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Bellanger N, Dereeper A, Koebnik R. Clustered Regularly Interspaced Short Palindromic Repeats in Xanthomonas citri—Witnesses to a Global Expansion of a Bacterial Pathogen over Time. Microorganisms 2022; 10:microorganisms10091715. [PMID: 36144317 PMCID: PMC9504256 DOI: 10.3390/microorganisms10091715] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
Xanthomonas citri pv. citri, a Gram-negative bacterium, is the causal agent of citrus canker, a significant threat to citrus production. Understanding of global expansion of the pathogen and monitoring introduction into new regions are of interest for integrated disease management at the local and global level. Genetic diversity can be assessed using genomic approaches or information from partial gene sequences, satellite markers or clustered regularly interspaced short palindromic repeats (CRISPR). Here, we compared CRISPR loci from 355 strains of X. citri pv. citri, including a sample from ancient DNA, and generated the genealogy of the spoligotypes, i.e., the absence/presence patterns of CRISPR spacers. We identified 26 novel spoligotypes and constructed their likely evolutionary trajectory based on the whole-genome information. Moreover, we analyzed ~30 additional pathovars of X. citri and found that the oldest part of the CRISPR array was present in the ancestor of several pathovars of X. citri. This work presents a framework for further analyses of CRISPR loci and allows drawing conclusions about the global spread of the citrus canker pathogen, as exemplified by two introductions in West Africa.
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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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Fan Q, Bibi S, Vallad GE, Goss EM, Hurlbert JC, Paret ML, Jones JB, Timilsina S. Identification of Genes in Xanthomonas euvesicatoria pv. rosa That Are Host Limiting in Tomato. PLANTS 2022; 11:plants11060796. [PMID: 35336678 PMCID: PMC8951399 DOI: 10.3390/plants11060796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/30/2022]
Abstract
Xanthomonas euvesicatoria pv. rosa strain Xer07 causes a leaf spot on a Rosa sp. and is closely related to X. euvesicatoria pv. euvesicatoria (Xee) and X. perforans (Xp), causal agents of bacterial spot of tomato. However, Xer07 is not pathogenic on tomato and elicits a hypersensitive reaction (HR). We compared the genomes of the three bacterial species to identify the factors that limit Xer07 on tomato. Comparison of pathogenicity associated factors including the type III secretion systems identified two genes, xopA and xer3856, in Xer07 that have lower sequence homology in tomato pathogens. xer3856 is a homolog of genes in X. citri (xac3856) and X. fuscans pv. aurantifolii, both of which have been reported to elicit HRs in tomato. When xer3856 was expressed in X. perforans and infiltrated in tomato leaflets, the transconjugant elicited an HR and significantly reduced bacterial populations compared to the wildtype X. perforans strain. When xer3856 was mutated in Xer07, the mutant strain still triggered an HR in tomato leaflets. The second gene identified codes for type III secreted effector XopA, which contains a harpin domain that is distinct from the xopA homologs in Xee and Xp. The Xer07-xopA, when expressed in X. perforans, did not elicit an HR in tomato leaflets, but significantly reduced bacterial populations. This indicates that xopA and xer3856 genes in combination with an additional factor(s) limit Xer07 in tomato.
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Affiliation(s)
- Qiurong Fan
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (Q.F.); (S.B.); (G.E.V.); (E.M.G.); (M.L.P.)
| | - Shaheen Bibi
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (Q.F.); (S.B.); (G.E.V.); (E.M.G.); (M.L.P.)
| | - Gary E. Vallad
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (Q.F.); (S.B.); (G.E.V.); (E.M.G.); (M.L.P.)
- Gulf Coast Research and Education Center, University of Florida, Balm, FL 33598, USA
| | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (Q.F.); (S.B.); (G.E.V.); (E.M.G.); (M.L.P.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Jason C. Hurlbert
- Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29733, USA;
| | - Matthews L. Paret
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (Q.F.); (S.B.); (G.E.V.); (E.M.G.); (M.L.P.)
- North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (Q.F.); (S.B.); (G.E.V.); (E.M.G.); (M.L.P.)
- Correspondence: (J.B.J.); (S.T.)
| | - Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (Q.F.); (S.B.); (G.E.V.); (E.M.G.); (M.L.P.)
- Correspondence: (J.B.J.); (S.T.)
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Chen NWG, Ruh M, Darrasse A, Foucher J, Briand M, Costa J, Studholme DJ, Jacques M. Common bacterial blight of bean: a model of seed transmission and pathological convergence. MOLECULAR PLANT PATHOLOGY 2021; 22:1464-1480. [PMID: 33942466 PMCID: PMC8578827 DOI: 10.1111/mpp.13067] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Xanthomonas citri pv. fuscans (Xcf) and Xanthomonas phaseoli pv. phaseoli (Xpp) are the causal agents of common bacterial blight of bean (CBB), an important disease worldwide that remains difficult to control. These pathogens belong to distinct species within the Xanthomonas genus and have undergone a dynamic evolutionary history including the horizontal transfer of genes encoding factors probably involved in adaptation to and pathogenicity on common bean. Seed transmission is a key point of the CBB disease cycle, favouring both vertical transmission of the pathogen and worldwide distribution of the disease through global seed trade. TAXONOMY Kingdom: Bacteria; phylum: Proteobacteria; class: Gammaproteobacteria; order: Lysobacterales (also known as Xanthomonadales); family: Lysobacteraceae (also known as Xanthomonadaceae); genus: Xanthomonas; species: X. citri pv. fuscans and X. phaseoli pv. phaseoli (Xcf-Xpp). HOST RANGE The main host of Xcf-Xpp is the common bean (Phaseolus vulgaris). Lima bean (Phaseolus lunatus) and members of the Vigna genus (Vigna aconitifolia, Vigna angularis, Vigna mungo, Vigna radiata, and Vigna umbellata) are also natural hosts of Xcf-Xpp. Natural occurrence of Xcf-Xpp has been reported for a handful of other legumes such as Calopogonium sp., Pueraria sp., pea (Pisum sativum), Lablab purpureus, Macroptilium lathyroides, and Strophostyles helvola. There are conflicting reports concerning the natural occurrence of CBB agents on tepary bean (Phaseolus acutifolius) and cowpea (Vigna unguiculata subsp. unguiculata). SYMPTOMS CBB symptoms occur on all aerial parts of beans, that is, seedlings, leaves, stems, pods, and seeds. Symptoms initially appear as water-soaked spots evolving into necrosis on leaves, pustules on pods, and cankers on twigs. In severe infections, defoliation and wilting may occur. DISTRIBUTION CBB is distributed worldwide, meaning that it is frequently encountered in most places where bean is cultivated in the Americas, Asia, Africa, and Oceania, except for arid tropical areas. Xcf-Xpp are regulated nonquarantine pathogens in Europe and are listed in the A2 list by the European and Mediterranean Plant Protection Organization (EPPO). GENOME The genome consists of a single circular chromosome plus one to four extrachromosomal plasmids of various sizes, for a total mean size of 5.27 Mb with 64.7% GC content and an average predicted number of 4,181 coding sequences. DISEASE CONTROL Management of CBB is based on integrated approaches that comprise measures aimed at avoiding Xcf-Xpp introduction through infected seeds, cultural practices to limit Xcf-Xpp survival between host crops, whenever possible the use of tolerant or resistant bean genotypes, and chemical treatments, mainly restricted to copper compounds. The use of pathogen-free seeds is essential in an effective management strategy and requires appropriate sampling, detection, and identification methods. USEFUL WEBSITES: https://gd.eppo.int/taxon/XANTPH, https://gd.eppo.int/taxon/XANTFF, and http://www.cost.eu/COST_Actions/ca/CA16107.
