diagnostics, estimating bacterial titres in infected material and for epidemiological studies. The UIC is fully synthetic, efficiently amplified and multiplex compatible with any other qPCR assay.
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Affiliation(s)
- S Ramachandran
- Foreign Disease and Weed Science Research Unit, USDA-ARS, Fort Detrick, MD, USA.,ARS Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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20
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Stackhouse T, Martinez-Espinoza AD, Ali ME. Turfgrass Disease Diagnosis: Past, Present, and Future. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1544. [PMID: 33187303 PMCID: PMC7697262 DOI: 10.3390/plants9111544] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 01/15/2023]
Abstract
Turfgrass is a multibillion-dollar industry severely affected by plant pathogens including fungi, bacteria, viruses, and nematodes. Many of the diseases in turfgrass have similar signs and symptoms, making it difficult to diagnose the specific problem pathogen. Incorrect diagnosis leads to the delay of treatment and excessive use of chemicals. To effectively control these diseases, it is important to have rapid and accurate detection systems in the early stages of infection that harbor relatively low pathogen populations. There are many methods for diagnosing pathogens on turfgrass. Traditional methods include symptoms, morphology, and microscopy identification. These have been followed by nucleic acid detection and onsite detection techniques. Many of these methods allow for rapid diagnosis, some even within the field without much expertise. There are several methods that have great potential, such as high-throughput sequencing and remote sensing. Utilization of these techniques for disease diagnosis allows for faster and accurate disease diagnosis and a reduction in damage and cost of control. Understanding of each of these techniques can allow researchers to select which method is best suited for their pathogen of interest. The objective of this article is to provide an overview of the turfgrass diagnostics efforts used and highlight prospects for disease detection.
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Affiliation(s)
- Tammy Stackhouse
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA;
| | | | - Md Emran Ali
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA;
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21
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Robène I, Maillot-Lebon V, Chabirand A, Moreau A, Becker N, Moumène A, Rieux A, Campos P, Gagnevin L, Gaudeul M, Baider C, Chiroleu F, Pruvost O. Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants. BMC Microbiol 2020; 20:296. [PMID: 33004016 PMCID: PMC7528614 DOI: 10.1186/s12866-020-01972-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/08/2020] [Indexed: 01/07/2023] Open
Abstract
Background Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols. Results Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD95% = 754 CFU ml− 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95% = 5234 CFU ml− 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays. Conclusions We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.
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Affiliation(s)
| | | | - Aude Chabirand
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Aurélie Moreau
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | - Amal Moumène
- Université de La Réunion, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Paola Campos
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | | | - Myriam Gaudeul
- Herbier national (P), Muséum National d'Histoire Naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound) Agricultural Services, Réduit, Mauritius
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Development of Real-Time and Colorimetric Loop Mediated Isothermal Amplification Assay for Detection of Xanthomonas gardneri. Microorganisms 2020; 8:microorganisms8091301. [PMID: 32858943 PMCID: PMC7563391 DOI: 10.3390/microorganisms8091301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 01/16/2023] Open
Abstract
Xanthomonas gardneri is one of the causal agents of bacterial spot (BS), an economically important bacterial disease of tomato and pepper. Field-deployable and portable loop-mediated isothermal amplification (LAMP)-based instruments provide rapid and sensitive detection of plant pathogens. In order to rapidly and accurately identify and differentiate X. gardneri from other BS-causing Xanthomonas spp., we optimized a new real-time monitoring LAMP-based method targeting the X. gardneri-specific hrpB gene. Specificity and sensitivity of real-time and colorimetric LAMP assays were tested on the complex of bacterial strains pathogenic to tomato and pepper and on plants infected by the pathogen. The assay detection limit was 1 pg/μL of genomic DNA with an assay duration of only 30 min. The use of portable and handheld instruments allows for fast analysis, reducing the diagnosis time, and can contribute to proper disease management and control of X. gardneri. Due to the high efficiency of this method, we suggest its use as a standard diagnostic tool during phytosanitary controls.
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Khojasteh M, Shah SMA, Haq F, Xu X, Taghavi SM, Osdaghi E, Chen G. Transcription Activator-Like Effectors Diversity in Iranian Strains of Xanthomonas translucens. PHYTOPATHOLOGY 2020; 110:758-767. [PMID: 31868568 DOI: 10.1094/phyto-11-19-0428-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf streak caused by different pathovars of Xanthomonas translucens is the most important seedborne bacterial disease of small grain cereals. However, variations in the virulence-associated genomic areas of the pathogen remain uninvestigated. In this study, the diversity of transcription activator-like effectors (TALE) was investigated using the Southern blotting of BamHI-digested genomic DNAs in the Iranian strains of X. translucens. All 65 X. translucens strains were assigned into 13 genotypes, where 57 X. translucens pv. undulosa strains were placed in genotypes 1 to 8, and seven X. translucens pv. translucens strains were placed in genotypes 9 to 12. Interestingly, we did not find any TALE genes in the strain XtKm7 (genotype 13), which showed to be pathogenic only on barley. Virulence and aggressiveness of these strains in greenhouse conditions were in agreement with the TALE-based clustering of the strains in the pathovar level, though variations were observed in the aggressiveness of X. translucens pv. undulosa strains. In general, strains containing higher numbers of putative TALE genes were more virulent on wheat and barley than strains containing fewer. This is the first TALE-based genetic diversity analysis on X. translucens strains and provides novel insights into the virulence repertories and genomic characteristics of the pathogen. Further investigations using TALE mutagenesis and complementation analysis are warranted to precisely elucidate the role of each detected X. translucens TALE in bacterial virulence and aggressiveness either on wheat or barley.
