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Sharma A, Timilsina S, Abrahamian P, Minsavage GV, Jones JB, Vallad GE, Goss EM. Bacterial Mutation During Seasonal Epidemics. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:93-97. [PMID: 38105425 DOI: 10.1094/mpmi-10-23-0164-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: 12/19/2023]
Abstract
Rapidly evolving bacterial pathogens pose a unique challenge for long-term plant disease management. In this study, we investigated the types and rate of mutations in bacterial populations during seasonal disease epidemics. Two phylogenetically distinct strains of the bacterial spot pathogen, Xanthomonas perforans, were marked, released in tomato fields, and recaptured at several time points during the growing season. Genomic variations in recaptured isolates were identified by comparative analysis of their whole-genome sequences. In total, 180 unique variations (116 substitutions, 57 insertions/deletions, and 7 structural variations) were identified from 300 genomes, resulting in the overall host-associated mutation rate of ∼0.3 to 0.9/genome/week. This result serves as a benchmark for bacterial mutation during epidemics in similar pathosystems. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, U.S.A
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Peter Abrahamian
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, U.S.A
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Gary E Vallad
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, U.S.A
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
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Subedi A, Barrera LBTDL, Ivey ML, Egel DS, Kebede M, Kara S, Aysan Y, Minsavage GV, Roberts PD, Jones JB, Goss EM. Population Genomics Reveals an Emerging Lineage of Xanthomonas perforans on Pepper. PHYTOPATHOLOGY 2024; 114:241-250. [PMID: 37432099 DOI: 10.1094/phyto-04-23-0128-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Xanthomonas perforans-the dominant causal agent of bacterial leaf spot of tomato-is an emerging pathogen of pepper, indicative of a potential host expansion across the southeastern United States. However, studies of the genetic diversity and evolution of X. perforans from pepper remain limited. In this study, the whole-genome sequences of 35 X. perforans strains isolated from pepper from four fields and two transplant facilities across southwest Florida between 2019 and 2021 were used to compare genomic divergence, evolution, and variation in type III secreted effectors. Phylogenetic analysis based on core genes revealed that all 35 X. perforans strains formed one genetic cluster with pepper and tomato strains from Alabama and Turkey and were closely related to strains isolated from tomato in Indiana, Mexico, and Louisiana. The in planta population growth of tomato strains isolated from Indiana, Mexico, Louisiana, and Turkey in pepper leaf mesophyll was on par with pepper X. perforans and X. euvesicatoria strains. Molecular clock analysis of the 35 Florida strains dated their emergence to approximately 2017. While strains varied in copper tolerance, all sequenced strains harbored the avrHah1 transcription activation-like effector located on a conjugative plasmid, not previously reported in Florida. Our findings suggest that there is a geographically distributed lineage of X. perforans strains on tomato that has the genetic background to cause disease on pepper. Moreover, this study clarifies potential adaptive variants of X. perforans on pepper that could help forecast the emergence of such strains and enable immediate or preemptive intervention.
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Affiliation(s)
- Aastha Subedi
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | | | - Melanie Lewis Ivey
- Department of Plant Pathology, The Ohio State University, Wooster, OH, U.S.A
| | - Daniel S Egel
- Botany and Plant Pathology Department, Purdue University, West Lafayette, IN, U.S.A
| | - Misrak Kebede
- Biotechnology Department, Collage of Biological and Chemical Engineering, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Serhat Kara
- Alata Horticulture Research Institute, Mersin, Turkey
| | - Yesim Aysan
- Department of Plant Protection, Cukurova University, Adana, Turkey
| | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Pamela D Roberts
- Southwest Florida Research & Education Center, University of Florida, Immokalee, FL, U.S.A
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL, U.S.A
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, U.S.A
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Bibi S, Weis K, Kaur A, Bhandari R, Goss E, Jones JB, Potnis N. A Brief Evaluation of a Copper Resistance Mobile Genetic Island in the Bacterial Leaf Spot Pathogen Xanthomonas euvesicatoria pv. perforans. PHYTOPATHOLOGY 2023; 113:1394-1398. [PMID: 37097444 DOI: 10.1094/phyto-02-23-0077-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Due to the continuous use of copper containing bactericides without effective alternative bactericides, copper resistance has become more prevalent in plant pathogens, including Xanthomonas euvesicatoria pv. perforans (formerly Xanthomonas perforans), a predominant cause of bacterial leaf spot disease of tomato and pepper in the Southeastern United States. Previously, reports of copper resistance have been associated with a large conjugative plasmid. However, we have characterized a copper resistance genomic island located within the chromosome of multiple X. euvesicatoria pv. perforans strains. The island is distinct from a previously described chromosomally encoded copper resistance island in X. vesicatoria strain XVP26. Computational analysis revealed the genomic island to contain multiple genes associated with genetic mobility, including both phage-related genes and transposase. Among copper-tolerant strains of X. euvesicatoria pv. perforans isolated from Florida, the majority of strains were found to have the copper resistance chromosomally encoded rather than plasmid borne. Our results suggest that this copper resistance island may have two modes of horizontal gene transfer and that chromosomally encoded copper resistance genes may provide a fitness advantage over plasmid-borne resistance.
