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Qiu Y, Wei F, Meng H, Peng M, Zhang J, He Y, Wei L, Ahmed W, Ji G. Whole-genome sequencing and comparative genome analysis of Xanthomonas fragariae YM2 causing angular leaf spot disease in strawberry. FRONTIERS IN PLANT SCIENCE 2023; 14:1267132. [PMID: 38192696 PMCID: PMC10773614 DOI: 10.3389/fpls.2023.1267132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
Abstract
Background Angular leaf spot disease caused by plant pathogenic bacterium Xanthomonas fragariae seriously threatens strawberry crop production globally. Methods In this study, we sequenced the whole genome of X. fragariae YM2, isolated from Yunnan Province, China. In addition, we performed a comparative genome analysis of X. fragariae YM2 with two existing strains of X. fragariae YL19 and SHQP01 isolated from Liaoning and Shanghai, respectively. Results The results of Nanopore sequencing showed that X. fragariae YM2 comprises one single chromosome with a contig size of 4,263,697 bp, one plasmid contig size of 0.39 Mb, a GC content ratio of 62.27%, and 3,958 predicted coding genes. The genome of YM2 comprises gum, hrp, rpf, and xps gene clusters and lipopolysaccharide (LPS), which are typical virulence factors in Xanthomonas species. By performing a comparative genomic analysis between X. fragariae strains YM2, YL19, and SHQP01, we found that strain YM2 is similar to YL19 and SHQP01 regarding genome size and GC contents. However, there are minor differences in the composition of major virulence factors and homologous gene clusters. Furthermore, the results of collinearity analysis demonstrated that YM2 has lower similarity and longer evolutionary distance with YL19 and SHQP01, but YL19 is more closely related to SHQP01. Conclusions The availability of this high-quality genetic resource will serve as a basic tool for investigating the biology, molecular pathogenesis, and virulence of X. fragariae YM2. In addition, unraveling the potential vulnerabilities in its genetic makeup will aid in developing more effective disease suppression control measures.
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Affiliation(s)
- Yue Qiu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- College of Agriculture, Anshun University, Anshun, Guizhou, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Fangjun Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Han Meng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Menglin Peng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Jinhao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yilu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Lanfang Wei
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Agricultural Foundation Experiment Teaching Center, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Waqar Ahmed
- College of Plant Protection, South China Agricultural University, Guangzhou, Guangdong, China
| | - Guanghai Ji
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan, China
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2
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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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3
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Liyanapathiranage P, Wagner N, Avram O, Pupko T, Potnis N. Phylogenetic Distribution and Evolution of Type VI Secretion System in the Genus Xanthomonas. Front Microbiol 2022; 13:840308. [PMID: 35495725 PMCID: PMC9048695 DOI: 10.3389/fmicb.2022.840308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
The type VI secretion system (T6SS) present in many Gram-negative bacteria is a contact-dependent apparatus that can directly deliver secreted effectors or toxins into diverse neighboring cellular targets including both prokaryotic and eukaryotic organisms. Recent reverse genetics studies with T6 core gene loci have indicated the importance of functional T6SS toward overall competitive fitness in various pathogenic Xanthomonas spp. To understand the contribution of T6SS toward ecology and evolution of Xanthomonas spp., we explored the distribution of the three distinguishable T6SS clusters, i3*, i3***, and i4, in approximately 1,740 Xanthomonas genomes, along with their conservation, genetic organization, and their evolutionary patterns in this genus. Screening genomes for core genes of each T6 cluster indicated that 40% of the sequenced strains possess two T6 clusters, with combinations of i3*** and i3* or i3*** and i4. A few strains of Xanthomonas citri, Xanthomonas phaseoli, and Xanthomonas cissicola were the exception, possessing a unique combination of i3* and i4. The findings also indicated clade-specific distribution of T6SS clusters. Phylogenetic analysis demonstrated that T6SS clusters i3* and i3*** were probably acquired by the ancestor of the genus Xanthomonas, followed by gain or loss of individual clusters upon diversification into subsequent clades. T6 i4 cluster has been acquired in recent independent events by group 2 xanthomonads followed by its spread via horizontal dissemination across distinct clades across groups 1 and 2 xanthomonads. We also noted reshuffling of the entire core T6 loci, as well as T6SS spike complex components, hcp and vgrG, among different species. Our findings indicate that gain or loss events of specific T6SS clusters across Xanthomonas phylogeny have not been random.
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Affiliation(s)
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Oren Avram
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
- *Correspondence: Neha Potnis,
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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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5
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Palomo Gómez JL, Shima M, Monterde A, Navarro I, Barbé S, Marco-Noales E. First report of bacterial leaf blight caused by Xanthomonas hortorum pv. carotae on carrots in Spain. PLANT DISEASE 2021; 105:2712. [PMID: 33622058 DOI: 10.1094/pdis-11-20-2493-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In September 2019, symptoms resembling those of bacterial leaf blight were observed on carrot plants (Daucus carota L. subsp. sativus Hoffm.) cv. Romance cultivated in commercial plots in Chañe (Segovia), Spain. Symptoms were observed in two plots surveyed representing three hectares, with an incidence greater than 90%, and also in some plots in other nearby municipalities sown with the same batch of seeds. The lesions observed at the ends of the leaves were initially yellow that develop dark brown to black with chlorotic halos on leaflets that turned necrotic. Yellow, Xanthomonas-like colonies were isolated onto YPGA medium (Ridé 1969) from leaf lesions. Two bacterial isolates were selected and confirmed by real-time PCR using a specific primer set for Xanthomonas hortorum pv. carotae (Temple et al. 2013). All isolates were gram-negative, aerobic rods positive for catalase, able of hydrolyzing casein and aesculin and growing at 2% NaCl, while were negative for oxidase and urease tests. Sequences of 16S rRNA gene showed 100% similarity with Xanthomonas campestris, X. arboricola, X. gardneri, X. cynarae strains (GenBank accession numbers: MW077507.1 and MW077508.1 for the isolates CRD19-206.3 and CRD19-206.4, respectively). However, the resulting phylogeny of multilocus sequence analysis (MLSA) of a concatenation of the housekeeping genes atpD, dnaK, and efp (Bui Thi Ngoc et al. 2010), by using neighbour-joining trees generated with 500 bootstrap replicates, grouped the two isolates with the X. hortorum pv. carotae M081 strain (Kimbrel et al. 2011) (GenBank accession numbers: MW161270 and MW161271 for atpD for the two isolates, respectively; MW161268 and MW161269 for dnaK; MW161272 and MW161273 for efp). A pairwise identity analysis revealed a 100% identity between all three isolates. Pathogenicity of the isolates was tested by spray inoculation (Christianson et al. 2015) with a bacterial suspension (108 CFU/ml) prepared in sterile distilled water at 3 to 4 true-leaf stage (six plants per isolate). Sterile distilled water was used as negative control. The inoculated plants were incubated in a growth chamber (25°C and 95% relative humidity [RH]) for 72 h, and then transferred to a greenhouse at 24 to 28°C and 65% RH. Characteristic leaf blight symptoms developed on inoculated carrot plants, while no symptoms were observed on the negative control plants 20 days after inoculation. The bacterium was re-isolated from symptomatic tissue and the identity confirmed through PCR analysis. Based on PCR, morphological and phenotypic tests, sequence analysis, and pathogenicity assays, the isolates were identified as X. hortorum pv. carotae. To our knowledge, this is the first report of bacterial leaf blight of carrot caused by X. hortorum pv. carotae in Spain, and the first molecular and pathological characterization. It is important to early detect this pathogen and take suitable measures to prevent its spread, since it could cause yield losses for a locally important crop such as carrot.