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Affiliation(s)
- Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
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Thapa SP, O'Leary M, Jacques MA, Gilbertson RL, Coaker G. Comparative Genomics to Develop a Specific Multiplex PCR Assay for Detection of Clavibacter michiganensis. PHYTOPATHOLOGY 2020; 110:556-566. [PMID: 31799900 DOI: 10.1094/phyto-10-19-0405-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clavibacter michiganensis is a Gram-positive bacterial pathogen that proliferates in the xylem vessels of tomato, causing bacterial wilt and canker symptoms. Accurate detection is a crucial step in confirming outbreaks of bacterial canker and developing management strategies. A major problem with existing detection methods are false-positive and -negative results. Here, we report the use of comparative genomics of 37 diverse Clavibacter strains, including 21 strains sequenced in this study, to identify specific sequences that are C. michiganensis detection targets. Genome-wide phylogenic analyses revealed additional diversity within the genus Clavibacter. Pathogenic C. michiganensis strains varied in plasmid composition, highlighting the need for detection methods based on chromosomal targets. We utilized sequences of C. michiganensis-specific loci to develop a multiplex PCR-based diagnostic platform using two C. michiganensis chromosomal genes (rhuM and tomA) and an internal control amplifying both bacterial and plant DNA (16s ribosomal RNA). The multiplex PCR assay specifically detected C. michiganensis strains from a panel of 110 additional bacteria, including other Clavibacter spp. and bacterial pathogens of tomato. The assay was adapted to detect the presence of C. michiganensis in seed and tomato plant materials with high sensitivity and specificity. In conclusion, the described method represents a robust, specific tool for detection of C. michiganensis in tomato seed and infected plants.
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Affiliation(s)
- Shree P Thapa
- Department of Plant Pathology, University of California, Davis, CA, U.S.A
| | - Michael O'Leary
- Department of Plant Pathology, University of California, Davis, CA, U.S.A
| | - Marie-Agnès Jacques
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 Quasav, Beaucouzé, France
| | | | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA, U.S.A
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Sapkota S, Mergoum M, Liu Z. The translucens group of Xanthomonas translucens: Complicated and important pathogens causing bacterial leaf streak on cereals. MOLECULAR PLANT PATHOLOGY 2020; 21:291-302. [PMID: 31967397 PMCID: PMC7036361 DOI: 10.1111/mpp.12909] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/14/2019] [Accepted: 12/21/2019] [Indexed: 05/31/2023]
Abstract
UNLABELLED Xanthomonas translucens is a group of gram-negative bacteria that can cause important diseases in cereal crops and forage grasses. Different pathovars have been defined according to their host ranges, and molecular and biochemical characteristics. Pathovars have been placed into two major groups: translucens and graminis. The translucens group contains the pathovars causing bacterial leaf streak (BLS) on cereal crops such as wheat, barley, triticale, rye, and oat. In recent years, BLS has re-emerged as a major problem for many wheat- and barley-producing areas worldwide. The biology of the pathogens and the host-pathogen interactions in cereal BLS diseases were poorly understood. However, recent genome sequence data have provided an insight into the bacterial phylogeny and identification and pathogenicity/virulence. Furthermore, identification of sources of resistance to BLS and mapping of the resistance genes have been initiated. TAXONOMY Kingdom Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species X. translucens; translucens group pathovars: undulosa, translucens, cerealis, hordei, and secalis; graminis group pathovars: arrhenatheri, graminis, poae, phlei; newly established pathovar: pistaciae. HOST RANGE X. translucens mainly infects plant species in the Poaceae with the translucens group on cereal crop species and the graminis group on forage grass species. However, some strains have been isolated from, and are able to infect, ornamental asparagus and pistachio trees. Most pathovars have a narrow host range, while a few can infect a broad range of hosts. GENOME The complete genome sequence is available for two X. translucens pv. undulosa strains and one pv. translucens strain. A draft genome sequence is also available for at least one strain from each pathovar. The X. translucens pv. undulosa strain Xt4699 was the first to have its complete genome sequenced, which consists of 4,561,137 bp with total GC content approximately at 68% and 3,528 predicted genes. VIRULENCE MECHANISMS Like most xanthomonads, X. translucens utilizes a type III secretion system (T3SS) to deliver a suite of T3SS effectors (T3Es) inside plant cells. Transcription activator-like effectors, a special group of T3Es, have been identified in most of the X. translucens genomes, some of which have been implicated in virulence. Genetic factors determining host range virulence have also been identified.