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Affiliation(s)
- Nicolas W. G. Chen
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Mylène Ruh
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Armelle Darrasse
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Justine Foucher
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Martial Briand
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Joana Costa
- University of Coimbra, Centre for Functional Ecology ‐ Science for People & the Planet, Department of Life SciencesCoimbraPortugal
| | - David J. Studholme
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK
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Potnis N. Harnessing Eco-Evolutionary Dynamics of Xanthomonads on Tomato and Pepper to Tackle New Problems of an Old Disease. ANNUAL REVIEW OF PHYTOPATHOLOGY 2021; 59:289-310. [PMID: 34030449 DOI: 10.1146/annurev-phyto-020620-101612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacterial spot is an endemic seedborne disease responsible for recurring outbreaks on tomato and pepper around the world. The disease is caused by four diverse species, Xanthomonas gardneri, Xanthomonas euvesicatoria, Xanthomonas perforans, and Xanthomonas vesicatoria. There are no commercially available disease-resistant tomato varieties, and the disease is managed by chemical/biological control options, although these have not reduced the incidence of outbreaks. The disease on peppers is managed by disease-resistant cultivars that are effective against X. euvesicatoria but not X. gardneri. A significant shift in composition and prevalence of different species and races of the pathogen has occurred over the past century. Here, I attempt to review ecological and evolutionary processes associated with the population dynamics leading to disease emergence and spread. The goal of this review is to integrate the knowledge on population genomics and molecular plant-microbe interactions for this pathosystem to tailor disease management strategies.
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Affiliation(s)
- Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama 36849, USA;
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Bacteriophage-Mediated Control of Phytopathogenic Xanthomonads: A Promising Green Solution for the Future. Microorganisms 2021; 9:microorganisms9051056. [PMID: 34068401 PMCID: PMC8153558 DOI: 10.3390/microorganisms9051056] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Xanthomonads, members of the family Xanthomonadaceae, are economically important plant pathogenic bacteria responsible for infections of over 400 plant species. Bacteriophage-based biopesticides can provide an environmentally friendly, effective solution to control these bacteria. Bacteriophage-based biocontrol has important advantages over chemical pesticides, and treatment with these biopesticides is a minor intervention into the microflora. However, bacteriophages’ agricultural application has limitations rooted in these viruses’ biological properties as active substances. These disadvantageous features, together with the complicated registration process of bacteriophage-based biopesticides, means that there are few products available on the market. This review summarizes our knowledge of the Xanthomonas-host plant and bacteriophage-host bacterium interaction’s possible influence on bacteriophage-based biocontrol strategies and provides examples of greenhouse and field trials and products readily available in the EU and the USA. It also details the most important advantages and limitations of the agricultural application of bacteriophages. This paper also investigates the legal background and industrial property right issues of bacteriophage-based biopesticides. When appropriately applied, bacteriophages can provide a promising tool against xanthomonads, a possibility that is untapped. Information presented in this review aims to explore the potential of bacteriophage-based biopesticides in the control of xanthomonads in the future.
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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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Vancheva T, Bogatzevska N, Moncheva P, Mitrev S, Vernière C, Koebnik R. Molecular Epidemiology of Xanthomonas euvesicatoria Strains from the Balkan Peninsula Revealed by a New Multiple-Locus Variable-Number Tandem-Repeat Analysis Scheme. Microorganisms 2021; 9:microorganisms9030536. [PMID: 33807692 PMCID: PMC8002079 DOI: 10.3390/microorganisms9030536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial spot of pepper and tomato is caused by at least three species of Xanthomonas, among them two pathovars of Xanthomonas euvesicatoria, which are responsible for significant yield losses on all continents. In order to trace back the spread of bacterial spot pathogens within and among countries, we developed the first multilocus variable number of tandem repeat analyses (MLVA) scheme for pepper- and tomato-pathogenic strains of X. euvesicatoria. In this work, we assessed the repeat numbers by DNA sequencing of 16 tandem repeat loci and applied this new tool to analyse a representative set of 88 X. euvesicatoria pepper strains from Bulgaria and North Macedonia. The MLVA-16 scheme resulted in a Hunter–Gaston Discriminatory Index (HGDI) score of 0.944 and allowed to resolve 36 MLVA haplotypes (MTs), thus demonstrating its suitability for high-resolution molecular typing. Strains from the different regions of Bulgaria and North Macedonia were found to be widespread in genetically distant clonal complexes or singletons. Sequence types of the variable number of tandem repeats (VNTR) amplicons revealed cases of size homoplasy and suggested the coexistence of different populations and different introduction events. The large geographical distribution of MTs and the existence of epidemiologically closely related strains in different regions and countries suggest long dispersal of strains on pepper in this area.