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Affiliation(s)
- José Luis Palomo Gómez
- Consejería de Agricultura y Ganadería de la Junta de Castilla y León, Centro Regional de Diagnóstico, Salamanca, Spain;
| | - Maria Shima
- Consejería de Agricultura y Ganadería de la Junta de Castilla y León, Centro Regional de Diagnóstico, Salamanca, Spain;
| | - Adela Monterde
- Instituto Valenciano de Investigaciones Agrarias, 70706, Moncada, Valencia, Spain;
| | - Inmaculada Navarro
- Instituto Valenciano de Investigaciones Agrarias, 70706, Moncada, Valencia, Spain;
| | - Silvia Barbé
- Instituto Valenciano de Investigaciones Agrarias, 70706, Moncada, Valenciana, Spain;
| | - Ester Marco-Noales
- Instituto Valenciano de Investigaciones Agrarias, 70706, CV-315 km 10,7, Moncada, Valencia, Spain, 46113;
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6
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Jeong K, Muñoz-Bodnar A, Arias Rojas N, Poulin L, Rodriguez-R LM, Gagnevin L, Vernière C, Pruvost O, Koebnik R. CRISPR elements provide a new framework for the genealogy of the citrus canker pathogen Xanthomonas citri pv. citri. BMC Genomics 2019; 20:917. [PMID: 31791238 PMCID: PMC6889575 DOI: 10.1186/s12864-019-6267-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/06/2019] [Indexed: 12/26/2022] Open
Abstract
Background Xanthomonads are an important clade of Gram-negative bacteria infecting a plethora of economically important host plants, including citrus. Knowledge about the pathogen’s diversity and population structure are prerequisite for epidemiological surveillance and efficient disease management. Rapidly evolving genetic loci, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are of special interest to develop new molecular typing tools. Results We analyzed CRISPR loci of 56 Xanthomonas citri pv. citri strains of world-wide origin, a regulated pathogen causing Asiatic citrus canker in several regions of the world. With one exception, 23 unique sequences built up the repertoire of spacers, suggesting that this set of strains originated from a common ancestor that already harbored these 23 spacers. One isolate originating from Pakistan contained a string of 14 additional, probably more recently acquired spacers indicating that this genetic lineage has or had until recently the capacity to acquire new spacers. Comparison of CRISPR arrays with previously obtained molecular typing data, such as amplified fragment length polymorphisms (AFLP), variable-number of tandem-repeats (VNTR) and genome-wide single-nucleotide polymorphisms (SNP), demonstrated that these methods reveal similar evolutionary trajectories. Notably, genome analyses allowed to generate a model for CRISPR array evolution in X. citri pv. citri, which provides a new framework for the genealogy of the citrus canker pathogen. Conclusions CRISPR-based typing will further improve the accuracy of the genetic identification of X. citri pv. citri outbreak strains in molecular epidemiology analyses, especially when used concomitantly with another genotyping method.
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Affiliation(s)
- Kwanho Jeong
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Alejandra Muñoz-Bodnar
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Current address: Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, USA
| | | | - Lucie Poulin
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Laboratoire de Biologie et de Pathologie Végétales, Université de Nantes, Nantes, France
| | - Luis Miguel Rodriguez-R
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,Present address: Department of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lionel Gagnevin
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.,CIRAD, UMR PVBMT, 97410, Saint Pierre, La Réunion, France
| | - Christian Vernière
- CIRAD, UMR PVBMT, 97410, Saint Pierre, La Réunion, France.,CIRAD, UMR BGPI, 34398, Montpellier, France
| | | | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France.
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7
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Dhakal U, Dobhal S, Alvarez AM, Arif M. Phylogenetic Analyses of Xanthomonads Causing Bacterial Leaf Spot of Tomato and Pepper: Xanthomonas euvesicatoria Revealed Homologous Populations Despite Distant Geographical Distribution. Microorganisms 2019; 7:microorganisms7100462. [PMID: 31623235 PMCID: PMC6843189 DOI: 10.3390/microorganisms7100462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/13/2019] [Accepted: 10/14/2019] [Indexed: 12/28/2022] Open
Abstract
Bacterial leaf spot of tomato and pepper (BLS), an economically important bacterial disease caused by four species of Xanthomonas (X. euvesicatoria (Xe), X. vesicatoria (Xv), X. gardneri (Xg), and X. perforans (Xp)), is a global problem and can cause over 50% crop loss under unfavorable conditions. Among the four species, Xe and Xv are prevalent worldwide. Characterization of the pathogens is crucial for disease management and regulatory purposes. In this study, we performed a multilocus sequence analysis (MLSA) with six genes (hrcN, dnaA gyrB, gapA, pdg, and hmbs) on BLS strains. Other Xanthomonas species were included to determine phylogenetic relationships within and among the tested strains. Four BLS species comprising 76 strains from different serological groups and diverse geographical locations were resolved into three major clades. BLS xanthomonads formed distinct clusters in the phylogenetic analyses. Three other xanthomonads, including X. albilineans, X. sacchari, and X. translucens pv. undolusa revealed less than 85%, 88%, and 89% average nucleotide identity (ANI), respectively, with the other species of Xanthomonas included in this study. Both antibody and MLSA data showed that Xv was clearly separated from Xe and that the latter strains were remarkably clonal, even though they originated from distant geographical locations. The Xe strains formed two separate phylogenetic groups; Xe group A1 consisted only of tomato strains, whereas Xe group A2 included strains from pepper and tomato. In contrast, the Xv group showed greater heterogeneity. Some Xv strains from South America were closely related to strains from California, while others grouped closer to a strain from Indiana and more distantly to a strain from Hawaii. Using this information molecular tests can now be devised to track distribution of clonal populations that may be introduced into new geographic areas through seeds and other infected plant materials.
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Affiliation(s)
- Upasana Dhakal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Manoa, HI 96822, USA.
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Manoa, HI 96822, USA.
| | - Anne M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Manoa, HI 96822, USA.
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Manoa, HI 96822, USA.
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8
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Fonseca NP, Patané JSL, Varani AM, Felestrino ÉB, Caneschi WL, Sanchez AB, Cordeiro IF, Lemes CGDC, Assis RDAB, Garcia CCM, Belasque J, Martins J, Facincani AP, Ferreira RM, Jaciani FJ, de Almeida NF, Ferro JA, Moreira LM, Setubal JC. Analyses of Seven New Genomes of Xanthomonas citri pv. aurantifolii Strains, Causative Agents of Citrus Canker B and C, Show a Reduced Repertoire of Pathogenicity-Related Genes. Front Microbiol 2019; 10:2361. [PMID: 31681223 PMCID: PMC6797930 DOI: 10.3389/fmicb.2019.02361] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/27/2019] [Indexed: 11/21/2022] Open
Abstract
Xanthomonas citri pv. aurantifolii pathotype B (XauB) and pathotype C (XauC) are the causative agents respectively of citrus canker B and C, diseases of citrus plants related to the better-known citrus canker A, caused by Xanthomonas citri pv. citri. The study of the genomes of strains of these related bacterial species has the potential to bring new understanding to the molecular basis of citrus canker as well as their evolutionary history. Up to now only one genome sequence of XauB and only one genome sequence of XauC have been available, both in draft status. Here we present two new genome sequences of XauB (both complete) and five new genome sequences of XauC (two complete). A phylogenomic analysis of these seven genome sequences along with 24 other related Xanthomonas genomes showed that there are two distinct and well-supported major clades, the XauB and XauC clade and the Xanthomonas citri pv. citri clade. An analysis of 62 Type III Secretion System effector genes showed that there are 42 effectors with variable presence/absence or pseudogene status among the 31 genomes analyzed. A comparative analysis of secretion-system and surface-structure genes showed that the XauB and XauC genomes lack several key genes in pathogenicity-related subsystems. These subsystems, the Types I and IV Secretion Systems, and the Type IV pilus, therefore emerge as important ones in helping explain the aggressiveness of the A type of citrus canker and the apparent dominance in the field of the corresponding strain over the B and C strains.