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Affiliation(s)
- Suraj Sapkota
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaGriffin Campus, GriffinGAUSA
| | - Mohamed Mergoum
- Institute of Plant Breeding, Genetics, and GenomicsUniversity of GeorgiaGriffin Campus, GriffinGAUSA
- Department of Crop and Soil SciencesUniversity of GeorgiaGriffin Campus, GriffinGAUSA
| | - Zhaohui Liu
- Department of Plant PathologyNorth Dakota State UniversityFargoNDUSA
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Curland RD, Gao L, Hirsch CD, Ishimaru CA. Localized Genetic and Phenotypic Diversity of Xanthomonas translucens Associated With Bacterial Leaf Streak on Wheat and Barley in Minnesota. PHYTOPATHOLOGY 2020; 110:257-266. [PMID: 31448998 DOI: 10.1094/phyto-04-19-0134-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf streak (BLS) of wheat and barley has been a disease of increasing concern in the Upper Midwest over the past decade. In this study, intra- and interfield genetic and pathogenic diversity of bacteria causing BLS in Minnesota was evaluated. In 2015, 89 strains were isolated from 100 leaf samples collected from two wheat and two barley fields naturally infected with BLS. Virulence assays and multilocus sequence alignments of four housekeeping genes supported pathovar identifications. All wheat strains were pathogenic on wheat and barley and belonged to the same lineage as the Xanthomonas translucens pv. undulosa-type strain. All barley strains were pathogenic on barley but not on wheat. Three lineages of barley strains were detected. The frequency and number of sequence types of each pathovar varied within and between fields. A significant population variance was detected between populations of X. translucens pv. undulosa collected from different wheat fields. Population stratification of X. translucens pv. translucens was not detected. Significant differences in virulence were detected among three dominant sequence types of X. translucens pv. undulosa but not those of X. translucens pv. translucens. Field trials with wheat and barley plants inoculated with strains of known sequence type and virulence did not detect significant race structures within either pathovar. Knowledge of virulence, sequence types, and population structures of X. translucens on wheat and barley can support studies on plant-bacterial interactions and breeding for BLS disease resistance.
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Affiliation(s)
- Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Liangliang Gao
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Cory D Hirsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Carol A Ishimaru
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
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Dai T, Yang X, Hu T, Li Z, Xu Y, Lu C. A Novel LAMP Assay for the Detection of Phytophthora cinnamomi Utilizing a New Target Gene Identified From Genome Sequences. PLANT DISEASE 2019; 103:3101-3107. [PMID: 31613192 DOI: 10.1094/pdis-04-19-0781-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phytophthora cinnamomi is an ecologically and agriculturally significant plant pathogen. Early and accurate detection of P. cinnamomi is paramount to disease prevention and management. In this study, a loop-mediated isothermal amplification (LAMP) assay utilizing a new target gene Pcinn100006 identified from genomic sequence data was developed and evaluated for the detection of P. cinnamomi. This Pcinn100006 LAMP assay was found highly specific to P. cinnamomi. All 10 tested isolates of P. cinnamomi yielded positive results, whereas 50 isolates belonging to 16 other Phytophthora species, Globisporangium ultimum, and 14 fungal species lacked detection. This assay was 10 times more sensitive (100 pg in a 25-µl reaction mixture) than a conventional PCR assay (2 ng in a 50-µl reaction mixture) for detecting the genomic DNA of P. cinnamomi. In addition, it detected P. cinnamomi from artificially inoculated leaves of Cedrus deodara. Moreover, detection rates of P. cinnamomi using environmental DNAs extracted from 13 naturally infested rhizosphere samples were 100% in the Pcinn100006 LAMP assay versus 46% in the conventional PCR assay. Considering its higher accuracy and shorter time span, this Pcinn100006 LAMP assay is a promising diagnostic tool to replace conventional PCR-based and culture-dependent assays for screening of P. cinnamomi in regions at risk of infection or contamination.
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Affiliation(s)
- Tingting Dai
- College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiao Yang
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA, U.S.A
| | - Tao Hu
- College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhongyan Li
- College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yue Xu
- College of Forestry, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Chenchen Lu
- Lianyungang Customs (formerly Lianyungang Entry-Exit Inspection and Quarantine Bureau), Lianyungang, China
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Karim S, McNally RR, Nasaruddin AS, DeReeper A, Mauleon RP, Charkowski AO, Leach JE, Ben-Hur A, Triplett LR. Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola. PLANT DISEASE 2019; 103:2893-2902. [PMID: 31436473 DOI: 10.1094/pdis-10-18-1819-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola. The remaining four amplified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field samples from across the United States that were previously submitted for testing. D. dianthicola was detected in 41 samples, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D. dianthicola in North America.