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Affiliation(s)
- Shaheen Bibi
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Kylie Weis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Amandeep Kaur
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Erica Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
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Shafique MS, Guo W, Chen X, Zhao K, Liu Y, Wang C, Ji Z. Genome resource of Xanthomonas oryzae pv. oryzae Chinese strain NE-8 causing bacterial blight of rice. Funct Integr Genomics 2023; 23:189. [PMID: 37246198 DOI: 10.1007/s10142-023-01109-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/11/2023] [Accepted: 05/16/2023] [Indexed: 05/30/2023]
Affiliation(s)
- Muhammad Sohaib Shafique
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China
| | - Wei Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Xifeng Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China
| | - Yapei Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China
| | - Chunlian Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572000, China.
| | - Zhiyuan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Sciences, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081, China.
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Coutinho TA, Jacques MA, Jones J. Editorial: Emergence and re-emergence of plant diseases caused by Xanthomonas species. Front Microbiol 2022; 13:1081601. [PMID: 36578575 PMCID: PMC9791255 DOI: 10.3389/fmicb.2022.1081601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Teresa A. Coutinho
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics/Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa,*Correspondence: Teresa A. Coutinho
| | - Marie-Agnes Jacques
- Institut Agro, INRAE, IRHS, SFR QUASAV, University of Angers, Angers, France
| | - Jeffrey Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
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Bernal E, Rotondo F, Roman-Reyna V, Klass T, Timilsina S, Minsavage GV, Iruegas-Bocardo F, Goss EM, Jones JB, Jacobs JM, Miller SA, Francis DM. Migration Drives the Replacement of Xanthomonas perforans Races in the Absence of Widely Deployed Resistance. Front Microbiol 2022; 13:826386. [PMID: 35369455 PMCID: PMC8971904 DOI: 10.3389/fmicb.2022.826386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Changes in Xanthomonas race and species composition causing bacterial spot of tomato have occurred throughout the world and are often associated with epidemics. Knowledge of bacterial population structure is key for resistance discovery and deployment. We surveyed Xanthomonas spp. composition from processing tomato fields in the Midwestern United States over a 4-year period between 2017 and 2020, compared these to strains collected previously, and found that X. perforans is currently the most prevalent species. We characterized 564 X. perforans isolates for sequence variation in avrXv3 to distinguish between race T3 and T4 and validated race designation using hypersensitive response (HR) assays for 106 isolates. Race T4 accounted for over 95% of X. perforans isolates collected in the Midwest between 2017 and 2020. Whole genome sequencing, Average Nucleotide Identity (ANI) analysis, core genome alignment and single nucleotide polymorphism (SNP) detection relative to a reference strain, and phylogenomic analysis suggest that the majority of Midwestern X. perforans strains collected between 2017 and 2020 were nearly identical, with greater than 99.99% ANI to X. perforans isolates collected from Collier County, Florida in 2012. These isolates shared a common SNP variant resulting an a premature stop codon in avrXv3. One sequenced isolate was identified with a deletion of avrXv3 and shared 99.99% ANI with a strain collected in Collier Co., Florida in 2006. A population shift to X. perforans T4 occurred in the absence of widely deployed resistance, with only 7% of tomato varieties tested having the resistant allele at the Xv3/Rx-4 locus. The persistence of nearly identical strains over multiple years suggests that migration led to the establishment of an endemic population. Our findings validate a genomics-based framework to track shifts in X. perforans populations due to migration, mutation, drift, or selection based on comparisons to 146 genomes.
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Affiliation(s)
- Eduardo Bernal
- Department of Horticulture and Crop Science, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - Francesca Rotondo
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - Veronica Roman-Reyna
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Taylor Klass
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Sujan Timilsina
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Gerald V. Minsavage
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Fernanda Iruegas-Bocardo
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Erica M. Goss
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Jeffrey B. Jones
- Department of Plant Pathology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jonathan M. Jacobs
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States
- Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Sally A. Miller
- Department of Plant Pathology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH, United States
| | - David M. Francis
- Department of Horticulture and Crop Science, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, OH, United States
- *Correspondence: David M. Francis,
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