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Affiliation(s)
- Natasha Peixoto Fonseca
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - José S L Patané
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
| | - Alessandro M Varani
- Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil
| | - Érica Barbosa Felestrino
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Washington Luiz Caneschi
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Angélica Bianchini Sanchez
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Isabella Ferreira Cordeiro
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Camila Gracyelle de Carvalho Lemes
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Renata de Almeida Barbosa Assis
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - Camila Carrião Machado Garcia
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil
| | - Joaquim Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Agda Paula Facincani
- Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil
| | - Rafael Marini Ferreira
- Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil
| | | | | | - Jesus Aparecido Ferro
- Departamento de Tecnologia, Universidade Estadual Paulista, UNESP, Campus de Jaboticabal, Jaboticabal, Brazil
| | - Leandro Marcio Moreira
- Programa de Pós-graduação em Biotecnologia, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil.,Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, Brazil
| | - João C Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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9
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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: 22] [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: 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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10
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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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11
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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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12
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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: 70] [Impact Index Per Article: 11.7] [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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13
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Tian Y, Zhao Y, Chen X, Dai Y, Zhao W, Hu B, Walcott RR. Evidence for a Novel Phylotype of Pseudomonas syringae Causing Bacterial Leaf Blight of Cantaloupe in China. PLANT DISEASE 2017; 101:1746-1752. [PMID: 30676919 DOI: 10.1094/pdis-01-17-0110-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacterial leaf blight (BLB) has caused severe yield losses in cantaloupe (Cucumis melo L.) in the major melon-growing regions of China since the beginning of the twentieth century. Historically, Pseudomonas syringae pv. lachrymans was considered to be the causal agent of BLB of cantaloupe and angular leaf spot of cucumber. In the process of characterizing bacteria isolated from cantaloupe, we observed that putative P. syringae pv. lachrymans yielded negative results in P. syringae pv. lachrymans-specific PCR assays. This suggested that the P. syringae pv. lachrymans-like strains from cantaloupe were distinct from those recovered from cucumber. To investigate the differences between P. syringae pv. lachrymans-like strains isolated from cantaloupe and cucumber, 13 P. syringae strains isolated from cantaloupe [12 from China and 1 from Zimbabwe (NCPPB2916)] and 7 additional P. syringae reference strains were analyzed by catabolic profiling, phylogenetic analysis by multilocus sequence analysis (MLSA) and pathogenicity tests on cantaloupe leaflets. Catabolic profiling and MLSA based on 10 housekeeping genes and 2 hypersensitive response and pathogenicity (hrp) genes allowed us to differentiate strains isolated from cantaloupe and cucumber. Pseudomonas syringae pv. lachrymans strains isolated from cucumber clustered with genomospecies 2, and 13 P. syringae strains isolated from cantaloupe belonged to genomospecies 1. While all cantaloupe strains were closely related to P. syringae pv. aptata, they could be differentiated from this pathovar based on metabolic tests and MLSA. Pathogenicity tests showed that all strains isolated from cantaloupe and cucumber were only pathogenic on their original hosts. Based on these observations we conclude that P. syringae pv. lachrymans strains recovered from cantaloupe in China represent a novel phylotype.
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Affiliation(s)
- Yanli Tian
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuqiang Zhao
- Institute of Botany, Jiangsu Province and the Chinese Academy of Sciences, Nanjing 210014, China
| | - Xuezi Chen
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanfeng Dai
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenjun Zhao
- Chinese Academy of Inspection and Quarantine, Beijing, 100029, China
| | - Baishi Hu
- College of Plant Protection and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China and National Engineering Research Center for Cucurbits, Changji 831100, China
| | - R R Walcott
- Department of Plant Pathology, The University of Georgia, Athens 30602
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14
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Bansal K, Midha S, Kumar S, Patil PB. Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity. Appl Environ Microbiol 2017; 83:e02993-16. [PMID: 28258140 PMCID: PMC5394309 DOI: 10.1128/aem.02993-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/22/2017] [Indexed: 11/20/2022] Open
Abstract
Citrus canker, caused by Xanthomonas citri pv. citri, is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed that X. citri pv. citri is related to many other pathovars, which can be collectively referred as Xanthomonas citri pathovars (XCPs). From the present study, we report the genome sequences of 18 XCPs and compared them with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster, suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, the majority of these XCPs were first noticed in India, corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role of interstrain genomic flux of these XCPs since their diversification from a common ancestor. Even though there are wide variations in type III gene effectomes, we identified three core effectors which can be valuable in resistance-breeding programs. Overall, genomic examination of ecological relatives allowed us to dissect the tremendous genomic potential of X. citri species to rapidly evolve into specialized strains infecting diverse crop plants.IMPORTANCE Host specialization is one of the characteristic features of highly evolved pathogens such as the Xanthomonas group of phytopathogenic bacteria. Since the hosts involve staple crops and economically important fruits such as citrus, detailed understanding of the diversity and evolution of such strains infecting diverse plants is important for quarantine purposes. In the present study, we carried out genomic investigation of members of a phylogenetically and ecologically defined group of Xanthomonas strains pathogenic to diverse plants, including citrus. This group includes the oldest Xanthomonas pathovars and also recently emerged pathovars in a particular country where they are endemic. Our high-throughput genomic study has provided novel insights into the evolution of a unique lineage consisting of serious pathogens and their ecological relatives, suggesting the nature, scope, and pattern of rapid and recent diversification. Further, from the level of species to that of clonal variants, the study revealed interesting genomic patterns in diversification of a Xanthomonas lineage and perhaps will inspire careful study of the host range of the included pathovars.
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Affiliation(s)
- Kanika Bansal
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Samriti Midha
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- CSIR-Institute of Microbial Technology, Chandigarh, India
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15
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High-Quality Draft Genome Sequences of Two Xanthomonas Pathotype Strains Infecting Aroid Plants. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00902-16. [PMID: 27587819 PMCID: PMC5009976 DOI: 10.1128/genomea.00902-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We present here the draft genome sequences of bacterial pathogens of the Araceae family, Xanthomonas axonopodis pv. dieffenbachiae LMG 695 and Xanthomonas campestris pv. syngonii LMG 9055, differing in host range. A comparison between genome sequences will help understand the mechanisms involved in tissue specificity and adaptation to host plants.
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16
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Zombre C, Sankara P, Ouédraogo SL, Wonni I, Boyer K, Boyer C, Terville M, Javegny S, Allibert A, Vernière C, Pruvost O. Natural Infection of Cashew (Anacardium occidentale) by Xanthomonas citri pv. mangiferaeindicae in Burkina Faso. PLANT DISEASE 2016; 100:718-723. [PMID: 30688624 DOI: 10.1094/pdis-10-15-1137-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Xanthomonas citri pv. mangiferaeindicae is the causal agent of bacterial canker of mango (Mangifera indica, Anacardiaceae), a disease of international importance. Since the original description of the bacterium in the 1940s, the status of cashew (Anacardium occidentale, Anacardiaceae) as a host species has been unclear. Here, we report the first outbreak of a cashew bacterial disease in Burkina Faso (Western Africa) where X. citri pv. mangiferaeindicae recently emerged on mango. A comprehensive molecular characterization, based on multilocus sequence analysis, supplemented with pathogenicity assays of isolates obtained during the outbreak, indicated that the causal agent on cashew in Burkina Faso is X. citri pv. mangiferaeindicae and not X. citri pv. anacardii, which was previously reported as the causal agent of a cashew bacterial leaf spot in Brazil. Pathogenicity data supported by population biology in Burkina Faso suggest a lack of host specialization. Therefore, the inoculum from each crop is potentially harmful to both host species. Symptoms induced on cashew leaves and fruit by X. citri pv. mangiferaeindicae and nonpigmented strains of X. citri pv. anacardii are similar, although the causative bacteria are genetically different. Thus, xanthomonads pathogenic on cashew may represent a new example of pathological convergence in this bacterial genus.