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Affiliation(s)
- Shaista Karim
- Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A
| | - R Ryan McNally
- Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A
| | - Afnan S Nasaruddin
- Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A
| | - Alexis DeReeper
- L'Institut de recherche pour le développement, IRD, Université Montpellier, IPME, Montpellier, France
| | - Ramil P Mauleon
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Amy O Charkowski
- Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A
| | - Jan E Leach
- Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A
| | - Asa Ben-Hur
- Colorado State University, Department of Computer Science, Fort Collins, CO 80523, U.S.A
| | - Lindsay R Triplett
- The Connecticut Agricultural Experiment Station, New Haven, CT 06511, U.S.A
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Molecular Typing Reveals High Genetic Diversity of Xanthomonas translucens Strains Infecting Small-Grain Cereals in Iran. Appl Environ Microbiol 2019; 85:AEM.01518-19. [PMID: 31420337 DOI: 10.1128/aem.01518-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/06/2019] [Indexed: 12/22/2022] Open
Abstract
This study provides a phylogeographic insight into the population diversity of Xanthomonas translucens strains causing bacterial leaf streak disease of small-grain cereals in Iran. Among the 65 bacterial strains isolated from wheat, barley, and gramineous weeds in eight Iranian provinces, multilocus sequence analysis and typing (MLSA and MLST) of four housekeeping genes (dnaK, fyuA, gyrB, and rpoD), identified 57 strains as X. translucens pv. undulosa, while eight strains were identified as X. translucens pv. translucens. Although the pathogenicity patterns on oat and ryegrass weed species varied among the strains, all X. translucens pv. undulosa strains were pathogenic on barley, Harding's grass, rye (except for XtKm35) and wheat, and all X. translucens pv. translucens strains were pathogenic on barley and Harding's grass, while none of the latter group was pathogenic on rye or wheat (except for XtKm18). MLST using the 65 strains isolated in Iran, as well as the sequences of the four genes from 112 strains of worldwide origin retrieved from the GenBank database, revealed higher genetic diversity (i.e., haplotype frequency, haplotype diversity, and percentage of polymorphic sites) among the Iranian population of X. translucens than among the North American strains of the pathogen. High genetic diversity of the BLS pathogen in Iran was in congruence with the fact that the Iranian Plateau is considered the center of origin of cultivated wheat. However, further studies using larger collections of strains are warranted to precisely elucidate the global population diversity and center of origin of the pathogen.IMPORTANCE Bacterial leaf streak (BLS) of small-grain cereals (i.e., wheat and barley) is one of the economically important diseases of gramineous crops worldwide. The disease occurs in many countries across the globe, with particular importance in regions characterized by high levels of precipitation. Two genetically distinct xanthomonads-namely, Xanthomonas translucens pv. undulosa and X. translucens pv. translucens-have been reported to cause BLS disease on small-grain cereals. As seed-borne pathogens, the causal agents are included in the A2 list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Despite its global distribution and high economic importance, the population structure, genetic diversity, and phylogeography of X. translucens remain undetermined. This study, using MLSA and MLST, provides a global-scale phylogeography of X. translucens strains infecting small-grain cereals. Based on the diversity parameters, neutrality indices, and population structure, we observe higher genetic diversity of the BLS pathogen in Iran, which is geographically close to the center of origin of common wheat, than has so far been observed in other areas of the world, including North America. The results obtained in this study provide a novel insight into the genetic diversity and population structure of the BLS pathogen of small-grain cereals on a global scale.
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Shah SMA, Haq F, Ma W, Xu X, Wang S, Xu Z, Zou L, Zhu B, Chen G. Tal1 NXtc01 in Xanthomonas translucens pv. cerealis Contributes to Virulence in Bacterial Leaf Streak of Wheat. Front Microbiol 2019; 10:2040. [PMID: 31551976 PMCID: PMC6737349 DOI: 10.3389/fmicb.2019.02040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Xanthomonas translucens pv. cerealis (Xtc) causes bacterial leaf streak (BLS) of important cereal crops, including wheat (Triticum aestivum) and barley (Hordeum vulgare). Transcription activator-like effectors (TALEs) play vital roles in many plant diseases caused by Xanthomonas spp., however, TALEs have not been previously characterized in Xtc. In this study, the whole genome of NXtc01, a virulent strain of Xtc from Xinjiang, China, was sequenced and compared with genomes of other Xanthomonas spp. Xtc NXtc01 consists of a single 4,622,298 bp chromosome that encodes 4,004 genes. Alignment of the NXtc01 sequence with the draft genome of Xtc strain CFBP 2541 (United States) revealed a single giant inversion and differences in the location of two tal genes, which were designated tal1 and tal2. In NXtc01, both tal genes are located on the chromosome, whereas tal2 is plasmid-encoded in CFBP 2541. The repeat variable diresidues (RVDs) at the 12th and 13th sites within Tal2 repeat units were identical in both strains, whereas Tal1 showed differences in the third RVD. Xtc NXtc01 and CFBP 2541 encoded 35 and 33 non-TALE type III effectors (T3Es), respectively. tal1, tal2, and tal-free deletion mutants of Xtc NXtc01 were constructed and evaluated for virulence. The tal1 and tal-free deletion mutants were impaired with respect to symptom development and growth in wheat, suggesting that tal1 is a virulence factor in NXtc01. This was confirmed in gain-of-function experiments that showed the introduction of tal1, but not tal2, restored virulence to the tal-free mutant. Furthermore, we generated a hrcC deletion mutant of NXtc01; the hrcC mutant was non-pathogenic on wheat and unable to elicit a hypersensitive response in the non-host Nicotiana benthamiana. Our data provide a platform for exploring the roles of both TALEs and non-TALEs in promoting BLS on wheat.
