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Yang CC, Wang ZY, Cheng CM. Insights into Superinfection Immunity Regulation of Xanthomonas axonopodis Filamentous Bacteriophage cf. Curr Microbiol 2023; 81:42. [PMID: 38112972 DOI: 10.1007/s00284-023-03539-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 10/26/2023] [Indexed: 12/21/2023]
Abstract
Filamentous bacteriophage cf infects Xanthomonas axonopodis pv. citri, a serious plant pathogen which causes citrus canker. To understand the immunity regulation of bacteria infected with bacteriophage cf, we applied DNA shuffling to mutate the cf intergenic region. One of the immunity mutants, cf-m3 (NCBI Taxonomy ID: 3050368) expressed a 106-109 fold greater superinfection ability compared with wild type cf. Nine mutations were identified on the cf-m3 phage, four of which were located within the coding region of an open reading frame (ORF165) for a hypothetical repressor, PT, and five located upstream of the PT coding region. A set of phages with mutations to the predicted PT protein or the upstream coding region were generated. All showed similarly low superinfection efficiency to wild type cf and no superinfection ability on cf lysogens. The results indicate that rather than superinfection inhibition, the PT protein and the un-transcribed cis element function individually as positive regulators of cf superinfection immunity. Greater superinfection ability depends on the simultaneous presence of both elements. This work yields further insight into the possible control of citrus canker disease through phages that overcome host superinfection immunity.
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Affiliation(s)
- Chia-Chin Yang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Zih-Yun Wang
- Department of Biomedical Sciences and Engineering, Tzu-Chi University, 701 Chung Yang Road Section 3, Hualien, 970, Taiwan
| | - Ching-Ming Cheng
- Department of Biomedical Sciences and Engineering, Tzu-Chi University, 701 Chung Yang Road Section 3, Hualien, 970, Taiwan.
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2
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Song D, Qi X, Huang Y, Jia A, Liang Y, Man C, Yang X, Jiang Y. Comparative proteomics reveals the antibiotic resistance and virulence of Cronobacter isolated from powdered infant formula and its processing environment. Int J Food Microbiol 2023; 407:110374. [PMID: 37678039 DOI: 10.1016/j.ijfoodmicro.2023.110374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Cronobacter species are opportunistic foodborne pathogens that can cause neonatal meningitis, sepsis, and necrotizing enterocolitis. In this genus, certain level strains have high mortality to infant (Cronobacter sakazakii and Cronobacter malonaticus) and antibiotic tolerance. Cronobacter has strong environmental tolerance (acid resistance, high temperature resistance, UV resistance, antibiotic resistance, etc.) and can survive in a variety of environments. It has been isolated in various production environments and products in several countries. However, the relationships between Cronobacter antibiotic tolerance and virulence remain unclear, especially at the molecular level. In this study, 96 strains of Cronobacter were isolated from powdered infant formula and its processing environment and screened for antibiotic tolerance, and proteomic maps of the representative strains of Cronobacter with antibiotic tolerance were generated by analyzing proteomics data using multiple techniques to identify protein that are implicated in Cronobacter virulence and antibiotic resistance. The increase in antibiotic tolerance of Cronobacter had a certain increase in the production of enterotoxin and hemolysin. Only triple tolerated Cronobacter sakazakii decreased the utilization of sialic acid. A total of 16,131 intracellular proteins were detected in eight representative strains, and different proteomes were present in strains with different antibiotic tolerance, including 56 virulence-related proteins. Multiple virulence proteins regulated by unknown genes were also found in the eight isolated representative strains.
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Affiliation(s)
- Danliangmin Song
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Xuehe Qi
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China.
| | - Yan Huang
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Ai Jia
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Yaqi Liang
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, Harbin 150030, China.
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, Harbin 150030, China.
| | - Yujun Jiang
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China.
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3
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Xu J, Zhang Y, Li J, Teper D, Sun X, Jones D, Wang Y, Tao J, Goss EM, Jones JB, Wang N. Phylogenomic analysis of 343 Xanthomonas citri pv. citri strains unravels introduction history and dispersal paths. PLoS Pathog 2023; 19:e1011876. [PMID: 38100539 PMCID: PMC10756548 DOI: 10.1371/journal.ppat.1011876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/29/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Xanthomonas citri pv. citri (Xcc) causes the devastating citrus canker disease. Xcc is known to have been introduced into Florida, USA in at least three different events in 1915, 1986 and 1995 with the first two claimed to be eradicated. It was questioned whether the Xcc introduction in 1986 has been successfully eradicated. Furthermore, it is unknown how Xcc has spread throughout the citrus groves in Florida. In this study, we investigated the population structure of Xcc to address these questions. We sequenced the whole genome of 343 Xcc strains collected from Florida groves between 1997 and 2016. Our analysis revealed two distinct clusters of Xcc. Our data strongly indicate that the claimed eradication of the 1986 Xcc introduction was not successful and Xcc strains from 1986 introduction were present in samples from at least 8 counties collected after 1994. Importantly, our data revealed that the Cluster 2 strains, which are present in all 20 citrus-producing counties sampled in Florida, originated from the Xcc introduction event in the Miami area in 1995. Our data suggest that Polk County is the epicenter of the dispersal of Cluster 2 Xcc strains, which is consistent with the fact that three major hurricanes passed through Polk County in 2004. As copper-based products have been extensively used to control citrus canker, we also investigated whether Xcc strains have developed resistance to copper. Notably, none of the 343 strains contained known copper resistance genes. Twenty randomly selected Xcc strains displayed sensitivity to copper. Overall, this study provides valuable insights into the introduction, eradication, spread, and copper resistance of Xcc in Florida.
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Affiliation(s)
- Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
| | - Yanan Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
| | - Jinyun Li
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
| | - Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
| | - Xiaoan Sun
- Florida Department of Agriculture and Consumer Services, Gainesville, Florida, United States of America
| | - Debra Jones
- Florida Department of Agriculture and Consumer Services, Gainesville, Florida, United States of America
| | - Yayu Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Jin Tao
- Guangdong Magigene Biotechnology Co., Ltd., Guangzhou, China
| | - Erica M. Goss
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Jeffrey B. Jones
- Department of Plant Pathology, IFAS, University of Florida, Gainesville, Florida, United States of America
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, Florida, United States of America
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4
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Wang Y, Xu X, Chen H, Yang F, Xu B, Wang K, Liu Q, Liang G, Zhang R, Jiao X, Zhang Y. Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers. BMC Genomics 2023; 24:530. [PMID: 37679681 PMCID: PMC10483869 DOI: 10.1186/s12864-023-09623-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
BACKGROUND Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a "generalist" species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive. RESULTS In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events. CONCLUSIONS A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers' gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.