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Affiliation(s)
- C Zombre
- Université de Ouagadougou, Ecole doctorale Science et Technologie, Ouagadougou, Burkina Faso
| | - P Sankara
- Université de Ouagadougou, Ecole doctorale Science et Technologie, Ouagadougou, Burkina Faso
| | - S L Ouédraogo
- Institut de l'Environnement et de Recherches Agricoles, Bobo Dioulasso, Burkina Faso
| | - I Wonni
- Institut de l'Environnement et de Recherches Agricoles, Bobo Dioulasso, Burkina Faso
| | - K Boyer
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
| | - C Boyer
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
| | - M Terville
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
| | - S Javegny
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
| | - A Allibert
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
| | - C Vernière
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
| | - O Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France
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17
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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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18
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Xue Y, Chu L. A rapid identification of barley varieties using DNA-AFLP. JOURNAL OF THE INSTITUTE OF BREWING 2015. [DOI: 10.1002/jib.253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Yongchang Xue
- School of Biological Engineering; Dalian Polytechnic University; Dalian 116034 People's Republic of China
| | - Lei Chu
- School of Biological Engineering; Dalian Polytechnic University; Dalian 116034 People's Republic of China
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19
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Leduc A, Traoré YN, Boyer K, Magne M, Grygiel P, Juhasz CC, Boyer C, Guerin F, Wonni I, Ouedraogo L, Vernière C, Ravigné V, Pruvost O. Bridgehead invasion of a monomorphic plant pathogenic bacterium:Xanthomonas citripv. citri, an emerging citrus pathogen in Mali and Burkina Faso. Environ Microbiol 2015; 17:4429-42. [DOI: 10.1111/1462-2920.12876] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/06/2015] [Indexed: 11/29/2022]
Affiliation(s)
- A. Leduc
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | | | - K. Boyer
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - M. Magne
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - P. Grygiel
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - C. C. Juhasz
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - C. Boyer
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - F. Guerin
- UMR PVBMT; Université de la Réunion; 97410 Saint Pierre La Réunion France
| | - I. Wonni
- Institut de l'Environnement et de Recherches agricoles; 01 BP910 Bobo Dioulasso Burkina Faso
| | - L. Ouedraogo
- Institut de l'Environnement et de Recherches agricoles; 01 BP910 Bobo Dioulasso Burkina Faso
| | - C. Vernière
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - V. Ravigné
- UMR BGPI; CIRAD; 34398 Montpellier France
| | - O. Pruvost
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
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20
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Rockey W, Potnis N, Timilsina S, Hong JC, Vallad GE, Jones JB, Norman DJ. Multilocus Sequence Analysis Reveals Genetic Diversity in Xanthomonads Associated With Poinsettia Production. PLANT DISEASE 2015; 99:874-882. [PMID: 30699531 DOI: 10.1094/pdis-08-14-0867-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Xanthomonas axonopodis pv. poinsettiicola is traditionally identified as the primary causal agent of bacterial leaf spot on poinsettia (family Euphorbiaceae). Sixty-seven strains of xanthomonads isolated from lesions associated with several species within the family Euphorbiaceae were collected over a 64-year period. The pathogenicity of these strains was compared on several potential hosts and they were analyzed by multilocus sequence analysis (MLSA) using six housekeeping genes. The 67 Xanthomonas strains associated with poinsettia production were separated into three distinct clades based on MLSA. The first clade identified contained the X. axonopodis pv. poinsettiicola reference strain (LMG849PT). A second clade was more closely related to X. hortorum pv. pelargonii (LMG7314PT) and the third clade contained the X. codiaei type strain (LMG8678T). This analysis indicated that there may also be other closely related pathovars or species of Xanthomonas that can infect poinsettia. Strains from the three clades could not be distinguished by symptoms or virulence on poinsettia plants. Strains capable of infecting geranium were found in all three clades, although the extent of leaf spot formation and number of systemic infections were significantly less than those produced by X. hortorum pv. pelargonii strains, typically the main causal agent of bacterial leaf spot on geranium. Clade III also contained strains isolated from zebra plant (Aphelandra squarrosa, family Acanthaceae), which is a newly recognized host for X. codiaei and X. axonopodis pv. poinsettiicola. Xanthomonas leaf spot is a serious threat to poinsettia production that can be caused by several Xanthomonas spp. that can infect different ornamental plant hosts. It is imperative that growers maintain a strict sanitation program because reservoirs of inoculum can occur on a number of ornamental hosts.
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Affiliation(s)
- W Rockey
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - N Potnis
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - S Timilsina
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - J C Hong
- U.S. Horticultural Research Laboratory, United States Department of Agriculture-Agricultural Research Service, Fort Pierce, FL 34945
| | - G E Vallad
- University of Florida, Gulf Coast Research and Education Center, Wimauma 33598
| | - J B Jones
- Department of Plant Pathology, University of Florida, Gainesville
| | - D J Norman
- University of Florida, Mid-Florida Research and Education Center, Apopka 32703
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21
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Timilsina S, Jibrin MO, Potnis N, Minsavage GV, Kebede M, Schwartz A, Bart R, Staskawicz B, Boyer C, Vallad GE, Pruvost O, Jones JB, Goss EM. Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and pepper plants reveals strains generated by recombination among species and recent global spread of Xanthomonas gardneri. Appl Environ Microbiol 2015; 81:1520-9. [PMID: 25527544 PMCID: PMC4309686 DOI: 10.1128/aem.03000-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/14/2014] [Indexed: 01/29/2023] Open
Abstract
Four Xanthomonas species are known to cause bacterial spot of tomato and pepper, but the global distribution and genetic diversity of these species are not well understood. A collection of bacterial spot-causing strains from the Americas, Africa, Southeast Asia, and New Zealand were characterized for genetic diversity and phylogenetic relationships using multilocus sequence analysis of six housekeeping genes. By examining strains from different continents, we found unexpected phylogeographic patterns, including the global distribution of a single multilocus haplotype of X. gardneri, possible regional differentiation in X. vesicatoria, and high species diversity on tomato in Africa. In addition, we found evidence of multiple recombination events between X. euvesicatoria and X. perforans. Our results indicate that there have been shifts in the species composition of bacterial spot pathogen populations due to the global spread of dominant genotypes and that recombination between species has generated genetic diversity in these populations.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Mustafa O. Jibrin
- Department of Crop Protection, Ahmadu Bello University, Zaria, Nigeria
| | - Neha Potnis
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Gerald V. Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Misrak Kebede
- Plant Pathology Department, School of Plant Science, Haramaya University, Dire Dawa, Ethiopia
| | - Allison Schwartz
- Department of Plant and Microbial Biology, University of California—Berkeley, California, USA
| | | | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California—Berkeley, California, USA
| | - Claudine Boyer
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France
| | - Gary E. Vallad
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Gulf Coast Research and Education Center, University of Florida, Wimauma, Florida, USA
| | - Olivier Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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22
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Pruvost O, Magne M, Boyer K, Leduc A, Tourterel C, Drevet C, Ravigné V, Gagnevin L, Guérin F, Chiroleu F, Koebnik R, Verdier V, Vernière C. A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage. PLoS One 2014; 9:e98129. [PMID: 24897119 PMCID: PMC4045669 DOI: 10.1371/journal.pone.0098129] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 04/28/2014] [Indexed: 11/18/2022] Open
Abstract
MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).
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Affiliation(s)
- Olivier Pruvost
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Maxime Magne
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Karine Boyer
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Alice Leduc
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Christophe Tourterel
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France
- Institut de Génétique et Microbiologie, UMR 8621, Université de Paris-Sud, Orsay, France
- Institut de Génétique et Microbiologie, UMR 8621, CNRS, Orsay, France
| | - Christine Drevet
- Institut de Génétique et Microbiologie, UMR 8621, Université de Paris-Sud, Orsay, France
- Institut de Génétique et Microbiologie, UMR 8621, CNRS, Orsay, France
| | - Virginie Ravigné
- UMR Biologie et Génétiques des Interactions Plante-Parasite (BGPI), CIRAD, Montpellier, France
| | - Lionel Gagnevin
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Fabien Guérin
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Université de la Réunion, Saint Pierre, La Réunion, France
| | - Frédéric Chiroleu
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
| | - Ralf Koebnik
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France
| | - Valérie Verdier
- Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs (RPB), IRD-CIRAD-UM2, Montpellier, France
| | - Christian Vernière
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France
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23
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Wonni I, Cottyn B, Detemmerman L, Dao S, Ouedraogo L, Sarra S, Tekete C, Poussier S, Corral R, Triplett L, Koita O, Koebnik R, Leach J, Szurek B, Maes M, Verdier V. Analysis of Xanthomonas oryzae pv. oryzicola population in Mali and Burkina Faso reveals a high level of genetic and pathogenic diversity. PHYTOPATHOLOGY 2014; 104:520-31. [PMID: 24199713 DOI: 10.1094/phyto-07-13-0213-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola was first reported in Africa in the 1980s. Recently, a substantial reemergence of this disease was observed in West Africa. Samples were collected at various sites in five and three different rice-growing regions of Burkina Faso and Mali, respectively. Sixty-seven X. oryzae pv. oryzicola strains were isolated from cultivated and wild rice varieties and from weeds showing BLS symptoms. X. oryzae pv. oryzicola strains were evaluated for virulence on rice and showed high variation in lesion length on a susceptible cultivar. X. oryzae pv. oryzicola strains were further characterized by multilocus sequence analysis (MLSA) using six housekeeping genes. Inferred dendrograms clearly indicated different groups among X. oryzae pv. oryzicola strains. Restriction fragment length polymorphism analysis using the transcriptional activator like effector avrXa7 as probe resulted in the identification of 18 haplotypes. Polymerase chain reaction-based analyses of two conserved type III effector (T3E) genes (xopAJ and xopW) differentiated the strains into distinct groups, with xopAJ not detected in most African X. oryzae pv. oryzicola strains. XopAJ functionality was confirmed by leaf infiltration on 'Kitaake' rice Rxo1 lines. Sequence analysis of xopW revealed four groups among X. oryzae pv. oryzicola strains. Distribution of 43 T3E genes shows variation in a subset of X. oryzae pv. oryzicola strains. Together, our results show that African X. oryzae pv. oryzicola strains are diverse and rapidly evolving, with a group endemic to Africa and another one that may have evolved from an Asian strain.