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Affiliation(s)
- Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiu Ma
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Zhu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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Ocenar J, Arizala D, Boluk G, Dhakal U, Gunarathne S, Paudel S, Dobhal S, Arif M. Development of a robust, field-deployable loop-mediated isothermal amplification (LAMP) assay for specific detection of potato pathogen Dickeya dianthicola targeting a unique genomic region. PLoS One 2019; 14:e0218868. [PMID: 31233546 PMCID: PMC6590888 DOI: 10.1371/journal.pone.0218868] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
Destructive maceration, a wide host range, and longevity in non-plant substrates has established Dickeya dianthicola (blackleg of potato) as a significant threat to potato industries worldwide. To protect these businesses, a specific and sensitive point-of-care D. dianthicola detection tool is necessary. We have developed a loop-mediated isothermal amplification (LAMP) assay for specific, sensitive, and rapid detection of D. dianthicola, which can be streamlined for point-of-care use. The developed LAMP assay targets a unique gene, alcohol dehydrogenase, of D. dianthicola. Assay specificity was assessed using strains present in inclusivity (16 D. dianthicola strains) and exclusivity panels (56 closely related, potato pathogenic, and other bacterial strains). Amplification with strains of inclusivity panel occurred, and cross-reactivity with non-target DNA was not observed. The limit of detection (LOD) was 10 CFU/ml when dilutions were made before isolating the genomic DNA; however, LOD was determined as 1 pg using 10-fold serially diluted D. dianthicola genomic DNA. Similar LOD of 1 pg was observed when serially diluted target genomic DNA was mixed with host genomic DNA. LOD (1 pg) was also calculated with 10-fold serially diluted synthetic DNA fragments containing primer target sites. Naturally and artificially inoculated plant samples were used for field adaptability tests with the field-deployable Optigene Plant Material Lysis Kit and a heat block (65°C); the results were obtained within 20 minutes. Despite the lack of method precision, no false positives or false negatives were observed. Therefore, with prepared reactions and a steady heat source, this assay can be used for rapid point-of-care detection, which is imperative for quarantine, eradication, disease management, and border protection.
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Affiliation(s)
- Jordie Ocenar
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- Department of Agriculture, State of Hawaii, Honolulu, Hawaii, United States of America
| | - Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Gamze Boluk
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Upasana Dhakal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Samudra Gunarathne
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Sujan Paudel
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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Liu F, McDonald M, Schwessinger B, Joe A, Pruitt R, Erickson T, Zhao X, Stewart V, Ronald PC. Variation and inheritance of the Xanthomonas raxX-raxSTAB gene cluster required for activation of XA21-mediated immunity. MOLECULAR PLANT PATHOLOGY 2019; 20:656-672. [PMID: 30773771 PMCID: PMC6637879 DOI: 10.1111/mpp.12783] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The rice XA21-mediated immune response is activated on recognition of the RaxX peptide produced by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The 60-residue RaxX precursor is post-translationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The 5-kb raxX-raxSTAB gene cluster of Xoo encodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type I secretion system. To assess raxX-raxSTAB gene cluster evolution and to determine its phylogenetic distribution, we first identified rax gene homologues in other genomes. We detected the complete raxX-raxSTAB gene cluster only in Xanthomonas spp., in five distinct lineages in addition to X. oryzae. The phylogenetic distribution of the raxX-raxSTAB gene cluster is consistent with the occurrence of multiple lateral (horizontal) gene transfer events during Xanthomonas speciation. RaxX natural variants contain a restricted set of missense substitutions, as expected if selection acts to maintain peptide hormone-like function. Indeed, eight RaxX variants tested all failed to activate the XA21-mediated immune response, yet retained peptide hormone activity. Together, these observations support the hypothesis that the XA21 receptor evolved specifically to recognize Xoo RaxX.