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Affiliation(s)
- Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Xiaomeng Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Fang Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Bo Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Kun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Qianwen Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Guixin Liang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Ruiqi Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Xin'an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
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Campos PE, Pruvost O, Boyer K, Chiroleu F, Cao TT, Gaudeul M, Baider C, Utteridge TMA, Becker N, Rieux A, Gagnevin L. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nat Commun 2023; 14:4306. [PMID: 37474518 PMCID: PMC10359311 DOI: 10.1038/s41467-023-39950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
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Affiliation(s)
- Paola E Campos
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | | | - Thuy Trang Cao
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
- Herbier national, Muséum national d'Histoire naturelle, CP39, 57 rue Cuvier, 75005, Paris, France
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security, R.E. Vaughan Building (MSIRI Compound), Reduit, 80835, Mauritius
| | | | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- CIRAD, UMR PHIM, Montpellier, France.
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Lovelace AH, Dorhmi S, Hulin MT, Li Y, Mansfield JW, Ma W. Effector Identification in Plant Pathogens. PHYTOPATHOLOGY 2023; 113:637-650. [PMID: 37126080 DOI: 10.1094/phyto-09-22-0337-kd] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Effectors play a central role in determining the outcome of plant-pathogen interactions. As key virulence proteins, effectors are collectively indispensable for disease development. By understanding the virulence mechanisms of effectors, fundamental knowledge of microbial pathogenesis and disease resistance have been revealed. Effectors are also considered double-edged swords because some of them activate immunity in disease resistant plants after being recognized by specific immune receptors, which evolved to monitor pathogen presence or activity. Characterization of effector recognition by their cognate immune receptors and the downstream immune signaling pathways is instrumental in implementing resistance. Over the past decades, substantial research effort has focused on effector biology, especially concerning their interactions with virulence targets or immune receptors in plant cells. A foundation of this research is robust identification of the effector repertoire from a given pathogen, which depends heavily on bioinformatic prediction. In this review, we summarize methodologies that have been used for effector mining in various microbial pathogens which use different effector delivery mechanisms. We also discuss current limitations and provide perspectives on how recently developed analytic tools and technologies may facilitate effector identification and hence generation of a more complete vision of host-pathogen interactions. [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)
| | - Sara Dorhmi
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
- Department of Microbiology and Plant Pathology, University of California Riverside, CA 92521, U.S.A
| | | | - Yufei Li
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
| | - John W Mansfield
- Faculty of Natural Sciences, Imperial College London, London, SW7 2BX, U.K
| | - Wenbo Ma
- The Sainsbury Laboratory, Norwich, NR4 7UH, U.K
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Shahbaz E, Ali M, Shafiq M, Atiq M, Hussain M, Balal RM, Sarkhosh A, Alferez F, Sadiq S, Shahid MA. Citrus Canker Pathogen, Its Mechanism of Infection, Eradication, and Impacts. PLANTS (BASEL, SWITZERLAND) 2022; 12:plants12010123. [PMID: 36616252 PMCID: PMC9824702 DOI: 10.3390/plants12010123] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/14/2022] [Accepted: 12/13/2022] [Indexed: 05/16/2023]
Abstract
Citrus canker is a ravaging bacterial disease threatening citrus crops. Its major types are Asiatic Canker, Cancrosis B, and Cancrosis C, caused by Xanthomonas citri pv. citri (Xcc), Xanthomonas citri pv. aurantifolii pathotype-B (XauB), and pathotype-C (XauC), respectively. The bacterium enters its host through stomata and wounds, from which it invades the intercellular spaces in the apoplast. It produces erumpent corky necrotic lesions often surrounded by a chlorotic halo on the leaves, young stems, and fruits, which causes dark spots, defoliation, reduced photosynthetic rate, rupture of leaf epidermis, dieback, and premature fruit drop in severe cases. Its main pathogenicity determinant gene is pthA, whose variants are present in all citrus canker-causing pathogens. Countries where citrus canker is not endemic adopt different methods to prevent the introduction of the pathogen into the region, eradicate the pathogen, and minimize its dissemination, whereas endemic regions require an integrated management program to control the disease. The main aim of the present manuscript is to shed light on the pathogen profile, its mechanism of infection, and fruitful strategies for disease management. Although an adequate method to completely eradicate citrus canker has not been introduced so far, many new methods are under research to abate the disease.
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Affiliation(s)
- Esha Shahbaz
- Department of Food Sciences, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Mobeen Ali
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Muhammad Shafiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Muhammad Atiq
- Department of Plant Pathology, University of Agriculture, Faisalabad 38000, Pakistan
| | - Mujahid Hussain
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA
| | - Rashad Mukhtar Balal
- Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| | - Ali Sarkhosh
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Fernando Alferez
- Horticultural Science Department, Southwest Florida Research and Education Center, University of Florida/IFAS, Immokalee, FL 34142, USA
| | - Saleha Sadiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore 54590, Pakistan
| | - Muhammad Adnan Shahid
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA
- Correspondence:
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Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
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Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
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9
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Yu J, Xu X, Wang Y, Zhai X, Pan Z, Jiao X, Zhang Y. Prophage-mediated genome differentiation of the Salmonella Derby ST71 population. Microb Genom 2022; 8. [PMID: 35451954 PMCID: PMC9453062 DOI: 10.1099/mgen.0.000817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although Salmonella Derby ST71 strains have been recognized as poultry-specific by previous studies, multiple swine-associated S. Derby ST71 strains were identified in this long-term, multi-site epidemic study. Here, 15 representative swine-associated S. Derby ST71 strains were sequenced and compared with 65 (one swine-associated and 64 poultry-associated) S. Derby ST71 strains available in the NCBI database at a pangenomic level through comparative genomics analysis to identify genomic features related to the differentiation of swine-associated strains and previously reported poultry-associated strains. The distribution patterns of known Salmonella pathogenicity islands (SPIs) and virulence factor (VF) encoding genes were not capable of differentiating between the two strain groups. The results demonstrated that the S. Derby ST71 population harbours an open pan-genome, and swine-associated ST71 strains contain many more genes than the poultry-associated strains, mainly attributed to the prophage sequence contents in the genomes. The numbers of prophage sequences identified in the swine-associated strains were higher than those in the poultry-associated strains. Prophages specifically harboured by the swine-associated strains were found to contain genes that facilitate niche adaptation for the bacterial hosts. Gene deletion experiments revealed that the dam gene specifically present in the prophage of the swine-associated strains is important for S. Derby to adhere onto the host cells. This study provides novel insights into the roles of prophages during the genome differentiation of Salmonella.