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24
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Scientific Opinion on the risk to plant health of Xanthomonas citri pv. citri and Xanthomonas citri pv. aurantifolii for the EU territory. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3556] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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Vernière C, Bui Thi Ngoc L, Jarne P, Ravigné V, Guérin F, Gagnevin L, Le Mai N, Chau NM, Pruvost O. Highly polymorphic markers reveal the establishment of an invasive lineage of the citrus bacterial pathogen Xanthomonas citri pv. citri in its area of origin. Environ Microbiol 2014; 16:2226-37. [PMID: 24373118 DOI: 10.1111/1462-2920.12369] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/13/2013] [Indexed: 11/28/2022]
Abstract
Investigating the population biology of plant pathogens in their native areas is essential to understand the factors that shape their population structure and favour their spread. Monomorphic pathogens dispatch extremely low genetic diversity in invaded areas, and native areas constitute a major reservoir for future emerging strains. One of these, the gammaproteobacterium Xanthomonas citri pv. citri, causes Asiatic canker and is a considerable threat to citrus worldwide. We studied its population genetic structure by genotyping 555 strains from 12 Vietnam provinces at 14 tandem repeat loci and insertion sequences. Discriminant analysis of principal components identified six clusters. Five of them were composed of endemic strains distributed heterogeneously across sampled provinces. A sixth cluster, VN6, displayed a much lower diversity and a clonal expansion structure, suggesting recent epidemic spread. No differences in aggressiveness on citrus or resistance to bactericides were detected between VN6 and other strains. VN6 likely represents a case of bioinvasion following introduction in a native area likely through contaminated plant propagative material. Highly polymorphic markers are useful for revealing migration patterns of recently introduced populations of a monomorphic bacterial plant pathogen.
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26
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Vinatzer BA, Monteil CL, Clarke CR. Harnessing population genomics to understand how bacterial pathogens emerge, adapt to crop hosts, and disseminate. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:19-43. [PMID: 24820995 DOI: 10.1146/annurev-phyto-102313-045907] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Crop diseases emerge without warning. In many cases, diseases cross borders, or even oceans, before plant pathologists have time to identify and characterize the causative agents. Genome sequencing, in combination with intensive sampling of pathogen populations and application of population genetic tools, is now providing the means to unravel how bacterial crop pathogens emerge from environmental reservoirs, how they evolve and adapt to crops, and what international and intercontinental routes they follow during dissemination. Here, we introduce the field of population genomics and review the population genomics research of bacterial plant pathogens over the past 10 years. We highlight the potential of population genomics for investigating plant pathogens, using examples of population genomics studies of human pathogens. We also describe the complementary nature of the fields of population genomics and molecular plant-microbe interactions and propose how to translate new insights into improved disease prevention and control.
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Affiliation(s)
- Boris A Vinatzer
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, Virginia 24061; ,
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27
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Vandroemme J, Cottyn B, Baeyen S, De Vos P, Maes M. Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content. BMC Genomics 2013; 14:829. [PMID: 24274055 PMCID: PMC4046712 DOI: 10.1186/1471-2164-14-829] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 11/20/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xanthomonas fragariae (Xf) is a bacterial strawberry pathogen and an A2 quarantine organism on strawberry planting stock in the EU. It is taxonomically and metabolically distinct within the genus Xanthomonas, and known for its host specificity. As part of a broader pathogenicity study, the genome of a Belgian, virulent Xf strain (LMG 25863) was assembled to draft status and examined for its pathogenicity related gene content. RESULTS The Xf draft genome (4.2 Mb) was considerably smaller than most known Xanthomonas genomes (~5 Mb). Only half of the genes coding for TonB-dependent transporters and cell-wall degrading enzymes that are typically present in other Xanthomonas genomes, were found in Xf. Other missing genes/regions with a possible impact on its plant-host interaction were: i) the three loci for xylan degradation and metabolism, ii) a locus coding for a ß-ketoadipate phenolics catabolism pathway, iii) xcs, one of two Type II Secretion System coding regions in Xanthomonas, and iv) the genes coding for the glyoxylate shunt pathway. Conversely, the Xf genome revealed a high content of externally derived DNA and several uncommon, possibly virulence-related features: a Type VI Secretion System, a second Type IV Secretion System and a distinct Type III Secretion System effector repertoire comprised of multiple rare effectors and several putative new ones. CONCLUSIONS The draft genome sequence of LMG 25863 confirms the distinct phylogenetic position of Xf within the genus Xanthomonas and reveals a patchwork of both lost and newly acquired genomic features. These features may help explain the specific, mostly endophytic association of Xf with the strawberry plant.
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Affiliation(s)
- Joachim Vandroemme
- />Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium
- />Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent, 9000 Belgium
| | - Bart Cottyn
- />Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium
| | - Steve Baeyen
- />Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium
| | - Paul De Vos
- />Laboratory of Microbiology, Ghent University, K. L. Ledeganckstraat 35, Ghent, 9000 Belgium
| | - Martine Maes
- />Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit - Crop Protection, Merelbeke, Belgium
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28
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Huang CH, Vallad GE, Adkison H, Summers C, Margenthaler E, Schneider C, Hong J, Jones JB, Ong K, Norman DJ. A Novel Xanthomonas sp. Causes Bacterial Spot of Rose (Rosa spp.). PLANT DISEASE 2013; 97:1301-1307. [PMID: 30722131 DOI: 10.1094/pdis-09-12-0851-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A bacterial spot of rose (Rosa spp.) caused by a xanthomonad was observed in Florida and Texas. Ten representative strains collected from the two states between 2004 and 2010 were used to determine the taxonomic position of this rose pathogen. Fatty acid methyl ester analysis was performed and a nearly 2-kb 16S-23S rRNA intergenic spacer along with flanking portions of the 16S and 23S rRNA genes were sequenced for selected strains, showing that they were members of the genus Xanthomonas. Multilocus sequence typing and analysis (MLST/MLSA) and pathogenicity tests were conducted to further characterize the Xanthomonas strains. The MLSA, based on six gene fragments-fusA, gapA, gltA, gyrB, lacF, and lepA-showed that the rose strains fell into Xanthomonas axonopodis subgroup 9.2 and shared the highest similarity values (98.8 to 99.7%) with X. alfalfae subsp. citrumelonis of the subgroup. However, principal coordinate analysis grouped the rose strains into a unique cluster distinct from other members of the subgroup according to virulence phenotypes on 11 plant species belonging to five plant families (Araceae, Euphorbiaceae, Rosaceae, Rutaceae, and Solanaceae). Moreover, the rose strains were aggressive on rose and Indian Hawthorn (Rhaphiolepsis indica). On the basis of the MLSA and virulence phenotypes, the pathovar epithet rosa is proposed.