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Affiliation(s)
- Taca Vancheva
- IPME, Univ Montpellier, Cirad, IRD, Montpellier, France;
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria;
| | - Nevena Bogatzevska
- Institute of Soil Science, Agrotechnologies and Plant Protection ‘Nikola Pushkarov’, Sofia, Bulgaria;
| | - Penka Moncheva
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria;
| | - Sasa Mitrev
- Department for Plant and Environment Protection, Faculty of Agriculture, Goce Delchev University, Štip, North Macedonia;
| | - Christian Vernière
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Insitut Agro, IRD, Montpellier, France;
| | - Ralf Koebnik
- IPME, Univ Montpellier, Cirad, IRD, Montpellier, France;
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Insitut Agro, IRD, Montpellier, France;
- Correspondence: ; Tel.: +33-467-416-228
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 DOI: 10.21203/rs.3.rs-17010/v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. RESULTS We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. CONCLUSIONS This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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10
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 PMCID: PMC7437933 DOI: 10.1186/s12864-020-06972-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. Results We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. Conclusions This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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11
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Studholme DJ, Wicker E, Abrare SM, Aspin A, Bogdanove A, Broders K, Dubrow Z, Grant M, Jones JB, Karamura G, Lang J, Leach J, Mahuku G, Nakato GV, Coutinho T, Smith J, Bull CT. Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov. PHYTOPATHOLOGY 2020; 110:1153-1160. [PMID: 31922946 DOI: 10.1094/phyto-03-19-0098-le] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present an amended description of the bacterial species Xanthomonas vasicola to include the causative agent of banana Xanthomonas wilt, as well as strains that cause disease on Areca palm, Tripsacum grass, sugarcane, and maize. Genome-sequence data reveal that these strains all share more than 98% average nucleotide with each other and with the type strain. Our analyses and proposals should help to resolve the taxonomic confusion that surrounds some of these pathogens and help to prevent future use of invalid names.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
| | - Emmanuel Wicker
- IPME, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Sadik Muzemil Abrare
- Southern Agricultural Research Institute (SARI), Areka Agricultural Research Center, Areka, Ethiopia
| | | | - Adam Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Kirk Broders
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Zoe Dubrow
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Murray Grant
- School of Life Sciences, Gibbet Hill, University of Warwick, Coventry, CV4 7AL, U.K
| | - Jeffrey B Jones
- University of Florida, Plant Pathology Department, 1453 Fifield Hall, Gainesville, FL 32611, U.S.A
| | | | - Jillian Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - Jan Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, U.S.A
| | - George Mahuku
- International Institute of Tropical Agiculture (IITA), East Africa Hub, IITA-Tanzania, P.O. Box 34441, Dar es Salaam, Tanzania
| | - Gloria Valentine Nakato
- International Institute of Tropical Agriculture (IITA), Plot 15B, Naguru East Road, Upper Naguru, P.O. Box 7878, Kampala, Uganda
| | - Teresa Coutinho
- Department of Microbiology and Plant Pathology, Centre for Microbial Ecology and Genomics (CMEG), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X28, Pretoria 0028, South Africa
| | | | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Penn State University, University Park, PA, U.S.A
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12
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Timilsina S, Potnis N, Newberry EA, Liyanapathiranage P, Iruegas-Bocardo F, White FF, Goss EM, Jones JB. Xanthomonas diversity, virulence and plant-pathogen interactions. Nat Rev Microbiol 2020; 18:415-427. [PMID: 32346148 DOI: 10.1038/s41579-020-0361-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.
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Affiliation(s)
- Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Neha Potnis
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric A Newberry
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | | | | | - Frank F White
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Erica M Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Jeffrey B Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, USA.
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13
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Khojasteh M, Shah SMA, Haq F, Xu X, Taghavi SM, Osdaghi E, Chen G. Transcription Activator-Like Effectors Diversity in Iranian Strains of Xanthomonas translucens. PHYTOPATHOLOGY 2020; 110:758-767. [PMID: 31868568 DOI: 10.1094/phyto-11-19-0428-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf streak caused by different pathovars of Xanthomonas translucens is the most important seedborne bacterial disease of small grain cereals. However, variations in the virulence-associated genomic areas of the pathogen remain uninvestigated. In this study, the diversity of transcription activator-like effectors (TALE) was investigated using the Southern blotting of BamHI-digested genomic DNAs in the Iranian strains of X. translucens. All 65 X. translucens strains were assigned into 13 genotypes, where 57 X. translucens pv. undulosa strains were placed in genotypes 1 to 8, and seven X. translucens pv. translucens strains were placed in genotypes 9 to 12. Interestingly, we did not find any TALE genes in the strain XtKm7 (genotype 13), which showed to be pathogenic only on barley. Virulence and aggressiveness of these strains in greenhouse conditions were in agreement with the TALE-based clustering of the strains in the pathovar level, though variations were observed in the aggressiveness of X. translucens pv. undulosa strains. In general, strains containing higher numbers of putative TALE genes were more virulent on wheat and barley than strains containing fewer. This is the first TALE-based genetic diversity analysis on X. translucens strains and provides novel insights into the virulence repertories and genomic characteristics of the pathogen. Further investigations using TALE mutagenesis and complementation analysis are warranted to precisely elucidate the role of each detected X. translucens TALE in bacterial virulence and aggressiveness either on wheat or barley.
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Affiliation(s)
- Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
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14
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de Paiva BAR, Wendland A, Teixeira NC, Ferreira MASV. Rapid Detection of Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli in Common Bean by Loop-Mediated Isothermal Amplification. PLANT DISEASE 2020; 104:198-203. [PMID: 31738688 DOI: 10.1094/pdis-02-19-0325-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A single loop-mediated isothermal amplification (LAMP) assay was developed for specific detection of both pathogens that cause bacterial blight in common bean, Xanthomonas phaseoli pv. phaseoli (Xpp) and Xanthomonas citri pv. fuscans (Xcf). The objective was to provide a simple, easy-to-use, specific, and sensitive method to investigate the presence of one or both pathogens in plant material and seeds for routine diagnosis. The detection limits for both pathogens were 10 CFU/ml for cell suspensions and 1 fg of DNA, whereas in conventional PCR, the primers detected up to 105 CFU/ml and 1 ng of DNA. Specificity was confirmed by testing DNA from bean leaves, other Xanthomonas species, common fungal and bacterial bean pathogens, and bacteria from the leaf microbiota. The method was tested with bean leaves inoculated with Xpp, and the pathogen could be detected from 4 h up to 15 days postinoculation, even before disease symptoms were visible. When the method was applied to bacterium detection (Xpp or Xcf) in seed lots from infected plants, the bacterium detection rate was 100% (24 of 24). The pathogens were detected in seeds incubated for just 1 h in saline solution (0.85%), reducing the time needed for bacterium detection. The LAMP assay could be useful as a tool in bean bacterial blight management. Rapid and sensitive detection of bacteria in bean seed lots would reduce the risks of planting highly contaminated seeds in environments favorable to blight multiplication.