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Affiliation(s)
- Jinyan Yu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xiaomeng Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xianyue Zhai
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Zhiming Pan
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Xinan Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China.,Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, PR China.,Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, PR China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, PR China
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10
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Lange HW, Tancos MA, Smart CD. Cruciferous Weeds Do Not Act as Major Reservoirs of Inoculum for Black Rot Outbreaks in New York State. PLANT DISEASE 2022; 106:174-181. [PMID: 34353128 DOI: 10.1094/pdis-05-21-0998-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: 06/13/2023]
Abstract
Cruciferous weeds have been shown to harbor diverse Xanthomonas campestris pathovars, including the agronomically damaging black rot of cabbage pathogen, X. campestris pv. campestris. However, the importance of weeds as inoculum sources for X. campestris pv. campestris outbreaks in New York remains unknown. To determine if cruciferous weeds act as primary reservoirs for X. campestris pv. campestris, fields that were rotating between cabbage or had severe black rot outbreaks were chosen for evaluation. Over a consecutive 3-year period, 148 cruciferous and noncruciferous weed samples were collected at 34 unique sites located across five New York counties. Of the 148 weed samples analyzed, 48 X. campestris isolates were identified, with a subset characterized using multilocus sequence analysis. All X. campestris isolates originated from weeds belonging to the Brassicaceae family, with predominant weed hosts being shepherd's purse (Capsella bursa-pastoris), wild mustard (Sinapis arvensis), yellow rocket (Barbarea vulgaris), and pennycress (Thlaspi arvense). Identifying pathogenic X. campestris weed isolates was rare, with only eight isolates causing brown necrotic leaf spots or typical V-shaped lesions on cabbage. There was no evidence of cabbage-infecting weed isolates persisting in an infected field by overwintering in weed hosts; however, similar cabbage and weed X. campestris haplotypes were identified in the same field during an active black rot outbreak. X. campestris weed isolates are genetically diverse both within and between fields, but our findings indicate that X. campestris weed isolates do not appear to act as primary sources of inoculum for B. oleracea fields in New York.
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Affiliation(s)
- Holly W Lange
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - Matthew A Tancos
- Foreign Disease-Weed Science Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Frederick, MD 21702
| | - Christine D Smart
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456
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11
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Li W, Li Z, Zhang L, Deng X, Zheng Z. Genome Sequence Resource of Xanthomonas citri pv. citri from Formalin-Fixed Citrus Leaves Specimen Showing Canker Lesions Collected in 1982. PLANT DISEASE 2022; 106:304-306. [PMID: 34328361 DOI: 10.1094/pdis-05-21-1100-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Xanthomonas citri pv. citri is the causative agent of citrus canker, one of the most devastating diseases threatening global citrus production. Here, we present the genome sequence of X. citri pv. citri strain GD82 from a formalin-fixed citrus leaf specimen showing canker lesions collected in 1982 in Guangdong Province, China. The GD82 genome consisted of 5,197,217 bp with G+C content of 64.8%, along with four circular plasmids: pXAC33 (32,377 bp), pXAC64 (63,972 bp), pXAC47 (47,810 bp), and pGD82.1 (219,560 bp). This is the oldest X. citri pv. citri genome from historical citrus canker specimens in China, which will enrich the current X. citri pv. citri genome database and facilitate genomic evolution research of X. citri pv. citri.
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Affiliation(s)
- Wenting Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Zhenxi Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Ling Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Xiaoling Deng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
| | - Zheng Zheng
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou, China
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12
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Huang CJ, Wu TL, Zheng PX, Ou JY, Ni HF, Lin YC. Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri. Front Microbiol 2021; 12:731711. [PMID: 34557177 PMCID: PMC8453159 DOI: 10.3389/fmicb.2021.731711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/18/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Worldwide citrus production is severely threatened by Asiatic citrus canker which is caused by the proteobacterium Xanthomonas citri subsp. citri. Foliar sprays of copper-based bactericides are frequently used to control plant bacterial diseases. Despite the sequencing of many X. citri strains, the genome diversity and distribution of genes responsible for metal resistance in X. citri subsp. citri strains from orchards with different management practices in Taiwan are not well understood. Results: The genomes of three X. citri subsp. citri strains including one copper-resistant strain collected from farms with different management regimes in Taiwan were sequenced by Illumina and Nanopore sequencing and assembled into complete circular chromosomes and plasmids. CRISPR spoligotyping and phylogenomic analysis indicated that the three strains were located in the same phylogenetic lineages and shared ∼3,000 core-genes with published X. citri subsp. citri strains. These strains differed mainly in the CRISPR repeats and pathogenicity-related plasmid-borne transcription activator-like effector (TALE)-encoding pthA genes. The copper-resistant strain has a unique, large copper resistance plasmid due to an unusual ∼40 kbp inverted repeat. Each repeat contains a complete set of the gene cluster responsible for copper and heavy metal resistance. Conversely, the copper sensitive strains carry no metal resistance genes in the plasmid. Through comparative analysis, the origin and evolution of the metal resistance clusters was resolved. Conclusion: Chromosomes remained constant among three strains collected in Taiwan, but plasmids likely played an important role in maintaining pathogenicity and developing bacterial fitness in the field. The evolution of pathogenicity factors and horizontal gene transfer events were observed in the three strains. These data suggest that agricultural management practices could be a potential trigger for the evolution of citrus canker pathogens. The decrease in the number of CRISPR repeats and pthA genes might be the result of adaptation to a less stressful environment. The metal resistance genes in the copper resistant X. citri strain likely originated from the Mauritian strain not the local copper-resistant X. euvesicatoria strain. This study highlights the importance of plasmids as 'vehicles' for exchanging genetic elements between plant pathogenic bacteria and contributing to bacterial adaptation to the environment.