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Affiliation(s)
- Cheng-Hua Huang
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Gary E Vallad
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Heather Adkison
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Carly Summers
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Elaina Margenthaler
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Christina Schneider
- Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma 33598
| | - Jason Hong
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville 32611
| | - Kevin Ong
- Texas Plant Disease Diagnostic Lab, Texas A&M University, College Station 77845
| | - David J Norman
- Mid-Florida Research and Education Center, University of Florida, IFAS, Apopka 32703
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29
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Escalon A, Javegny S, Vernière C, Noël LD, Vital K, Poussier S, Hajri A, Boureau T, Pruvost O, Arlat M, Gagnevin L. Variations in type III effector repertoires, pathological phenotypes and host range of Xanthomonas citri pv. citri pathotypes. MOLECULAR PLANT PATHOLOGY 2013; 14:483-96. [PMID: 23437976 PMCID: PMC6638789 DOI: 10.1111/mpp.12019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The mechanisms determining the host range of Xanthomonas are still undeciphered, despite much interest in their potential roles in the evolution and emergence of plant pathogenic bacteria. Xanthomonas citri pv. citri (Xci) is an interesting model of host specialization because of its pathogenic variants: pathotype A strains infect a wide range of Rutaceous species, whereas pathotype A*/A(W) strains have a host range restricted to Mexican lime (Citrus aurantifolia) and alemow (Citrus macrophylla). Based on a collection of 55 strains representative of Xci worldwide diversity assessed by amplified fragment length polymorphism (AFLP), we investigated the distribution of type III effectors (T3Es) in relation to host range. We examined the presence of 66 T3Es from xanthomonads in Xci and identified a repertoire of 28 effectors, 26 of which were shared by all Xci strains, whereas two (xopAG and xopC1) were present only in some A*/A(W) strains. We found that xopAG (=avrGf1) was present in all A(W) strains, but also in three A* strains genetically distant from A(W) , and that all xopAG-containing strains induced the hypersensitive response (HR) on grapefruit and sweet orange. The analysis of xopAD and xopAG suggested horizontal transfer between X. citri pv. bilvae, another citrus pathogen, and some Xci strains. A strains were genetically less diverse, induced identical phenotypic responses and possessed indistinguishable T3E repertoires. Conversely, A*/A(W) strains exhibited a wider genetic diversity in which clades correlated with geographical origin and T3E repertoire, but not with pathogenicity, according to T3E deletion experiments. Our data outline the importance of taking into account the heterogeneity of Xci A*/A(W) strains when analysing the mechanisms of host specialization.
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Affiliation(s)
- Aline Escalon
- UMR PVBMT, CIRAD, F-97410 Saint-Pierre, La Réunion, France
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30
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Mhedbi-Hajri N, Hajri A, Boureau T, Darrasse A, Durand K, Brin C, Saux MFL, Manceau C, Poussier S, Pruvost O, Lemaire C, Jacques MA. Evolutionary history of the plant pathogenic bacterium Xanthomonas axonopodis. PLoS One 2013; 8:e58474. [PMID: 23505513 PMCID: PMC3591321 DOI: 10.1371/journal.pone.0058474] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 02/05/2013] [Indexed: 01/02/2023] Open
Abstract
Deciphering mechanisms shaping bacterial diversity should help to build tools to predict the emergence of infectious diseases. Xanthomonads are plant pathogenic bacteria found worldwide. Xanthomonas axonopodis is a genetically heterogeneous species clustering, into six groups, strains that are collectively pathogenic on a large number of plants. However, each strain displays a narrow host range. We address the question of the nature of the evolutionary processes--geographical and ecological speciation--that shaped this diversity. We assembled a large collection of X. axonopodis strains that were isolated over a long period, over continents, and from various hosts. Based on the sequence analysis of seven housekeeping genes, we found that recombination occurred as frequently as point mutation in the evolutionary history of X. axonopodis. However, the impact of recombination was about three times greater than the impact of mutation on the diversity observed in the whole dataset. We then reconstructed the clonal genealogy of the strains using coalescent and genealogy approaches and we studied the diversification of the pathogen using a model of divergence with migration. The suggested scenario involves a first step of generalist diversification that spanned over the last 25,000 years. A second step of ecology-driven specialization occurred during the past two centuries. Eventually, secondary contacts between host-specialized strains probably occurred as a result of agricultural development and intensification, allowing genetic exchanges of virulence-associated genes. These transfers may have favored the emergence of novel pathotypes. Finally, we argue that the largest ecological entity within X. axonopodis is the pathovar.
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Affiliation(s)
- Nadia Mhedbi-Hajri
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Ahmed Hajri
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Tristan Boureau
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Armelle Darrasse
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Karine Durand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Chrystelle Brin
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Marion Fischer-Le Saux
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Charles Manceau
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Stéphane Poussier
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | | | - Christophe Lemaire
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Marie-Agnès Jacques
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
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Delcourt S, Vernière C, Boyer C, Pruvost O, Hostachy B, Robène-Soustrade I. Revisiting the Specificity of PCR Primers for Diagnostics of Xanthomonas citri pv. citri by Experimental and In Silico Analyses. PLANT DISEASE 2013; 97:373-378. [PMID: 30722361 DOI: 10.1094/pdis-04-12-0351-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Asiatic citrus canker disease, caused by Xanthomonas citri pv. citri, seriously impacts citrus production worldwide. Two pathogenic variants, A and A*/Aw, have been described within this pathovar. Two additional pathovars of X. citri with a limited geographic distribution and reduced pathogenicity, namely X. citri pvs. aurantifolii and bilvae, are also pathogenic to citrus and some rutaceous species. Rapid and reliable identification is required for these citrus pathogens, which are classified as a quarantine organism in citrus-producing countries. The specificity of nine polymerase chain reaction primers previously designed for the identification of X. citri pv. citri or citrus bacterial canker strains (both pvs. citri and aurantifolii) was assayed on a large strain collection (n = 87), including the two pathotypes of X. citri pv. citri, other genetic related or unrelated pathogenic xanthomonads, and saprophytic xanthomonads. This study gave congruent results with the original articles when testing the same strains or pathovars but the use of a broad inclusivity and exclusivity panel of strains highlighted new findings. Particularly, primers 2/3, 4/7, and KingF/R failed to provide amplification for three strains from the pathotype A*/Aw. Moreover, all pairs of primers detected at least one non-target strain. These data were supported by in silico analysis of the DNA sequences available from National Center for Biotechnology Information databases.
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Affiliation(s)
- Suzy Delcourt
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre, La Réunion, France
| | | | - Claudine Boyer
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre, La Réunion, France
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Donahoo RS, Jones JB, Lacy GH, Stromberg VK, Norman DJ. Genetic analyses of Xanthomonas axonopodis pv. dieffenbachiae strains reveal distinct phylogenetic groups. PHYTOPATHOLOGY 2013; 103:237-244. [PMID: 23134337 DOI: 10.1094/phyto-08-12-0191-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A comprehensive analysis of 175 Xanthomonas axonopodis pv. dieffenbachiae strains isolated from 10 Araceae hosts was done to identify pathogen variation. The strains were subjected to repetitive extragenic palindromic sequence polymerase chain reaction and four major phylogenetic clusters were generated. A subset of 40 strains isolated from Anthurium, Dieffenbachia, and Syngonium was further defined by amplified fragment length polymorphism and fatty acid methyl ester analysis and the same four phylogenetic clusters were observed. Comparison of representative strains in the first three clusters using DNA-DNA hybridization and multilocus sequence analysis supports the previous reclassification of strains in cluster I, including the X. axonopodis pv. dieffenbachiae pathovar reference strain (LMG695), to X. citri. Our research findings indicate that strains in cluster I, isolated primarily from anthurium, probably represent an undescribed pathovar. Other phylogenetic subclusters consisting primarily of strains isolated from xanthosoma and philodendron in clusters III and IV, respectively, may yet represent other undescribed species or pathovars of Xanthomonas.