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Affiliation(s)
| | - Adriane Wendland
- Embrapa Arroz e Feijão, 75375-000 Santo Antônio de Goiás, Goiás, Brazil
| | | | - Marisa A S V Ferreira
- Department of Plant Pathology, University of Brasilia, 70910-900 Brasilia, Distrito Federal, Brazil
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15
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Liu F, McDonald M, Schwessinger B, Joe A, Pruitt R, Erickson T, Zhao X, Stewart V, Ronald PC. Variation and inheritance of the Xanthomonas raxX-raxSTAB gene cluster required for activation of XA21-mediated immunity. MOLECULAR PLANT PATHOLOGY 2019; 20:656-672. [PMID: 30773771 PMCID: PMC6637879 DOI: 10.1111/mpp.12783] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The rice XA21-mediated immune response is activated on recognition of the RaxX peptide produced by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The 60-residue RaxX precursor is post-translationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The 5-kb raxX-raxSTAB gene cluster of Xoo encodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type I secretion system. To assess raxX-raxSTAB gene cluster evolution and to determine its phylogenetic distribution, we first identified rax gene homologues in other genomes. We detected the complete raxX-raxSTAB gene cluster only in Xanthomonas spp., in five distinct lineages in addition to X. oryzae. The phylogenetic distribution of the raxX-raxSTAB gene cluster is consistent with the occurrence of multiple lateral (horizontal) gene transfer events during Xanthomonas speciation. RaxX natural variants contain a restricted set of missense substitutions, as expected if selection acts to maintain peptide hormone-like function. Indeed, eight RaxX variants tested all failed to activate the XA21-mediated immune response, yet retained peptide hormone activity. Together, these observations support the hypothesis that the XA21 receptor evolved specifically to recognize Xoo RaxX.
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Affiliation(s)
- Furong Liu
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Megan McDonald
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Anna Joe
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Rory Pruitt
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Teresa Erickson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Xiuxiang Zhao
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Valley Stewart
- Department of Microbiology & Molecular GeneticsUniversity of CaliforniaDavisCA95616USA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
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16
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Ferreira MASV, Bonneau S, Briand M, Cesbron S, Portier P, Darrasse A, Gama MAS, Barbosa MAG, Mariano RDLR, Souza EB, Jacques MA. Xanthomonas citri pv. viticola Affecting Grapevine in Brazil: Emergence of a Successful Monomorphic Pathogen. FRONTIERS IN PLANT SCIENCE 2019; 10:489. [PMID: 31057588 PMCID: PMC6482255 DOI: 10.3389/fpls.2019.00489] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
The pathovar viticola of Xanthomonas citri causes bacterial canker of grapevine. This disease was first recorded in India in 1972, and later in Brazil in 1998, where its distribution is currently restricted to the northeastern region. A multilocus sequence analysis (MLSA) based on seven housekeeping genes and a multilocus variable number of tandem repeat analysis (MLVA) with eight loci were performed in order to assess the genetic relatedness among strains from India and Brazil. Strains isolated in India from three related pathovars affecting Vitaceae species and pathogenic strains isolated from Amaranthus sp. found in bacterial canker-infected vineyards in Brazil were also included. MLSA revealed lack of diversity in all seven genes and grouped grapevine and Amaranthus strains in a monophyletic group in X. citri. The VNTR (variable number of tandem repeat) typing scheme conducted on 107 strains detected 101 haplotypes. The total number of alleles per locus ranged from 5 to 12. A minimum spanning tree (MST) showed that Brazilian strains were clearly separated from Indian strains, which showed unique alleles at three loci. The two strains isolated from symptomatic Amaranthus sp. presented unique alleles at two loci. STRUCTURE analyses revealed three groups congruent with MST and a fourth group with strains from India and Brazil. Admixture among populations were observed in all groups. MST, STRUCTURE and e-BURST analyses showed that the strains collected in 1998 belong to two distinct groups, with predicted founder genotypes from two different vineyards in the same region. This suggest that one introduction of grape planting materials contaminated with genetically distinct strains took place, which was followed by pathogen adaptation. Genome sequencing of one Brazilian strain confirmed typical attributes of pathogenic xanthomonads and allowed the design of a complementary VNTR typing scheme dedicated to X. citri pv. viticola that will allow further epidemiological survey of this genetically monomorphic pathovar.
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Affiliation(s)
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Sophie Cesbron
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Perrine Portier
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Armelle Darrasse
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
| | - Marco A. S. Gama
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | | | - Rosa de L. R. Mariano
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Elineide B. Souza
- Laboratório de Fitobacteriologia, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d’Angers, Beaucouzé, France
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17
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Bansal K, Kumar S, Patil PB. Complete Genome Sequence Reveals Evolutionary Dynamics of an Emerging and Variant Pathovar of Xanthomonas euvesicatoria. Genome Biol Evol 2018; 10:3104-3109. [PMID: 30346514 PMCID: PMC6257573 DOI: 10.1093/gbe/evy238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2018] [Indexed: 11/13/2022] Open
Abstract
Xanthomonas, a complex group of pathogens, infects more than 400 plants, which is expanding to new hosts causing serious diseases. Genome-based studies are transforming our understanding on diversity and relationship of host-specific members, known as pathovars. In this study, we report complete genome sequence of a novel pathovar Xanthomonas axonopodis pv. commiphorae (Xcom) from India. It causes gumming disease of Commiphora wightii, a medicinally important plant. Genome-based phylogenetic and taxonomic investigation revealed that the pathovar belongs to Xanthomonas euvesicatoria and not X. axonopodis as reported earlier. Interestingly, it is a novel host and novel geographic origin for a X. euvesicatoria pathovar. A core-genome-based phylogenetic analysis resolved the pathovar complex of this species on the basis of their hosts. Interestingly, this pathovar harbors a unique 35-kb plasmid encoding type III effectors and toxin-antitoxin gene that is absent in other X. euvesicatoria pathovars and infects tomato, pepper, rose, onion, philodendron, alfalfa, and citrus plants. The pathovar contains two TAL (transcription activator-like) genes, one on plasmid and another on genomic region with an additional pseudo TAL gene flanked by IS elements in the plasmid. Further, Xcom has acquired a novel set of lipopolysaccharide biosynthesis genes after its divergence from the closely related pathovar that infects rose and supports the role of horizontal gene transfer in hypervariation at this locus in the species. Complete genome sequence of this variant pathovar has provided novel insights into evolution of an emerging pathovar in Xanthomonas and will be valuable resource in pathogenomics of X. euvesicatoria.