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Affiliation(s)
- Chien-Jui Huang
- Department of Plant Medicine, National Chiayi University, Chiayi, Taiwan
| | - Ting-Li Wu
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Hui-Fang Ni
- Department of Plant Protection, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
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13
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Teper D, Xu J, Pandey SS, Wang N. PthAW1, a Transcription Activator-Like Effector of Xanthomonas citri subsp. citri, Promotes Host-Specific Immune Responses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1033-1047. [PMID: 33970668 DOI: 10.1094/mpmi-01-21-0026-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Citrus canker disease caused by Xanthomonas citri subsp. citri is one of the most destructive diseases in citrus. X. citri subsp. citri pathotypes display different host ranges. X. citri subsp. citri strain A (XccA) causes canker disease in most commercial citrus varieties, whereas strain AW (XccAW), which is genetically similar to XccA, infects only lime and alemow. Understanding the mechanism that determines the host range of pathogens is critical to investigating and utilizing host resistance. We hypothesized that XccAW would undergo mutations in genes that restrict its host range when artificially inoculated into incompatible citrus varieties. To test this hypothesis, we used an experimental evolution approach to identify phenotypic traits and genetic loci associated with the adaptation of XccAW to incompatible sweet orange. Repeated inoculation and reisolation cycles improved the ability of three independent XccAW strains to colonize sweet orange. Adapted XccAW strains displayed increased expression of type III secretion system and effector genes. Genome sequencing analysis indicated that two of the adapted strains harbored mutations in pthAW1, a transcription activator-like effector (TALE) gene, that corresponded to the removal of one or two repeats from the central DNA-binding repeat region. Introduction of the original but not the adapted pthAW1 variants into XccA abolished its ability to cause canker symptoms in sweet orange, Meyer lemon, and clementine but not in other XccAW-resistant citrus varieties. The original pthAW1, when expressed in XccA, induced ion leakage and the expression of pathogenesis-related genes but had no effect on CsLOB1 expression in sweet orange. Our study has identified a novel host-specific avirulence TALE and demonstrated active adaptive rearrangements of the TALE repeat array during host adaptation.[Formula: see text] Copyright © 2021 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)
- Doron Teper
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Sheo Shankar Pandey
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, U.S.A
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14
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Webster J, Bogema D, Chapman TA. Comparative Genomics of Xanthomonas citri pv. citri A* Pathotype Reveals Three Distinct Clades with Varying Plasmid Distribution. Microorganisms 2020; 8:microorganisms8121947. [PMID: 33302542 PMCID: PMC7764509 DOI: 10.3390/microorganisms8121947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/23/2022] Open
Abstract
Citrus bacterial canker (CBC) is an important disease of citrus cultivars worldwide that causes blister-like lesions on host plants and leads to more severe symptoms such as plant defoliation and premature fruit drop. The causative agent, Xanthomonas citri pv. citri, exists as three pathotypes—A, A*, and Aw—which differ in their host range and elicited host response. To date, comparative analyses have been hampered by the lack of closed genomes for the A* pathotype. In this study, we sequenced and assembled six CBC isolates of pathotype A* using second- and third-generation sequencing technologies to produce complete, closed assemblies. Analysis of these genomes and reference A, A*, and Aw sequences revealed genetic groups within the A* pathotype. Investigation of accessory genomes revealed virulence factors, including type IV secretion systems and heavy metal resistance genes, differentiating the genetic groups. Genomic comparisons of closed genome assemblies also provided plasmid distribution information for the three genetic groups of A*. The genomes presented here complement existing closed genomes of A and Aw pathotypes that are publicly available and open opportunities to investigate the evolution of X. citri pv. citri and the virulence factors that contribute to this serious pathogen.
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15
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Li L, Liu Z, Zhang M, Meng D, Liu X, Wang P, Li X, Jiang Z, Zhong S, Jiang C, Yin H. Insights into the Metabolism and Evolution of the Genus Acidiphilium, a Typical Acidophile in Acid Mine Drainage. mSystems 2020; 5:e00867-20. [PMID: 33203689 PMCID: PMC7677001 DOI: 10.1128/msystems.00867-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/28/2020] [Indexed: 01/05/2023] Open
Abstract
Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions.IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.
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Affiliation(s)
- Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Min Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Pei Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiutong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zhen Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuiping Zhong
- College of Zijin Mining, Fuzhou University, Fuzhou, China
- National Key Laboratory of Comprehensive Utilization of Low-Grade Refractory Gold Ores, Shanghang, China
| | - Chengying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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16
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Pang Z, Zhang L, Coaker G, Ma W, He SY, Wang N. Citrus CsACD2 Is a Target of Candidatus Liberibacter Asiaticus in Huanglongbing Disease. PLANT PHYSIOLOGY 2020; 184:792-805. [PMID: 32759268 PMCID: PMC7536665 DOI: 10.1104/pp.20.00348] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/27/2020] [Indexed: 05/06/2023]
Abstract
Citrus Huanglongbing (HLB), caused by Candidatus Liberibacter asiaticus (Las), is one of the most destructive citrus diseases worldwide, yet how Las causes HLB is poorly understood. Here we show that a Las-secreted protein, SDE15 (CLIBASIA_04025), suppresses plant immunity and promotes Las multiplication. Transgenic expression of SDE15 in Duncan grapefruit (Citrus × paradisi) suppresses the hypersensitive response induced by Xanthomonas citri ssp. citri (Xcc) and reduces the expression of immunity-related genes. SDE15 also suppresses the hypersensitive response triggered by the Xanthomonas vesicatoria effector protein AvrBsT in Nicotiana benthamiana, suggesting that it may be a broad-spectrum suppressor of plant immunity. SDE15 interacts with the citrus protein CsACD2, a homolog of Arabidopsis (Arabidopsis thaliana) ACCELERATED CELL DEATH 2 (ACD2). SDE15 suppression of plant immunity is dependent on CsACD2, and overexpression of CsACD2 in citrus suppresses plant immunity and promotes Las multiplication, phenocopying overexpression of SDE15. Identification of CsACD2 as a susceptibility target has implications in genome editing for novel plant resistance against devastating HLB.