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A genome sequence-based approach to taxonomy of the genus Nocardia. Antonie van Leeuwenhoek 2012; 102:481-91. [DOI: 10.1007/s10482-012-9780-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
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34
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MultiLocus Sequence Analysis- and Amplified Fragment Length Polymorphism-based characterization of xanthomonads associated with bacterial spot of tomato and pepper and their relatedness to Xanthomonas species. Syst Appl Microbiol 2012; 35:183-90. [DOI: 10.1016/j.syapm.2011.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 12/07/2011] [Accepted: 12/16/2011] [Indexed: 11/21/2022]
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35
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Hajri A, Brin C, Zhao S, David P, Feng JX, Koebnik R, Szurek B, Verdier V, Boureau T, Poussier S. Multilocus sequence analysis and type III effector repertoire mining provide new insights into the evolutionary history and virulence of Xanthomonas oryzae. MOLECULAR PLANT PATHOLOGY 2012; 13:288-302. [PMID: 21929565 PMCID: PMC6638859 DOI: 10.1111/j.1364-3703.2011.00745.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Multilocus sequence analysis (MLSA) and type III effector (T3E) repertoire mining were performed to gain new insights into the genetic relatedness of Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), two major bacterial pathogens of rice. Based on a collection of 45 African and Asian strains, we first sequenced and analysed three housekeeping genes by MLSA, Bayesian clustering and a median-joining network approach. Second, we investigated the distribution of 32 T3E genes, which are known to be major virulence factors of plant pathogenic bacteria, in all selected strains, by polymerase chain reaction and dot-blot hybridization methods. The diversity observed within housekeeping genes, as well as within T3E repertoires, clearly showed that both pathogens belong to closely related, but distinct, phylogenetic groups. Interestingly, these evolutionary groups are differentiated according to the geographical origin of the strains, suggesting that populations of Xoo and Xoc might be endemic in Africa and Asia, and thus have evolved separately. We further revealed that T3E gene repertoires of both pathogens comprise core and variable gene suites that probably have distinct roles in pathogenicity and different evolutionary histories. In this study, we carried out a functional analysis of xopO, a differential T3E gene between Xoo and Xoc, to determine the involvement of this gene in tissue specificity. Altogether, our data contribute to a better understanding of the evolutionary history of Xoo and Xoc in Africa and Asia, and provide clues for functional studies aiming to understand the virulence, host and tissue specificity of both rice pathogens.
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Affiliation(s)
- Ahmed Hajri
- Département Santé des Plantes et Environnement, Institut National de la Recherche Agronomique, UMR 077 PaVé, 42 rue Georges Morel, 49071 Beaucouzé cedex, France
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36
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Rodriguez-R LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A. Genomes-based phylogeny of the genus Xanthomonas. BMC Microbiol 2012; 12:43. [PMID: 22443110 PMCID: PMC3359215 DOI: 10.1186/1471-2180-12-43] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 03/23/2012] [Indexed: 11/24/2022] Open
Abstract
Background The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus. Results Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines. Conclusions Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.
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Affiliation(s)
- Luis M Rodriguez-R
- Laboratory of Mycology and Plant Pathology, Biological Sciences Department, Universidad de Los Andes, Cra 1 No 18A-12, Bogotá, Colombia
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37
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Jaciani FJ, Ferro JA, Ferro MIT, Vernière C, Pruvost O, Belasque J. Genetic Diversity of a Brazilian Strain Collection of Xanthomonas citri subsp. citri Based on the Type III Effector Protein Genes. PLANT DISEASE 2012; 96:193-203. [PMID: 30731808 DOI: 10.1094/pdis-04-11-0357] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Exclusion and eradication or management based on an integrated approach with less susceptible varieties, copper-based bactericides, and windbreaks are the two main strategies used to prevent or control citrus canker. Field tolerance or resistance to citrus canker is not found in the most important commercial sweet orange cultivars, and pathogen-derived resistance has been developed and applied in different crops to obtain resistant genotypes to plant pathogens. We describe the development of DNA primers and probes based on the type III effector genes avrXacE1, avrXacE2, avrXacE3, avrBs2, pthA4, hpaF, and XAC3090 (leucine rich protein), and their application in the evaluation of the genetic diversity of the pathogen. A total of 49 haplotypes were identified in 157 strains by Southern blot analysis. No genetic polymorphism was detected by BOX elements - and enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) analysis, nor with the genes avrBs2, XAC3090, and hpaF. Nei's genetic diversity indexes varied from 0.65 to 0.96 for subcollections of the pathogen. One or few haplotypes were most frequent in the strain collection, but several haplotypes were represented by solely one or few strains. The PthA4 probe resulted in the higher number of haplotypes identified in the Brazilian subcollections. Greater variation in the frequency of haplotypes occurred within subcollections (93.7%) than among subcollections. Only some haplotypes were genetically distant from all others, especially those originated from Rio Grande do Sul and Santa Catarina states. These bacterial effectors are widely spread in the collections and are useful for a better understanding of the host-pathogen interaction and the search for resistance genes in host and nonhost plants.
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Affiliation(s)
- F J Jaciani
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ. Estadual Paulista, Campus de Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - J A Ferro
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ. Estadual Paulista, Campus de Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - M I T Ferro
- Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ. Estadual Paulista, Campus de Jaboticabal, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - C Vernière
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7, chemin de l'Irat, 97410 Saint Pierre, Réunion, France
| | - O Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7, chemin de l'Irat, 97410 Saint Pierre, Réunion, France
| | - J Belasque
- Fundo de Defesa da Citricultura, Araraquara, SP, Brazil
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38
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Sakamoto M, Ohkuma M. Identification and classification of the genus Bacteroides by multilocus sequence analysis. MICROBIOLOGY-SGM 2011; 157:3388-3397. [PMID: 21948050 DOI: 10.1099/mic.0.052332-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5% gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.
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Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Moriya Ohkuma
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
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39
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Marguerettaz M, Pieretti I, Gayral P, Puig J, Brin C, Cociancich S, Poussier S, Rott P, Royer M. Genomic and evolutionary features of the SPI-1 type III secretion system that is present in Xanthomonas albilineans but is not essential for xylem colonization and symptom development of sugarcane leaf scald. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:246-59. [PMID: 20955079 DOI: 10.1094/mpmi-08-10-0188] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Xanthomonas albilineans is the causal agent of sugarcane leaf scald. Interestingly, this bacterium, which is not known to be insect or animal associated, possesses a type III secretion system (T3SS) belonging to the injectisome family Salmonella pathogenicity island 1 (SPI-1). The T3SS SPI-1 of X. albilineans shares only low similarity with other available T3SS SPI-1 sequences. Screening of a collection of 128 plant-pathogenic bacteria revealed that this T3SS SPI-1 is present in only two species of Xanthomonas: X. albilineans and X. axonopodis pv. phaseoli. Inoculation of sugarcane with knockout mutants showed that this system is not required by X. albilineans to spread within xylem vessels and to cause disease symptoms. This result was confirmed by the absence of this T3SS SPI-1 in an X. albilineans strain isolated from diseased sugarcane. To investigate the importance of the T3SS SPI-1 during the life cycle of X. albilineans, we analyzed T3SS SPI-1 sequences from 11 strains spanning the genetic diversity of this species. No nonsense mutations or frameshifting indels were observed in any of these strains, suggesting that the T3SS SPI-1 system is maintained within the species X. albilineans. Evolutionary features of T3SS SPI-1 based on phylogenetic, recombination, and selection analyses are discussed in the context of the possible functional importance of T3SS SPI-1 in the ecology of X. albilineans.
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Affiliation(s)
- Mélanie Marguerettaz
- UMR BGPI CIRAD, Campus International de Baillarguet, TA A-54/K, 34398 Montpellier Cedex 5, France
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40
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SAWADA H, WATAUCHI K, KUNUGI Y. Polyphasic comparison of bacterial spot pathogen of grapevine (Xanthomonas arboricola) with that of stone fruits (X. arboricola pv. pruni). ACTA ACUST UNITED AC 2011. [DOI: 10.3186/jjphytopath.77.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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41
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Fargier E, Fischer-Le Saux M, Manceau C. A multilocus sequence analysis of Xanthomonas campestris reveals a complex structure within crucifer-attacking pathovars of this species. Syst Appl Microbiol 2010; 34:156-65. [PMID: 21193279 DOI: 10.1016/j.syapm.2010.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 07/28/2010] [Accepted: 09/27/2010] [Indexed: 10/18/2022]
Abstract
Previous classification of Xanthomonas campestris has defined six pathovars (aberrans, armoraciae, barbareae, campestris, incanae, and raphani) that cause diseases on cruciferous plants. However, pathogenicity assays with a range of strains and different hosts identifies only three types of symptom: black rot, leaf spot and bacterial blight. These findings raise the question of the genetic relatedness between strains assigned to different pathovars or symptom phenotypes. Here we have addressed this issue by multilocus sequence analysis of 42 strains. The X. campestris species was polymorphic at the 8 loci analysed and had a high genetic diversity; 23 sequence types were identified of which 16 were unique. All strains that induce black rot (pathovars aberrans and campestris) were genetically close but split in two groups. Only three clonal complexes were found, all within pathovar campestris. The assignment of the genome-sequenced strain 756C to pathovar raphani suggested from disease symptoms was confirmed, although this group of strains was particularly polymorphic. Strains belonging to pathovars barbareae and incanae were closely related, but distinct from pathovar campestris. There is evidence of genetic exchanges of housekeeping genes within this species as deduced from a clear incongruence between individual gene phylogenies and from network structures from SplitsTree analysis. Overall this study showed that the high genetic diversity derived equally from recombination and point mutation accumulation. However, X. campestris remains a species with a clonal evolution driven by a differential adaptation to cruciferous hosts.