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Affiliation(s)
- Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR—Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR—Institute of Microbial Technology, Chandigarh, India
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18
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da Gama MAS, Mariano RDLR, da Silva Júnior WJ, de Farias ARG, Barbosa MAG, Ferreira MÁDSV, Costa Júnior CRL, Santos LA, de Souza EB. Taxonomic Repositioning of Xanthomonas campestris pv. viticola (Nayudu 1972) Dye 1978 as Xanthomonas citri pv. viticola (Nayudu 1972) Dye 1978 comb. nov. and Emendation of the Description of Xanthomonas citri pv. anacardii to Include Pigmented Isolates Pathogenic to Cashew Plant. PHYTOPATHOLOGY 2018; 108:1143-1153. [PMID: 29688131 DOI: 10.1094/phyto-02-18-0037-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Grapevine bacterial canker, which is caused by Xanthomonas campestris pv. viticola, is one of the most important grapevine diseases in the northeastern region of Brazil. This disease causes severe damage and represents a high potential risk to the development of Brazilian viticulture. In turn, pigmented isolates pathogenic to cashew plant, making cashew fruit unfit for sale, also have been detected in Northeastern Brazil. Given that the taxonomic position of these bacteria is unclear, the multilocus sequence analysis (MLSA) technique, average nucleotide identity (ANI) values and tetranucleotide frequency correlation coefficients (TETRA) were used to analyze their phylogenetic relationship in relation to other Xanthomonas species. X. campestris pv. viticola was closely related to X. citri pv. mangiferaeindicae (repetitive-polymerase chain reaction [rep-PCR], MLSA, and ANI) and X. citri subsp. citri (MLSA and ANI). Pigmented isolates pathogenic to cashew plant were closely related to X. citri pv. anacardii (rep-PCR, MLSA, ANI, and TETRA). The results obtained in this study support the emendation of the description of X. citri pv. anacardii to include pigmented isolates of Xanthomonas pathogenic to cashew plant. In addition, the reclassification of X. campestris pv. viticola as X. citri pv. viticola comb. nov. is suggested.
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Affiliation(s)
- Marco Aurélio Siqueira da Gama
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Rosa de Lima Ramos Mariano
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Wilson José da Silva Júnior
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Antônio Roberto Gomes de Farias
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Maria Angélica Guimarães Barbosa
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Marisa Álvares da Silva Velloso Ferreira
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - César Raimundo Lima Costa Júnior
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Liliana Andréa Santos
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
| | - Elineide Barbosa de Souza
- First, second, third, fourth, and eighth authors: Área de Fitossanidade, Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil; fifth author: Empresa Brasileira de Pesquisa Agropecuária, Semiárido; BR 428, Km 152, Zona Rural, CEP 56302-970 Petrolina-PE, Brazil; sixth author: Departamento de Fitopatologia, Instituto de Ciências Biológicas, Universidade de Brasília, Campus Universitário, Asa Norte, CEP 70910-900, Brasília-DF, Brazil; seventh author: Departamento de Genética, Universidade Federal de Pernambuco, Av. Professor Moraes Rego, 1235, Cidade Universitária, CEP 50670-901, Recife-PE, Brazil; and ninth author: Área de Microbiologia, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Av. Dom Manoel de Medeiros, s/n, Dois Irmãos, CEP 52171-900, Recife-PE, Brazil
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19
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Zhang X, Babadoost M. Characteristics of Xanthomonas cucurbitae Isolates from Pumpkins and Survival of the Bacterium in Pumpkin Seeds. PLANT DISEASE 2018; 102:1779-1784. [PMID: 30125182 DOI: 10.1094/pdis-08-17-1216-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This study was conducted to determine characteristics of Xanthomonas cucurbitae, the causal agent of bacterial spot of pumpkin, and survival of the bacterium in pumpkin seeds. Fourteen X. cucurbitae isolates from the north central region of the United States, along with the X. cucurbitae strain 23378 from the American Type Culture Collection, were included in this study. The range of minimum, optimum, and maximum temperatures for colony development of X. cucurbitae were 4 to 6°C, 24 to 30°C, and 34 to 36°C, respectively. Optimum pH for colony development ranged from 6.5 to 8.0. Leaves of 3-week-old pumpkins 'Howden' and 'Dickinson' were inoculated with X. cucurbitae isolates (108 CFU/ml). There was a significant difference in the postinoculation periods for appearance of bacterial lesions on the leaves among the isolates; however, there was no significant difference in diameters of the lesions on each of the pumpkin cultivar 7 days after inoculation. Four of the isolates caused significantly larger lesions on 'Dickinson' leaves than 'Howden' leaves. Naturally infected 'Howden' pumpkin and inoculated 'Dickinson' pumpkin seeds with X. cucurbitae were stored at 4 and 22°C. X. cucurbitae was isolated from both naturally infected and inoculated seeds 24 months after storage at both 4 and 22°C, and the isolated bacteria were pathogenic.
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Affiliation(s)
- X Zhang
- Department of Crop Sciences, University of Illinois, Urbana 61801
| | - M Babadoost
- Department of Crop Sciences, University of Illinois, Urbana 61801
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Chen NWG, Serres-Giardi L, Ruh M, Briand M, Bonneau S, Darrasse A, Barbe V, Gagnevin L, Koebnik R, Jacques MA. Horizontal gene transfer plays a major role in the pathological convergence of Xanthomonas lineages on common bean. BMC Genomics 2018; 19:606. [PMID: 30103675 PMCID: PMC6090828 DOI: 10.1186/s12864-018-4975-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 07/31/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Host specialization is a hallmark of numerous plant pathogens including bacteria, fungi, oomycetes and viruses. Yet, the molecular and evolutionary bases of host specificity are poorly understood. In some cases, pathological convergence is observed for individuals belonging to distant phylogenetic clades. This is the case for Xanthomonas strains responsible for common bacterial blight of bean, spread across four genetic lineages. All the strains from these four lineages converged for pathogenicity on common bean, implying possible gene convergences and/or sharing of a common arsenal of genes conferring the ability to infect common bean. RESULTS To search for genes involved in common bean specificity, we used a combination of whole-genome analyses without a priori, including a genome scan based on k-mer search. Analysis of 72 genomes from a collection of Xanthomonas pathovars unveiled 115 genes bearing DNA sequences specific to strains responsible for common bacterial blight, including 20 genes located on a plasmid. Of these 115 genes, 88 were involved in successive events of horizontal gene transfers among the four genetic lineages, and 44 contained nonsynonymous polymorphisms unique to the causal agents of common bacterial blight. CONCLUSIONS Our study revealed that host specificity of common bacterial blight agents is associated with a combination of horizontal transfers of genes, and highlights the role of plasmids in these horizontal transfers.