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Affiliation(s)
- Zhiqian Pang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida/Institute of Food and Agricultural Sciences, Lake Alfred, Florida 33850
| | - Li Zhang
- MSU-DOE Plant Research Laboratory, Plant Resilient Institute, Michigan State University, East Lansing, Michigan 48824
- Howard Hughes Medical Institute, Michigan State University, East Lansing, Michigan 48824
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, California 95616
| | - Wenbo Ma
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California 92521
| | - Sheng-Yang He
- MSU-DOE Plant Research Laboratory, Plant Resilient Institute, Michigan State University, East Lansing, Michigan 48824
- Howard Hughes Medical Institute, Michigan State University, East Lansing, Michigan 48824
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida/Institute of Food and Agricultural Sciences, Lake Alfred, Florida 33850
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17
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Patané JSL, Martins J, Rangel LT, Belasque J, Digiampietri LA, Facincani AP, Ferreira RM, Jaciani FJ, Zhang Y, Varani AM, Almeida NF, Wang N, Ferro JA, Moreira LM, Setubal JC. Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses. BMC Genomics 2019; 20:700. [PMID: 31500575 PMCID: PMC6734499 DOI: 10.1186/s12864-019-6007-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a broad host spectrum, while A* and Aw are more restricted both in hosts and in geography. Two previous phylogenomic studies led to contrasting well-supported clades for sequenced genomes of these pathotypes. No extensive biogeographical or divergence dating analytic approaches have been so far applied to available genomes. RESULTS Based on a larger sampling of genomes than in previous studies (including six new genomes sequenced by our group, adding to a total of 95 genomes), phylogenomic analyses resulted in different resolutions, though overall indicating that A + AW is the most likely true clade. Our results suggest the high degree of recombination at some branches and the fast diversification of lineages are probable causes for this phylogenetic blurring effect. One of the genomes analyzed, X. campestris pv. durantae, was shown to be an A* strain; this strain has been reported to infect a plant of the family Verbenaceae, though there are no reports of any X. citri subsp. citri pathotypes infecting any plant outside the Citrus genus. Host reconstruction indicated the pathotype ancestor likely had plant hosts in the family Fabaceae, implying an ancient jump to the current Rutaceae hosts. Extensive dating analyses indicated that the origin of X. citri subsp. citri occurred more recently than the main phylogenetic splits of Citrus plants, suggesting dispersion rather than host-directed vicariance as the main driver of geographic expansion. An analysis of 120 pathogenic-related genes revealed pathotype-associated patterns of presence/absence. CONCLUSIONS Our results provide novel insights into the evolutionary history of X. citri subsp. citri as well as a sound phylogenetic foundation for future evolutionary and genomic studies of its pathotypes.
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Affiliation(s)
- José S L Patané
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Joaquim Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luiz Thiberio Rangel
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Luciano A Digiampietri
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Agda Paula Facincani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Rafael Marini Ferreira
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Fabrício José Jaciani
- Departamento de Pesquisa e Desenvolvimento, Fundo de Defesa da Citricultura (Fundecitrus), Araraquara, SP, Brazil
| | - Yunzeng Zhang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Alessandro M Varani
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, FL, USA
| | - Jesus A Ferro
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil
| | - Leandro M Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
- Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA.
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18
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Pruvost O, Boyer K, Ravigné V, Richard D, Vernière C. Deciphering how plant pathogenic bacteria disperse and meet: Molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity. Evol Appl 2019; 12:1523-1538. [PMID: 31462912 PMCID: PMC6708428 DOI: 10.1111/eva.12788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/25/2019] [Accepted: 02/24/2019] [Indexed: 12/15/2022] Open
Abstract
Although some plant pathogenic bacteria represent a significant threat to agriculture, the determinants of their ecological success and evolutionary potential are still poorly understood. Refining our understanding of bacterial strain circulation at small spatial scales and the biological significance and evolutionary consequences of co-infections are key questions. The study of bacterial population biology can be challenging, because it requires high-resolution markers that can be genotyped with a high throughput. Here, we overcame this difficulty for Xanthomonas citri pv. citri, a genetically monomorphic bacterium causing Asiatic citrus canker (ACC). Using a genotyping method that did not require cultivating the bacterium or purifying DNA, we deciphered the pathogen's spatial genetic structure at several microgeographic scales, down to single lesion, in a situation of ACC endemicity. In a grove where copper was recurrently applied for ACC management, copper-susceptible and copper-resistant X. citri pv. citri coexisted and the bacterial population structured as three genetic clusters, suggesting a polyclonal contamination. The range of spatial dependency, estimated for the two largest clusters, was four times greater for the cluster predominantly composed of copper-resistant bacteria. Consistently, the evenness value calculated for this cluster was indicative of increased transmission. Linkage disequilibrium was high even at a tree scale, probably due to a combination of clonality and admixture. Approximately 1% of samples exhibited within-lesion multilocus polymorphism, explained at least in part by polyclonal infections. Canker lesions, which are of major biological significance as an inoculum source, may also represent a preferred niche for horizontal gene transfer. This study points out the potential of genotyping data for estimating the range of spatial dependency of plant bacterial pathogens, an important parameter for guiding disease management strategies.
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Affiliation(s)
| | | | | | - Damien Richard
- CIRADUMR PVBMTSaint Pierre, La RéunionFrance
- ANSESSaint Pierre, La RéunionFrance
- Université de la RéunionUMR PVBMTSaint Denis, La RéunionFrance
| | - Christian Vernière
- CIRADUMR PVBMTSaint Pierre, La RéunionFrance
- CIRADUMR BGPIMontpellierFrance
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19
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A duplex quantitative real-time PCR assay for the detection and quantification of Xanthomonas phaseoli pv. dieffenbachiae from diseased and latently infected anthurium tissue. J Microbiol Methods 2019; 161:74-83. [PMID: 30858003 DOI: 10.1016/j.mimet.2019.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 11/22/2022]
Abstract
Anthurium bacterial blight caused by Xanthomonas phaseoli pv. dieffenbachiae (formerly Xanthomonas axonopodis pv. dieffenbachiae) is the major phytosanitary threat in many anthurium growing areas worldwide. Reliable and sensitive diagnostic tools are required for surveillance and certification programs. A duplex real-time quantitative PCR assay was developed for the detection and quantification of X. phaseoli pv. dieffenbachiae from anthurium tissue. This PCR assay targeted a X. phaseoli pv. dieffenbachiae-specific gene encoding an ABC transporter and an internal control encoding for chalcone synthase in Anthurium andreanum. A cycle threshold (Ct), using a receiver-operating characteristic approach (ROC), was implemented to ensure that the declaration of a positive sample was reliable. The duplex real-time assay displayed very high performance with regards to analytical specificity (100% inclusivity, 98.9% exclusivity), analytical sensitivity (LOD95% = 894 bacteria/ml corresponding to 18 bacteria per reaction) and repeatability. We demonstrated the pertinence of this real-time quantitative PCR assay for detecting X. phaseoli pv. dieffenbachiae from diseased leaf tissue (collected from outbreaks on anthurium) and from asymptomatic, latently infected anthurium plants. This assay could be useful for surveillance, as well as for indexing propagative plant material for the presence of X. phaseoli pv. dieffenbachiae.