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Affiliation(s)
- Furong Liu
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Megan McDonald
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Anna Joe
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Rory Pruitt
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Teresa Erickson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Xiuxiang Zhao
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Valley Stewart
- Department of Microbiology & Molecular GeneticsUniversity of CaliforniaDavisCA95616USA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
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Juanillas V, Dereeper A, Beaume N, Droc G, Dizon J, Mendoza JR, Perdon JP, Mansueto L, Triplett L, Lang J, Zhou G, Ratharanjan K, Plale B, Haga J, Leach JE, Ruiz M, Thomson M, Alexandrov N, Larmande P, Kretzschmar T, Mauleon RP. Rice Galaxy: an open resource for plant science. Gigascience 2019; 8:giz028. [PMID: 31107941 PMCID: PMC6527052 DOI: 10.1093/gigascience/giz028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/29/2018] [Accepted: 02/12/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Rice molecular genetics, breeding, genetic diversity, and allied research (such as rice-pathogen interaction) have adopted sequencing technologies and high-density genotyping platforms for genome variation analysis and gene discovery. Germplasm collections representing rice diversity, improved varieties, and elite breeding materials are accessible through rice gene banks for use in research and breeding, with many having genome sequences and high-density genotype data available. Combining phenotypic and genotypic information on these accessions enables genome-wide association analysis, which is driving quantitative trait loci discovery and molecular marker development. Comparative sequence analyses across quantitative trait loci regions facilitate the discovery of novel alleles. Analyses involving DNA sequences and large genotyping matrices for thousands of samples, however, pose a challenge to non-computer savvy rice researchers. FINDINGS The Rice Galaxy resource has shared datasets that include high-density genotypes from the 3,000 Rice Genomes project and sequences with corresponding annotations from 9 published rice genomes. The Rice Galaxy web server and deployment installer includes tools for designing single-nucleotide polymorphism assays, analyzing genome-wide association studies, population diversity, rice-bacterial pathogen diagnostics, and a suite of published genomic prediction methods. A prototype Rice Galaxy compliant to Open Access, Open Data, and Findable, Accessible, Interoperable, and Reproducible principles is also presented. CONCLUSIONS Rice Galaxy is a freely available resource that empowers the plant research community to perform state-of-the-art analyses and utilize publicly available big datasets for both fundamental and applied science.
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Affiliation(s)
- Venice Juanillas
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Alexis Dereeper
- Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
| | - Nicolas Beaume
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Gaetan Droc
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Joshua Dizon
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - John Robert Mendoza
- Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, Philippines
| | - Jon Peter Perdon
- Advanced Science and Technology Institute, Department of Science and Technology, Quezon City, Philippines
| | - Locedie Mansueto
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Lindsay Triplett
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Jillian Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Gabriel Zhou
- Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USA
| | | | - Beth Plale
- Indiana University, 107 S Indiana Ave, Bloomington, IN 47405, USA
| | - Jason Haga
- National Institute of Advanced Industrial Science and Technology, AIST Tsukuba Central 1,1-1-1 Umezono, Tsukuba, Ibaraki 305-8560, Japan
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Manuel Ruiz
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Michael Thomson
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
- Department of Soil and Crop Sciences, Texas A&M University, Houston, TX, USA
| | - Nickolai Alexandrov
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
| | - Pierre Larmande
- Institut de recherche pour le développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
| | - Tobias Kretzschmar
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| | - Ramil P Mauleon
- International Rice Research Institute, DAPO Box 7777, Metro Manila 1301, Philippines
- Southern Cross Plant Science, Southern Cross University, Lismore, Australia
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Dang Z, McLenachan PA, Lockhart PJ, Waipara N, Er O, Reynolds C, Blanchon D. Metagenome Profiling Identifies Potential Biocontrol Agents for Selaginella kraussiana in New Zealand. Genes (Basel) 2019; 10:genes10020106. [PMID: 30709012 PMCID: PMC6409722 DOI: 10.3390/genes10020106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/18/2019] [Accepted: 01/22/2019] [Indexed: 11/16/2022] Open
Abstract
Metagenomics can be used to identify potential biocontrol agents for invasive species and was used here to identify candidate species for biocontrol of an invasive club moss in New Zealand. Profiles were obtained for Selaginella kraussiana collected from nine geographically disjunct locations in Northern New Zealand. These profiles were distinct from those obtained for the exotic club moss Selaginella moellendorffii and the native club mosses Lycopodium deuterodensum and Lycopodium volubile also collected in Northern New Zealand. Fungi and bacteria implicated elsewhere in causing plant disease were identified on plants of Selaginella that exhibited signs of necrosis. Most notably, high densities of sequence reads from Xanthomonas translucens and Pseudomonas syringae were associated with some populations of Selaginella but not Lycopodium. Since these bacteria are already in use as biocontrol agents elsewhere, further investigation into their potential as biocontrol of Selaginella in New Zealand is suggested.
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Affiliation(s)
- Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China.
| | - Patricia A McLenachan
- Institute of Fundamental Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand.
| | - Peter J Lockhart
- Institute of Fundamental Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand.
| | - Nick Waipara
- The New Zealand Institute for Plant & Food Research Limited, Mt Albert, Auckland 1142, New Zealand.
| | - Orhan Er
- Arborlab Consultancy Services, Auckland 0632, New Zealand.
| | | | - Dan Blanchon
- School of Environmental and Animal Sciences, Unitec Institute of Technology, Private Bag 92025, Auckland 1142, New Zealand.