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Affiliation(s)
- Nicolas W. G. Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Laurana Serres-Giardi
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Armelle Darrasse
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
| | - Valérie Barbe
- CEA/DSV/IG/Genoscope, 2 rue Gaston Crémieux, BP5706, 91057 Evry, France
| | - Lionel Gagnevin
- CIRAD, UMR PVBMT, F-97410 Saint-Pierre, La Réunion France
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071 Beaucouzé, France
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21
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Ferraz HGM, Badel JL, da Silva Guimarães LM, Reis BP, Tótola MR, Gonçalves RC, Alfenas AC. Xanthomonas axonopodis pv. eucalyptorum pv. nov. Causing Bacterial Leaf Blight on Eucalypt in Brazil. THE PLANT PATHOLOGY JOURNAL 2018; 34:269-285. [PMID: 30140181 PMCID: PMC6097821 DOI: 10.5423/ppj.oa.01.2018.0014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/02/2018] [Accepted: 04/17/2018] [Indexed: 06/08/2023]
Abstract
Bacterial leaf blight is a major disease of eucalypt, especially under nursery conditions. Different bacterial species have been associated with the disease in several countries, and despite its importance worldwide, it is not clear to date whether similar disease symptoms are caused by the same or by different etiological agents. In this study, 43 bacterial strains were isolated from blighted eucalypt leaves collected in different geographic areas of Brazil and inoculated onto a susceptible eucalypt clone. Polyphasic taxonomy, including morphological, physiological, biochemical, molecular, and pathogenicity tests showed that only certain strains of Xanthomonas axonopodis caused symptoms of the disease. Strains varied in their aggressiveness, but no correlation with geographic origin was observed. MLSA-based phylogenetic analysis using concatenated dnaK, fyuA, gyrB and rpoD gene sequences allocated the strains in a well-defined clade, corresponding to Rade-marker's group RG 9.6. Inoculation of nineteen plant species belonging to seven botanical families with representative strain LPF 602 showed it to be pathogenic only on Eucalyptus spp, and Corymbia spp. Based on distinct biochemical and pathogenic characteristics that differentiate the eucalypt strains from other pathovars of the X. axonopodis species, here we propose their allocation into the new pathovar X. axonopodis pv. eucalyptorum pv. nov.
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Affiliation(s)
| | - Jorge Luis Badel
- Department of Phytopathology, Universidade Federal de Viçosa, Viçosa, MG 36570-900,
Brazil
| | | | - Bruna Paolinelli Reis
- Department of Phytopathology, Universidade Federal de Viçosa, Viçosa, MG 36570-900,
Brazil
| | - Marcos Rogério Tótola
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, MG 36570-900,
Brazil
| | | | - Acelino Couto Alfenas
- Department of Phytopathology, Universidade Federal de Viçosa, Viçosa, MG 36570-900,
Brazil
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22
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Curland RD, Gao L, Bull CT, Vinatzer BA, Dill-Macky R, Van Eck L, Ishimaru CA. Genetic Diversity and Virulence of Wheat and Barley Strains of Xanthomonas translucens from the Upper Midwestern United States. PHYTOPATHOLOGY 2018; 108:443-453. [PMID: 29165007 DOI: 10.1094/phyto-08-17-0271-r] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial leaf streak (BLS) of wheat and barley, caused by Xanthomonas translucens pv. undulosa and X. translucens pv. translucens, has been of growing concern in small grains production in the Upper Midwestern United States. To optimize disease resistance breeding, a greater awareness is needed of the pathovars and genetic diversity within the pathogens causing BLS in the region. Multilocus sequencing typing (MLST) and analysis (MLSA) of four common housekeeping genes (rpoD, dnaK, fyuA, and gyrB) was used to evaluate the genetic diversity of 82 strains of X. translucens isolated between 2006 and 2013 from wheat, barley, rye, and intermediate wheatgrass. In addition, in planta disease assays were conducted on 75 strains to measure relative virulence in wheat and barley. All strains were determined by MLSA to be related to X. translucens pv. undulosa and X. translucens pv. translucens. Clustering of strains based on Bayesian, network, and minimum spanning trees correlated with relative virulence levels in inoculated wheat and barley. Thus, phylogeny based on rpoD, dnaK, fyuA, and gyrB correlated with host of isolation and was an effective means for predicting virulence of strains belonging to X. translucens pv. translucens and X. translucens pv. undulosa.
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Affiliation(s)
- Rebecca D Curland
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Liangliang Gao
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Carolee T Bull
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Boris A Vinatzer
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Ruth Dill-Macky
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Leon Van Eck
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
| | - Carol A Ishimaru
- First, fifth, sixth, and seventh authors: Department of Plant Pathology, University of Minnesota, 495 Borlaug Hall, 1991 Upper Buford Circle, St. Paul 55108; second author: Department of Plant Pathology, Kansas State University, 4024 Throckmorton Hall, 1712 Claflin Road, Manhattan 66506; third author: U.S. Department of Agriculture, 1636 E. Alisal Street, Salinas, CA 93905 and Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, 16802; and fourth author: Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg 24061
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23
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Lang JM, DuCharme E, Ibarra Caballero J, Luna E, Hartman T, Ortiz-Castro M, Korus K, Rascoe J, Jackson-Ziems TA, Broders K, Leach JE. Detection and Characterization of Xanthomonas vasicola pv. vasculorum (Cobb 1894) comb. nov. Causing Bacterial Leaf Streak of Corn in the United States. PHYTOPATHOLOGY 2017; 107:1312-1321. [PMID: 28677478 DOI: 10.1094/phyto-05-17-0168-r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial leaf streak of corn (Zea mays) recently reached epidemic levels in three corn-growing states, and has been detected in another six states in the central United States. Xanthomonas vasicola was identified as the causal agent of this disease. A multilocus sequence alignment of six housekeeping genes and comparison of average nucleotide identity from draft genome sequence were used to confirm phylogenetic relationships and classification of this bacteria relative to other X. vasicola strains. X. vasicola isolates from Nebraska and South Africa were highly virulent on corn and sugarcane and less virulent on sorghum but caused water-soaking symptoms that are typical of X. vasicola infection on the leaves of all three hosts. Based on host range and phylogenetic comparison, we propose the taxonomic designation of this organism to X. vasicola pv. vasculorum ( Cobb 1894 ) comb. nov. Polymerase chain reaction-based diagnostic assays were developed that distinguish X. vasicola pv. vasculorum and X. vasicola pv. holcicola from each other and from other Xanthomonas spp.