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20
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Ference CM, Gochez AM, Behlau F, Wang N, Graham JH, Jones JB. Recent advances in the understanding of Xanthomonas citri ssp. citri pathogenesis and citrus canker disease management. MOLECULAR PLANT PATHOLOGY 2018; 19:1302-1318. [PMID: 29105297 PMCID: PMC6638175 DOI: 10.1111/mpp.12638] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/29/2017] [Accepted: 10/31/2017] [Indexed: 05/09/2023]
Abstract
Taxonomic status: Bacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species Xanthomonas citri ssp. citri (Xcc). Host range: Compatible hosts vary in their susceptibility to citrus canker (CC), with grapefruit, lime and lemon being the most susceptible, sweet orange being moderately susceptible, and kumquat and calamondin being amongst the least susceptible. Microbiological properties: Xcc is a rod-shaped (1.5-2.0 × 0.5-0.75 µm), Gram-negative, aerobic bacterium with a single polar flagellum. The bacterium forms yellow colonies on culture media as a result of the production of xanthomonadin. Distribution: Present in South America, the British Virgin Islands, Africa, the Middle East, India, Asia and the South Pacific islands. Localized incidence in the USA, Argentina, Brazil, Bolivia, Uruguay, Senegal, Mali, Burkina Faso, Tanzania, Iran, Saudi Arabia, Yemen and Bangladesh. Widespread throughout Paraguay, Comoros, China, Japan, Malaysia and Vietnam. Eradicated from South Africa, Australia and New Zealand. Absent from Europe.
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Affiliation(s)
- Christopher M. Ference
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research LaboratoryFort PierceFL 34945USA
- Department of Plant PathologyUniversity of FloridaGainesvilleFL 32611USA
| | - Alberto M. Gochez
- Citrus Pathology, EEA INTA Bella VistaBella VistaCorrientes 3432Argentina
| | - Franklin Behlau
- Department of Research & DevelopmentFundo de Defesa da Citricultura (Fundecitrus)AraraquaraSão Paulo 14.807‐040Brazil
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, University of FloridaLake AlfredFL 33850USA
| | - James H. Graham
- Department of Soil and Water Science, Citrus Research and Education Center, University of FloridaLake AlfredFL 33850USA
| | - Jeffrey B. Jones
- Department of Plant PathologyUniversity of FloridaGainesvilleFL 32611USA
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21
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Where are we going with genomics in plant pathogenic bacteria? Genomics 2018; 111:729-736. [PMID: 29678682 DOI: 10.1016/j.ygeno.2018.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022]
Abstract
Genome sequencing is commonly used in research laboratories right now thanks to the rise of high-throughput sequencing with higher speed and output-to-cost ratios. Here, we summarized the application of genomics in different aspects of plant bacterial pathosystems. Genomics has been used in studying the mechanisms of plant-bacteria interactions, and host specificity. It also helps with taxonomy, study of non-cultured bacteria, identification of causal agent, single cell sequencing, population genetics, and meta-transcriptomic. Overall, genomics has significantly improved our understanding of plant-microbe interaction.
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22
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Duan S, Jia H, Pang Z, Teper D, White F, Jones J, Zhou C, Wang N. Functional characterization of the citrus canker susceptibility gene CsLOB1. MOLECULAR PLANT PATHOLOGY 2018; 19:1908-1916. [PMID: 29461671 PMCID: PMC6638005 DOI: 10.1111/mpp.12667] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/29/2018] [Accepted: 02/16/2018] [Indexed: 05/08/2023]
Abstract
Xanthomonas citri ssp. citri (Xcc) is an important plant-pathogenic bacterium that causes citrus canker disease worldwide. PthA, a transcriptional activator-like (TAL) effector, directs the expression of the canker susceptibility gene CsLOB1. Here, we report our recent progress in the functional characterization of CsLOB1. Subcellular localization analysis of CsLOB1 protein in citrus protoplast revealed that CsLOB1 is primarily localized in the nucleus. We showed that CsLOB1 expression driven by dexamethasone (DEX) in CsLOB1-GR transgenic plants is associated with pustule formation following treatment with DEX. Pustule formation was not observed in DEX-treated wild-type plants and in non-treated CsLOB1-GR transgenic plants. Water soaking is typically associated with symptoms of citrus canker. Weaker water soaking was observed with pustule formation in CsLOB1-GR transgenic plants following DEX treatment. When CsLOB1-GR-transgenic Duncan grapefruit leaves were inoculated with Xcc306ΔpthA4 and treated with DEX, typical canker symptoms, including hypertrophy, hyperplasia and water soaking symptoms, were observed on DEX-treated transgenic plant leaves, but not on mock-treated plants. Twelve citrus genes that are induced by PthA4 are also stimulated by the DEX-induced expression of CsLOB1. As CsLOB1 acts as a transcriptional factor, we identified putative targets of CsLOB1 via bioinformatic and electrophoretic mobility shift assays. Cs2g20600, which encodes a zinc finger C3HC4-type RING finger protein, has been identified to be a direct target of CsLOB1. This study advances our understanding of the function of CsLOB1 and the molecular mechanism of how Xcc causes canker symptoms via CsLOB1.