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Affiliation(s)
- E Fargier
- INRA, UMR A77 Pathologie Végétale, 42 rue Georges Morel, B.P. 60057, F-49070 Beaucouzé, France
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42
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Hamza AA, Robène-Soustrade I, Jouen E, Gagnevin L, Lefeuvre P, Chiroleu F, Pruvost O. Genetic and Pathological Diversity Among Xanthomonas Strains Responsible for Bacterial Spot on Tomato and Pepper in the Southwest Indian Ocean Region. PLANT DISEASE 2010; 94:993-999. [PMID: 30743480 DOI: 10.1094/pdis-94-8-0993] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacterial spot of tomato and pepper, a major problem in tropical climates, can be caused by several Xanthomonas genospecies. We examined the genetic and pathological diversity of a collection of 72 strains from the southwest Indian Ocean region as part of a regional research and development program to update inventories of agricultural pests and pathogens. Xanthomonas euvesicatoria, X. perforans, X. gardneri, and X. vesicatoria were identified in our strain collection. The identification of strains at the species level was consistently achieved by amplified fragment length polymorphism (AFLP) and multilocus sequence analysis (MLSA). Overall, X. euvesicatoria was the species recovered prevalently. MLSA data based on four housekeeping genes identified two to three sequence types per genospecies. It suggested that sequence variations primarily consisted of synonymous mutations, although a recombination event spanning several hundred nucleotides was detected for some strains of X. euvesicatoria on the atpD gene coding for the F1-F0-ATPase β subunit. The pathogenicity of strains was consistent with data found in the literature. Some pathological variations were primarily observed among strains identified as X. euvesicatoria. This study provides the first ever comprehensive description of the status of Xanthomonas species that cause bacterial spot of tomato and pepper in the southwest Indian Ocean region.
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Affiliation(s)
- A A Hamza
- Research Plant Pathologists, 97410 Saint Pierre, La Réunion, France
| | | | - E Jouen
- Research Plant Pathologists, 97410 Saint Pierre, La Réunion, France
| | - L Gagnevin
- Research Plant Pathologists, 97410 Saint Pierre, La Réunion, France
| | - P Lefeuvre
- Research Plant Pathologists, 97410 Saint Pierre, La Réunion, France
| | - F Chiroleu
- Statistician, CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7, chemin de l'Irat, France
| | - O Pruvost
- Research Plant Pathologist, 97410 Saint Pierre, La Réunion, France
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Robène-Soustrade I, Legrand D, Gagnevin L, Chiroleu F, Laurent A, Pruvost O. Multiplex nested PCR for detection of Xanthomonas axonopodis pv. allii from onion seeds. Appl Environ Microbiol 2010; 76:2697-703. [PMID: 20208024 PMCID: PMC2863456 DOI: 10.1128/aem.02697-09] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Accepted: 02/22/2010] [Indexed: 11/20/2022] Open
Abstract
Bacterial blight of onion (BBO) is an emerging disease that is present in many onion-producing areas. The causal agent, Xanthomonas axonopodis pv. allii, is seed transmitted. A reliable and sensitive diagnostic tool for testing seed health is needed. Detection of X. axonopodis pv. allii was achieved using a multiplex nested PCR assay developed using two randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) sequences corresponding to pilus assembly genes (pilW and pilX) and the avrRxv gene, respectively. The multiplex nested PCR was used with a large collection of X. axonopodis pv. allii strains pathogenic to onion and/or other Allium species isolated in different regions of the world. The internal primers used in the multiplex PCR assay directed amplification for all 86 X. axonopodis pv. allii strains tested, resulting in a 401-bp amplicon, a 444- to 447-bp amplicon, or both amplicons, depending on the strain. No amplification was obtained for 41 unrelated phytopathogenic bacteria and for 14 saprophytic bacteria commonly isolated from onion leaves and seeds. Most Xanthomonas strains also did not produce amplicons, except for nine strains classified in X. axonopodis genetic subgroup 9.1 or 9.2 and not pathogenic to onion. Nevertheless, sequence signatures distinguished most of these strains from X. axonopodis pv. allii. The assay detected X. axonopodis pv. allii in seed lots with contamination levels of 5 x 10(2) CFU g(-1) or higher. The sensitivity threshold of the multiplex nested PCR assay was found to be 1 infected seed in 27,340 seeds. This PCR-based assay should be useful for certifying that commercial seed lots are free of this important seed-borne pathogen.
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Affiliation(s)
- Isabelle Robène-Soustrade
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7 chemin de l'Irat, Saint Pierre, La Réunion, France.
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Moreira LM, Almeida NF, Potnis N, Digiampietri LA, Adi SS, Bortolossi JC, da Silva AC, da Silva AM, de Moraes FE, de Oliveira JC, de Souza RF, Facincani AP, Ferraz AL, Ferro MI, Furlan LR, Gimenez DF, Jones JB, Kitajima EW, Laia ML, Leite RP, Nishiyama MY, Rodrigues Neto J, Nociti LA, Norman DJ, Ostroski EH, Pereira HA, Staskawicz BJ, Tezza RI, Ferro JA, Vinatzer BA, Setubal JC. Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii. BMC Genomics 2010; 11:238. [PMID: 20388224 PMCID: PMC2883993 DOI: 10.1186/1471-2164-11-238] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 04/13/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C. RESULTS We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. CONCLUSION We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.
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Affiliation(s)
- Leandro M Moreira
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Campus Morro do Cruzeiro, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal do Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Neha Potnis
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Luciano A Digiampietri
- Escola de Artes, Ciências, e Humanidades, Universidade de São Paulo, São Paulo, SP, Brazil
- Laboratório de Bioinformática, Instituto de Computação, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Said S Adi
- Faculdade de Computação, Universidade Federal do Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Julio C Bortolossi
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | | | - Aline M da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fabrício E de Moraes
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - Julio C de Oliveira
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
- Departamento de Ciências Biológicas, Campus de Diadema, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Robson F de Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Agda P Facincani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - André L Ferraz
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - Maria I Ferro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - Luiz R Furlan
- Departamento de Melhoramento e Nutrição Animal, Faculdade de Medicina Veterinária e Zootecnia de Botucatu, UNESP - Univ. Estadual Paulista, SP, Brazil
| | - Daniele F Gimenez
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Elliot W Kitajima
- Núcleo de apoio à pesquisa em microscopia eletrônica aplicada à pesquisa agropecuária, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Marcelo L Laia
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
- Departamento de Engenharia Florestal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Rui P Leite
- Instituto Agronômico do Paraná, Londrina, PR, Brazil
| | - Milton Y Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Julio Rodrigues Neto
- Laboratório de Bacteriologia Vegetal, Instituto Biológico Campinas, Campinas, SP, Brazil
| | - Letícia A Nociti
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - David J Norman
- Institute of Food and Agricultural Sciences, Mid-Florida Research & Education Center, University of Florida, Gainesville, FL, USA
| | - Eric H Ostroski
- Laboratório de Bioinformática, Instituto de Computação, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Haroldo A Pereira
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - Brian J Staskawicz
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Renata I Tezza
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - Jesus A Ferro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal, UNESP - Univ. Estadual Paulista, Jaboticabal, SP, Brazil
| | - Boris A Vinatzer
- Department of Plant Pathology, Physiology and Weed Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - João C Setubal
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
- Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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