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Affiliation(s)
- J M Lang
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - E DuCharme
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J Ibarra Caballero
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - E Luna
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - T Hartman
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - M Ortiz-Castro
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - K Korus
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J Rascoe
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - T A Jackson-Ziems
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - K Broders
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
| | - J E Leach
- First, second, third, fourth, sixth, tenth, and eleventh authors: Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, 80523-1177; fifth, seventh, and ninth authors: University of Nebraska-Lincoln, Lincoln 68583; seventh author: Alachua County Extension, University of Florida, Gainesville 32609; and eighth author: United States Department of Agriculture-Animal Plant Health Inspection Service-Plant Protection and Quarantine-CPHST, Beltsville, MD 20705
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Ruh M, Briand M, Bonneau S, Jacques MA, Chen NWG. Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors. BMC Genomics 2017; 18:670. [PMID: 28854875 PMCID: PMC5577687 DOI: 10.1186/s12864-017-4087-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022] Open
Abstract
Background Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance. Their capacity to bind to a specific host DNA sequence suggests that they are potential candidates for host adaption. Results To study the diversity of tal genes from Xanthomonas strains responsible for common bacterial blight of bean, whole genome sequences of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli pv. phaseoli were obtained by single molecule real time sequencing. Analysis of these genomes revealed the existence of four tal genes named tal23A, tal20F, tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A and tal18H were carried on plasmids and shared between phylogenetically distant strains, therefore suggesting recent horizontal transfers of these genes between X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was present in all strains studied, suggesting that it played an important role in adaptation to common bean. In silico predictions of TAL effectors targets in the common bean genome suggested that TAL effectors shared by X. citri pv. fuscans and X. phaseoli pv. phaseoli strains target the promoters of genes of similar functions. This could be a trace of convergent evolution among TAL effectors from different phylogenetic groups, and comforts the hypothesis that TAL effectors have been implied in the adaptation to common bean. Conclusions Altogether, our results favour a model where plasmidic TAL effectors are able to contribute to host adaptation by being horizontally transferred between distant lineages. Electronic supplementary material The online version of this article (10.1186/s12864-017-4087-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France.
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Barak JD, Vancheva T, Lefeuvre P, Jones JB, Timilsina S, Minsavage GV, Vallad GE, Koebnik R. Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors. FRONTIERS IN PLANT SCIENCE 2016; 7:1805. [PMID: 28018370 PMCID: PMC5146329 DOI: 10.3389/fpls.2016.01805] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/15/2016] [Indexed: 05/11/2023]
Abstract
Multiple species of Xanthomonas cause bacterial spot of tomato (BST) and pepper. We sequenced five Xanthomonas euvesicatoria strains isolated from three continents (Africa, Asia, and South America) to provide a set of representative genomes with temporal and geographic diversity. LMG strains 667, 905, 909, and 933 were pathogenic on tomato and pepper, except LMG 918 elicited a hypersensitive reaction (HR) on tomato. Furthermore, LMG 667, 909, and 918 elicited a HR on Early Cal Wonder 30R containing Bs3. We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating X. euvesicatoria from X. perforans, both causal agents of BST. LMG strains 905, 909, 918, and 933 were nonpectolytic while only LMG 918 was amylolytic. These results suggest that LMG 918 is atypical of X. euvesicatoria. Sequence analysis of all the publicly available X. euvesicatoria and X. perforans strains comparing seven housekeeping genes identified seven haplotypes with few polymorphisms. Whole genome comparison by average nucleotide identity (ANI) resulted in values of >99% among the LMG strains 667, 905, 909, 918, and 933 and X. euvesicatoria strains and >99.6% among the LMG strains and a subset of X. perforans strains. These results suggest that X. euvesicatoria and X. perforans should be considered a single species. ANI values between strains of X. euvesicatoria, X. perforans, X. allii, X. alfalfa subsp. citrumelonis, X. dieffenbachiae, and a recently described pathogen of rose were >97.8% suggesting these pathogens should be a single species and recognized as X. euvesicatoria. Analysis of the newly sequenced X. euvesicatoria strains revealed interesting findings among the type 3 (T3) effectors, relatively ancient stepwise erosion of some T3 effectors, additional X. euvesicatoria-specific T3 effectors among the causal agents of BST, orthologs of avrBs3 and avrBs4, and T3 effectors shared among xanthomonads pathogenic against various hosts. The results from this study supports the finding that T3 effector repertoire and host range are fundamental for the study of host-microbe interaction but of little relevance to bacterial speciation.
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Affiliation(s)
- Jeri D. Barak
- UMR Interactions – Plantes – Microorganismes – Environnement, IRD-Cirad-Université MontpellierMontpellier, France
- Department of Plant Pathology, University of WisconsinMadison, WI, USA
| | - Taca Vancheva
- UMR Interactions – Plantes – Microorganismes – Environnement, IRD-Cirad-Université MontpellierMontpellier, France
- Faculty of Biology, Sofia University St. Kliment OhridskiSofia, Bulgaria
| | - Pierre Lefeuvre
- Pôle de Protection des Plantes, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Cirad-Université de la RéunionSaint-Pierre, Ile de la Réunion, France
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of FloridaGainsville, FL, USA
| | - Sujan Timilsina
- Department of Plant Pathology, University of FloridaGainsville, FL, USA
| | | | - Gary E. Vallad
- Gulf Coast Research and Education Center, University of FloridaWimauma, FL, USA
| | - Ralf Koebnik
- UMR Interactions – Plantes – Microorganismes – Environnement, IRD-Cirad-Université MontpellierMontpellier, France
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Liu Q, Ravanlou A, Babadoost M. Occurrence of Bacterial Spot on Pumpkin and Squash Fruit in the North Central Region of the United States and Bacteria Associated with the Spots. PLANT DISEASE 2016; 100:2377-2382. [PMID: 30686176 DOI: 10.1094/pdis-01-16-0107-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Since 2006, a bacterial spot disease has been widely observed on pumpkin and squash fruit in the North Central region (NCR) of the United States. Surveys were conducted during 2011 to 2013 to determine the occurrence of the disease on pumpkin and winter squash in the NCR. In each state, at least five commercial pumpkin and squash fields were visited each year within 3 weeks of harvest, and 60 fruit were inspected in each field. In nine states surveyed, 217 of 245 fields had fruit with bacterial spot. The average incidence of the symptomatic fruit in all pumpkin fields surveyed was 27.1, 30.3, and 25.3% in 2011, 2012, and 2013, respectively. The average incidence of fruit with bacterial spot in all squash fields surveyed was 20.2% in 2012 and 16.9% in 2013. The incidence of symptomatic fruit was more than 90% in some fields. Xanthomonas cucurbitae and non-X. cucurbitae bacteria were isolated from all of the symptomatic fruit collected. X. cucurbitae was identified based on colony characteristics on yeast extract-dextrose-CaCO3 agar, a polymerase chain reaction test using primers RST2 and RST3, and pathogenicity on pumpkin leaves. All X. cucurbitae isolates tested were pathogenic on 'Howden' pumpkin. In total, 312 non-X. cucurbitae isolates were identified into 10 genera based on the restriction fragment length polymorphism analysis. None of the non-X. cucurbitae isolates was pathogenic on Howden. In vitro studies of interactions between non-X. cucurbitae and X. cucurbitae showed that Pantoea isolates had antagonistic activity against X. cucurbitae. Identified Pantoea agglomerans showed the highest antagonistic activity against X. cucurbitae.