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Affiliation(s)
- Shuo Duan
- Citrus Research InstituteSouthwest University, Chongqing400712, China
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
| | - Hongge Jia
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
| | - Zhiqian Pang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
| | - Doron Teper
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
| | - Frank White
- Department of Plant PathologyUniversity of FloridaGainesvilleFL 32611USA
| | - Jeffrey Jones
- Department of Plant PathologyUniversity of FloridaGainesvilleFL 32611USA
| | - Changyong Zhou
- Citrus Research InstituteSouthwest University, Chongqing400712, China
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, Institute of Food and Agricultural Sciences (IFAS)University of FloridaLake AlfredFL 33850USA
- China‐USA Citrus Huanglongbing Joint Laboratory (A joint laboratory of The University of Florida's Institute of Food and Agricultural Sciences and Gannan Normal University)National Navel Orange Engineering Research Center, Gannan Normal UniversityGanzhouJiangxiChina
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23
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Gochez AM, Huguet-Tapia JC, Minsavage GV, Shantaraj D, Jalan N, Strauß A, Lahaye T, Wang N, Canteros BI, Jones JB, Potnis N. Pacbio sequencing of copper-tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator-like effectors among X. citri strains. BMC Genomics 2018; 19:16. [PMID: 29301493 PMCID: PMC5755412 DOI: 10.1186/s12864-017-4408-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 12/21/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Xanthomonas citri, a causal agent of citrus canker, has been a well-studied model system due to recent availability of whole genome sequences of multiple strains from different geographical regions. Major limitations in our understanding of the evolution of pathogenicity factors in X. citri strains sequenced by short-read sequencing methods have been tracking plasmid reshuffling among strains due to inability to accurately assign reads to plasmids, and analyzing repeat regions among strains. X. citri harbors major pathogenicity determinants, including variable DNA-binding repeat region containing Transcription Activator-like Effectors (TALEs) on plasmids. The long-read sequencing method, PacBio, has allowed the ability to obtain complete and accurate sequences of TALEs in xanthomonads. We recently sequenced Xanthomonas citri str. Xc-03-1638-1-1, a copper tolerant A group strain isolated from grapefruit in 2003 from Argentina using PacBio RS II chemistry. We analyzed plasmid profiles, copy number and location of TALEs in complete genome sequences of X. citri strains. RESULTS We utilized the power of long reads obtained by PacBio sequencing to enable assembly of a complete genome sequence of strain Xc-03-1638-1-1, including sequences of two plasmids, 249 kb (plasmid harboring copper resistance genes) and 99 kb (pathogenicity plasmid containing TALEs). The pathogenicity plasmid in this strain is a hybrid plasmid containing four TALEs. Due to the intriguing nature of this pathogenicity plasmid with Tn3-like transposon association, repetitive elements and multiple putative sites for origins of replication, we might expect alternative structures of this plasmid in nature, illustrating the strong adaptive potential of X. citri strains. Analysis of the pathogenicity plasmid among completely sequenced X. citri strains, coupled with Southern hybridization of the pathogenicity plasmids, revealed clues to rearrangements of plasmids and resulting reshuffling of TALEs among strains. CONCLUSIONS We demonstrate in this study the importance of long-read sequencing for obtaining intact sequences of TALEs and plasmids, as well as for identifying rearrangement events including plasmid reshuffling. Rearrangement events, such as the hybrid plasmid in this case, could be a frequent phenomenon in the evolution of X. citri strains, although so far it is undetected due to the inability to obtain complete plasmid sequences with short-read sequencing methods.
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Affiliation(s)
- Alberto M Gochez
- Citrus Pathology, INTA EEA Bella Vista, Bella Vista, Corrientes, Argentina
| | | | - Gerald V Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Deepak Shantaraj
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Neha Jalan
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Annett Strauß
- University of Tübingen, ZMBP - General Genetics, Tuebingen, Germany
| | - Thomas Lahaye
- University of Tübingen, ZMBP - General Genetics, Tuebingen, Germany
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Blanca I Canteros
- Citrus Pathology, INTA EEA Bella Vista, Bella Vista, Corrientes, Argentina
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA.
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36830, USA.
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24
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Moreira LM, Soares MR, Facincani AP, Ferreira CB, Ferreira RM, Ferro MIT, Gozzo FC, Felestrino ÉB, Assis RAB, Garcia CCM, Setubal JC, Ferro JA, de Oliveira JCF. Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection. BMC Microbiol 2017; 17:155. [PMID: 28693412 PMCID: PMC5504864 DOI: 10.1186/s12866-017-1063-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 07/01/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker. A proteomic analysis under in planta infectious and non-infectious conditions was conducted in order to increase our knowledge about the adaptive process of Xac during infection. RESULTS For that, a 2D-based proteomic analysis of Xac at 1, 3 and 5 days after inoculation, in comparison to Xac growth in NB media was carried out and followed by MALDI-TOF-TOF identification of 124 unique differentially abundant proteins. Among them, 79 correspond to up-regulated proteins in at least one of the three stages of infection. Our results indicate an important role of proteins related to biofilm synthesis, lipopolysaccharides biosynthesis, and iron uptake and metabolism as possible modulators of plant innate immunity, and revealed an intricate network of proteins involved in reactive oxygen species adaptation during Plants` Oxidative Burst response. We also identified proteins previously unknown to be involved in Xac-Citrus interaction, including the hypothetical protein XAC3981. A mutant strain for this gene has proved to be non-pathogenic in respect to classical symptoms of citrus canker induced in compatible plants. CONCLUSIONS This is the first time that a protein repertoire is shown to be active and working in an integrated manner during the infection process in a compatible host, pointing to an elaborate mechanism for adaptation of Xac once inside the plant.
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Affiliation(s)
- Leandro M Moreira
- Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas (ICEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil. .,Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil.
| | - Márcia R Soares
- Departamento de Bioquímica (DBq), Instituto de Química (IQ), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Agda P Facincani
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil.
| | - Cristiano B Ferreira
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Rafael M Ferreira
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Maria I T Ferro
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Fábio C Gozzo
- Instituto de Química, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil
| | - Érica B Felestrino
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Renata A B Assis
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Camila Carrião M Garcia
- Departamento de Ciências Biológicas (DECBI), Instituto de Ciências Exatas e Biológicas (ICEB), Universidade Federal de Ouro Preto (UFOP), Ouro Preto, MG, Brazil.,Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - João C Setubal
- Departamento de Bioquímica (DB), Instituto de Química (IQ), Universidade de São Paulo (USP), São Paulo, SP, Brazil.,Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA
| | - Jesus A Ferro
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Universidade Estadual Paulista, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Julio C F de Oliveira
- Departamento de Ciências Biológicas (DCB), Universidade Federal de São Paulo (UNIFESP), Diadema, SP, Brazil
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25
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Di Lorenzo F, Silipo A, Andersen Gersby LB, Palmigiano A, Lanzetta R, Garozzo D, Boyer C, Pruvost O, Newman MA, Molinaro A. Xanthomonas citri pv. citri Pathotypes: LPS Structure and Function as Microbe-Associated Molecular Patterns. Chembiochem 2017; 18:772-781. [PMID: 28186388 DOI: 10.1002/cbic.201600671] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Indexed: 12/13/2022]
Abstract
Xanthomonas citri pv. citri is the pathogen responsible for Asiatic citrus canker, one of the most serious citrus diseases worldwide. The lipopolysaccharide (LPS) molecule has been demonstrated to be involved in X. citri pv. citri virulence. Despite enormous progress in investigations of the molecular mechanisms for bacterial pathogenicity, determination of the detailed LPS structure-activity relationship is limited, as the current knowledge is mainly based on structural determination of one X. citri pv. citri strain. As X. citri pv. citri strains are distinguished into three main pathogenicity groups, we characterized the full structure of the LPS from two pathotypes that differ in their host-range specificity. This revealed an intriguing difference in LPS O-chain structure. We also tested the LPSs and isolated lipid A moieties for their ability to act as microbe-associated molecular patterns in Arabidopsis thaliana. Both LPS/lipid As induced ROS accumulation, but no difference was observed between the two pathotypes.