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Nagel R, Bieber JE, Schmidt-Dannert MG, Nett RS, Peters RJ. A Third Class: Functional Gibberellin Biosynthetic Operon in Beta-Proteobacteria. Front Microbiol 2018; 9:2916. [PMID: 30546353 PMCID: PMC6278637 DOI: 10.3389/fmicb.2018.02916] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/13/2018] [Indexed: 11/13/2022] Open
Abstract
The ability of plant-associated microbes to produce gibberellin A (GA) phytohormones was first described for the fungal rice pathogen Gibberella fujikuroi in the 1930s. Recently the capacity to produce GAs was shown for several bacteria, including symbiotic alpha-proteobacteria (α-rhizobia) and gamma-proteobacteria phytopathogens. All necessary enzymes for GA production are encoded by a conserved operon, which appears to have undergone horizontal transfer between and within these two phylogenetic classes of bacteria. Here the operon was shown to be present and functional in a third class, the beta-proteobacteria, where it is found in several symbionts (β-rhizobia). Conservation of function was examined by biochemical characterization of the enzymes encoded by the operon from Paraburkholderia mimosarum LMG 23256T. Despite the in-frame gene fusion between the short-chain alcohol dehydrogenase/reductase and ferredoxin, the encoded enzymes exhibited the expected activity. Intriguingly, together these can only produce GA9, the immediate precursor to the bioactive GA4, as the cytochrome P450 (CYP115) that catalyzes the final hydroxylation reaction is missing, similar to most α-rhizobia. However, phylogenetic analysis indicates that the operon from β-rhizobia is more closely related to examples from gamma-proteobacteria, which almost invariably have CYP115 and, hence, can produce bioactive GA4. This indicates not only that β-rhizobia acquired the operon by horizontal gene transfer from gamma-proteobacteria, rather than α-rhizobia, but also that they independently lost CYP115 in parallel to the α-rhizobia, further hinting at the possibility of detrimental effects for the production of bioactive GA4 by these symbionts.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
| | - John E Bieber
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States.,Science Department, Newton Senior High School, Newton, IA, United States
| | - Mark G Schmidt-Dannert
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Ryan S Nett
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
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Curland RD, Gao L, Bull CT, Vinatzer BA, Dill-Macky R, Van Eck L, Ishimaru CA. Genetic Diversity and Virulence of Wheat and Barley Strains of Xanthomonas translucens from the Upper Midwestern United States. PHYTOPATHOLOGY 2018; 108:443-453. [PMID: 29165007 DOI: 10.1094/phyto-08-17-0271-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial leaf streak (BLS) of wheat and barley, caused by Xanthomonas translucens pv. undulosa and X. translucens pv. translucens, has been of growing concern in small grains production in the Upper Midwestern United States. To optimize disease resistance breeding, a greater awareness is needed of the pathovars and genetic diversity within the pathogens causing BLS in the region. Multilocus sequencing typing (MLST) and analysis (MLSA) of four common housekeeping genes (rpoD, dnaK, fyuA, and gyrB) was used to evaluate the genetic diversity of 82 strains of X. translucens isolated between 2006 and 2013 from wheat, barley, rye, and intermediate wheatgrass. In addition, in planta disease assays were conducted on 75 strains to measure relative virulence in wheat and barley. All strains were determined by MLSA to be related to X. translucens pv. undulosa and X. translucens pv. translucens. Clustering of strains based on Bayesian, network, and minimum spanning trees correlated with relative virulence levels in inoculated wheat and barley. Thus, phylogeny based on rpoD, dnaK, fyuA, and gyrB correlated with host of isolation and was an effective means for predicting virulence of strains belonging to X. translucens pv. translucens and X. translucens pv. undulosa.
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Affiliation(s)
- Rebecca D Curland
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Liangliang Gao
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Carolee T Bull
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Boris A Vinatzer
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Ruth Dill-Macky
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Leon Van Eck
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Carol A Ishimaru
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
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Wen A, Jayawardana M, Fiedler J, Sapkota S, Shi G, Peng Z, Liu S, White FF, Bogdanove AJ, Li X, Liu Z. Genetic mapping of a major gene in triticale conferring resistance to bacterial leaf streak. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:649-658. [PMID: 29218377 DOI: 10.1007/s00122-017-3026-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/21/2017] [Indexed: 06/07/2023]
Abstract
A major gene conferring resistance to bacterial leaf streak was mapped to chromosome 5R in triticale. Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Xtu), is an important disease of wheat and triticale around the world. Although resistance to BLS is limited in wheat, several triticale accessions have high levels of resistance. To characterize the genetic basis of this resistance, we developed triticale mapping populations using a resistant accession (Siskiyou) and two susceptible accessions (UC38 and Villax St. Jose). Bulked segregant analysis in an F2 population derived from the cross of Siskiyou × UC38 led to the identification of a simple sequence repeat (SSR) marker (XSCM138) on chromosome 5R that co-segregated with the resistance gene. The cross of Siskiyou × Villax St. Jose was advanced into an F2:5 recombinant inbred line population and evaluated for BLS reaction. Genetic linkage maps on this population were assembled with markers generated using genotyping-by-sequencing as well as several SSR markers previously identified on 5R. Quantitative trait locus (QTL) mapping revealed a single major QTL on chromosome 5R, underlined by the same SSR marker as in the Siskiyou × UC38 population. The F1 hybrids of the two crosses were highly resistant to BLS, indicating that resistance is largely dominant. This work will facilitate introgression of this rye-derived BLS resistance gene into the wheat genome by molecular marker-mediated chromosome engineering.