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Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | | | - Angelo Palmigiano
- CNR-Istituto per i Polimeri, Compositi e Biomateriali IPCB, via Gaifami 18, 95126, Catania, Italy
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - Domenico Garozzo
- CNR-Istituto per i Polimeri, Compositi e Biomateriali IPCB, via Gaifami 18, 95126, Catania, Italy
| | - Claudine Boyer
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Réunion, France
| | - Olivier Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, La Réunion, France
| | - Mari-Anne Newman
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Copenhagen, Denmark
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
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26
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Quibod IL, Perez-Quintero A, Booher NJ, Dossa GS, Grande G, Szurek B, Vera Cruz C, Bogdanove AJ, Oliva R. Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment. Sci Rep 2016; 6:34137. [PMID: 27667260 PMCID: PMC5035989 DOI: 10.1038/srep34137] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/07/2016] [Indexed: 01/01/2023] Open
Abstract
Understanding the processes that shaped contemporary pathogen populations in agricultural landscapes is quite important to define appropriate management strategies and to support crop improvement efforts. Here, we took advantage of an historical record to examine the adaptation pathway of the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo) in a semi-isolated environment represented in the Philippine archipelago. By comparing genomes of key Xoo groups we showed that modern populations derived from three Asian lineages. We also showed that diversification of virulence factors occurred within each lineage, most likely driven by host adaptation, and it was essential to shape contemporary pathogen races. This finding is particularly important because it expands our understanding of pathogen adaptation to modern agriculture.
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Affiliation(s)
- Ian Lorenzo Quibod
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Alvaro Perez-Quintero
- Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Gerbert S Dossa
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Genelou Grande
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Boris Szurek
- Résistance des Plantes aux Bioagresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Casiana Vera Cruz
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, USA
| | - Ricardo Oliva
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
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27
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Jacques MA, Arlat M, Boulanger A, Boureau T, Carrère S, Cesbron S, Chen NWG, Cociancich S, Darrasse A, Denancé N, Fischer-Le Saux M, Gagnevin L, Koebnik R, Lauber E, Noël LD, Pieretti I, Portier P, Pruvost O, Rieux A, Robène I, Royer M, Szurek B, Verdier V, Vernière C. Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:163-87. [PMID: 27296145 DOI: 10.1146/annurev-phyto-080615-100147] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strains usually cause disease on only a few plant species and are highly adapted to their hosts, making them pertinent models to study host specificity. This review summarizes our current understanding of the molecular basis of host specificity in the Xanthomonas genus, with a particular focus on the ecology, physiology, and pathogenicity of the bacterium. Despite our limited understanding of the basis of host specificity, type III effectors, microbe-associated molecular patterns, lipopolysaccharides, transcriptional regulators, and chemotactic sensors emerge as key determinants for shaping host specificity.
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Affiliation(s)
- Marie-Agnès Jacques
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Matthieu Arlat
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, F-31062 Toulouse, France
| | - Alice Boulanger
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, F-31062 Toulouse, France
| | - Tristan Boureau
- Université Angers, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France;
| | - Sébastien Carrère
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
| | - Sophie Cesbron
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Nicolas W G Chen
- Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France;
| | - Stéphane Cociancich
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Armelle Darrasse
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Nicolas Denancé
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Marion Fischer-Le Saux
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Lionel Gagnevin
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Ralf Koebnik
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Emmanuelle Lauber
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
| | - Laurent D Noël
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
| | - Isabelle Pieretti
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Perrine Portier
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Olivier Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Adrien Rieux
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Isabelle Robène
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Monique Royer
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Boris Szurek
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Valérie Verdier
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Christian Vernière
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
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Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O. Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges. BMC Genomics 2015; 16:1098. [PMID: 26699528 PMCID: PMC4690215 DOI: 10.1186/s12864-015-2310-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/15/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The identification of factors involved in the host range definition and evolution is a pivotal challenge in the goal to predict and prevent the emergence of plant bacterial disease. To trace the evolution and find molecular differences between three pathotypes of Xanthomonas citri pv. citri that may explain their distinctive host ranges, 42 strains of X. citri pv. citri and one outgroup strain, Xanthomonas citri pv. bilvae were sequenced and compared. RESULTS The strains from each pathotype form monophyletic clades, with a short branch shared by the A(w) and A pathotypes. Pathotype-specific recombination was detected in seven regions of the alignment. Using Ancestral Character Estimation, 426 SNPs were mapped to the four branches at the base of the A, A*, A(w) and A/A(w) clades. Several genes containing pathotype-specific nonsynonymous mutations have functions related to pathogenicity. The A pathotype is enriched for SNP-containing genes involved in defense mechanisms, while A* is significantly depleted for genes that are involved in transcription. The pathotypes differ by four gene islands that largely coincide with regions of recombination and include genes with a role in virulence. Both A* and A(w) are missing genes involved in defense mechanisms. In contrast to a recent study, we find that there are an extremely small number of pathotype-specific gene presences and absences. CONCLUSIONS The three pathotypes of X. citri pv. citri that differ in their host ranges largely show genomic differences related to recombination, horizontal gene transfer and single nucleotide polymorphism. We detail the phylogenetic relationship of the pathotypes and provide a set of candidate genes involved in pathotype-specific evolutionary events that could explain to the differences in host range and pathogenicity between them.
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Affiliation(s)
- Jonathan L Gordon
- Université de la Réunion, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France.
- Current Address: CIRAD, UMR CMAEE, F-97170, Petit-Bourg, Guadeloupe, France.
| | | | - Aline Escalon
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France.
| | - Valérie Barbe
- CEA/DSV/IG/Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France.
| | | | - Lionel Gagnevin
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France.
- Current Address: UMR IPME, IRD-CIRAD-Université Montpellier, 34394, Montpellier, France.
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