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Affiliation(s)
- Aimin Wen
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Malini Jayawardana
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Jason Fiedler
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA
| | - Suraj Sapkota
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Gongjun Shi
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA.
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Lang JM, DuCharme E, Ibarra Caballero J, Luna E, Hartman T, Ortiz-Castro M, Korus K, Rascoe J, Jackson-Ziems TA, Broders K, Leach JE. Detection and Characterization of Xanthomonas vasicola pv. vasculorum (Cobb 1894) comb. nov. Causing Bacterial Leaf Streak of Corn in the United States. PHYTOPATHOLOGY 2017; 107:1312-1321. [PMID: 28677478 DOI: 10.1094/phyto-05-17-0168-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial leaf streak of corn (Zea mays) recently reached epidemic levels in three corn-growing states, and has been detected in another six states in the central United States. Xanthomonas vasicola was identified as the causal agent of this disease. A multilocus sequence alignment of six housekeeping genes and comparison of average nucleotide identity from draft genome sequence were used to confirm phylogenetic relationships and classification of this bacteria relative to other X. vasicola strains. X. vasicola isolates from Nebraska and South Africa were highly virulent on corn and sugarcane and less virulent on sorghum but caused water-soaking symptoms that are typical of X. vasicola infection on the leaves of all three hosts. Based on host range and phylogenetic comparison, we propose the taxonomic designation of this organism to X. vasicola pv. vasculorum ( Cobb 1894 ) comb. nov. Polymerase chain reaction-based diagnostic assays were developed that distinguish X. vasicola pv. vasculorum and X. vasicola pv. holcicola from each other and from other Xanthomonas spp.
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Affiliation(s)
- J M Lang
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - E DuCharme
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J Ibarra Caballero
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - E Luna
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - T Hartman
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - M Ortiz-Castro
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - K Korus
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J Rascoe
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - T A Jackson-Ziems
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - K Broders
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J E Leach
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
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Falahi Charkhabi N, Booher NJ, Peng Z, Wang L, Rahimian H, Shams-Bakhsh M, Liu Z, Liu S, White FF, Bogdanove AJ. Complete Genome Sequencing and Targeted Mutagenesis Reveal Virulence Contributions of Tal2 and Tal4b of Xanthomonas translucens pv. undulosa ICMP11055 in Bacterial Leaf Streak of Wheat. Front Microbiol 2017; 8:1488. [PMID: 28848509 PMCID: PMC5554336 DOI: 10.3389/fmicb.2017.01488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022] Open
Abstract
Bacterial leaf streak caused by Xanthomonas translucens pv. undulosa (Xtu) is an important disease of wheat (Triticum aestivum) and barley (Hordeum vulgare) worldwide. Transcription activator-like effectors (TALEs) play determinative roles in many of the plant diseases caused by the different species and pathovars of Xanthomonas, but their role in this disease has not been characterized. ICMP11055 is a highly virulent Xtu strain from Iran. The aim of this study was to better understand genetic diversity of Xtu and to assess the role of TALEs in bacterial leaf streak of wheat by comparing the genome of this strain to the recently completely sequenced genome of a U.S. Xtu strain, and to several other draft X. translucens genomes, and by carrying out mutational analyses of the TALE (tal) genes the Iranian strain might harbor. The ICMP11055 genome, including its repeat-rich tal genes, was completely sequenced using single molecule, real-time technology (Pacific Biosciences). It consists of a single circular chromosome of 4,561,583 bp, containing 3,953 genes. Whole genome alignment with the genome of the United States Xtu strain XT4699 showed two major re-arrangements, nine genomic regions unique to ICMP11055, and one region unique to XT4699. ICMP110055 harbors 26 non-TALE type III effector genes and seven tal genes, compared to 25 and eight for XT4699. The tal genes occur singly or in pairs across five scattered loci. Four are identical to tal genes in XT4699. In addition to common repeat-variable diresidues (RVDs), the tal genes of ICMP11055, like those of XT4699, encode several RVDs rarely observed in Xanthomonas, including KG, NF, Y∗, YD, and YK. Insertion and deletion mutagenesis of ICMP11055 tal genes followed by genetic complementation analysis in wheat cv. Chinese Spring revealed that Tal2 and Tal4b of ICMP11055 each contribute individually to the extent of disease caused by this strain. A largely conserved ortholog of tal2 is present in XT4699, but for tal4b, only a gene with partial, fragmented RVD sequence similarity can be found. Our results lay the foundation for identification of important host genes activated by Xtu TALEs as targets for the development of disease resistant varieties.
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Affiliation(s)
- Nargues Falahi Charkhabi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States.,Department of Plant Pathology, Tarbiat Modares UniversityTehran, Iran
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Zhao Peng
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States.,Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Heshmat Rahimian
- Department of Plant Protection, Sari Agricultural Science and Natural Resources UniversitySari, Iran
| | | | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, FargoND, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States
| | - Frank F White
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States.,Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
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