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Affiliation(s)
- Qiong Liu
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana 61801
| | - Abbasali Ravanlou
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana 61801
| | - Mohammad Babadoost
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana 61801
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27
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Genome editing: the road of CRISPR/Cas9 from bench to clinic. Exp Mol Med 2016; 48:e265. [PMID: 27741224 PMCID: PMC5099421 DOI: 10.1038/emm.2016.111] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/14/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022] Open
Abstract
Molecular scissors engineered for site-specific modification of the genome hold great promise for effective functional analyses of genes, genomes and epigenomes and could improve our understanding of the molecular underpinnings of disease states and facilitate novel therapeutic applications. Several platforms for molecular scissors that enable targeted genome engineering have been developed, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and, most recently, clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated-9 (Cas9). The CRISPR/Cas9 system's simplicity, facile engineering and amenability to multiplexing make it the system of choice for many applications. CRISPR/Cas9 has been used to generate disease models to study genetic diseases. Improvements are urgently needed for various aspects of the CRISPR/Cas9 system, including the system's precision, delivery and control over the outcome of the repair process. Here, we discuss the current status of genome engineering and its implications for the future of biological research and gene therapy.
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28
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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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29
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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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Segarra G, Puopolo G, Porcel-Rodríguez E, Giovannini O, Pertot I. Monitoring Lysobacter capsici AZ78 using strain specific qPCR reveals the importance of the formulation for its survival in vineyards. FEMS Microbiol Lett 2015; 363:fnv243. [PMID: 26691736 DOI: 10.1093/femsle/fnv243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 11/12/2022] Open
Abstract
Survival in the phyllosphere is a critical feature for biofungicides based on non-spore forming bacteria. Moreover, knowledge of their persistence on plants is important to design effective formulations and application techniques. With this scope, the aim of this work was to develop a specific method to monitor the fate in the environment of Lysobacter capsici AZ78, a biocontrol agent of Plasmopara viticola, and to evaluate the contribution of formulation in its persistence on grapevine leaves. A strain-specific primer pair derived from REP-PCR fingerprinting was used in quantitative PCR experiments to track the evolution of L. capsici AZ78 population in vineyards. The population reached between 5 and 6 log10 cells gram of leaf(-1) after application and decreased by more than 100 times in one week. Multiple regression analysis showed that unfavourable temperature was the main environmental factor correlating with the decrease of L. capsici AZ78 persistence on grapevine leaves. Importantly, the use of formulation additives protected L. capsici AZ78 against environmental factors and improved its persistence on the leaves by more than 10 times compared to nude cells. Formulation and the knowledge about the persistence of L. capsici AZ78 in vineyards will be useful to develop commercial biofungicides for foliar application.
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Affiliation(s)
- Guillem Segarra
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Edmund Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Gerardo Puopolo
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Edmund Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Elena Porcel-Rodríguez
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Edmund Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Oscar Giovannini
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Edmund Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Ilaria Pertot
- Department of Sustainable Agro-Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Edmund Mach 1, 38010 San Michele all'Adige, Trento, Italy
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Aritua V, Harrison J, Sapp M, Buruchara R, Smith J, Studholme DJ. Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans. Front Microbiol 2015; 6:1080. [PMID: 26500625 PMCID: PMC4595841 DOI: 10.3389/fmicb.2015.01080] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 09/22/2015] [Indexed: 11/13/2022] Open
Abstract
Common bacterial blight is a devastating seed-borne disease of common beans that also occurs on other legume species including lablab and Lima beans. We sequenced and analyzed the genomes of 26 strains of Xanthomonas axonopodis pv. phaseoli and X. fuscans subsp. fuscans, the causative agents of this disease, collected over four decades and six continents. This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread. The bacterial strain from Lima bean fell within the previously described Genetic Lineage 1, along with the pathovar type strain (NCPPB 3035). The strains from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines. Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.
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Affiliation(s)
- Valente Aritua
- International Center for Tropical Agriculture Kampala, Uganda
| | | | | | - Robin Buruchara
- Africa Regional Office, International Center for Tropical Agriculture, Consultative Group for International Agricultural Research (CGIAR) Nairobi, Kenya
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Essakhi S, Cesbron S, Fischer-Le Saux M, Bonneau S, Jacques MA, Manceau C. Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System. Appl Environ Microbiol 2015; 81:5395-410. [PMID: 26048944 PMCID: PMC4510168 DOI: 10.1128/aem.00835-15] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 05/21/2015] [Indexed: 01/13/2023] Open
Abstract
Xanthomonas arboricola is conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. This study showed that X. arboricola also encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. The aim of this study was to assess the X. arboricola population structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. A multilocus sequence analysis (MLSA) was performed on a collection of 100 X. arboricola strains, including 27 nonpathogenic strains isolated from walnut. Nonpathogenic strains grouped outside clusters defined by pathovars and formed separate genetic lineages. A multilocus variable-number tandem-repeat analysis (MLVA) conducted on a collection of X. arboricola strains isolated from walnut showed that nonpathogenic strains clustered separately from clonal complexes containing Xanthomonas arboricola pv. juglandis strains. Some nonpathogenic strains of X. arboricola did not contain the canonical type III secretion system (T3SS) and harbored only one to three type III effector (T3E) genes. In the nonpathogenic strains CFBP 7640 and CFBP 7653, neither T3SS genes nor any of the analyzed T3E genes were detected. This finding raises a question about the origin of nonpathogenic strains and the evolution of plant pathogenicity in X. arboricola. T3E genes that were not detected in any nonpathogenic isolates studied represent excellent candidates to be those responsible for pathogenicity in X. arboricola.
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Affiliation(s)
- Salwa Essakhi
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Sophie Cesbron
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | | | - Sophie Bonneau
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Marie-Agnès Jacques
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Charles Manceau
- INRA, UMR 1345, Institut de Recherche en Horticulture et Semences, Beaucouzé, France Anses, Laboratoire de la Santé des Végétaux, Unité Expertise-Risques Biologiques, Angers, France
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Robène I, Perret M, Jouen E, Escalon A, Maillot MV, Chabirand A, Moreau A, Laurent A, Chiroleu F, Pruvost O. Development and validation of a real-time quantitative PCR assay to detect Xanthomonas axonopodis pv. allii from onion seed. J Microbiol Methods 2015; 114:78-86. [DOI: 10.1016/j.mimet.2015.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/30/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
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Fischer-Le Saux M, Bonneau S, Essakhi S, Manceau C, Jacques MA. Aggressive Emerging Pathovars of Xanthomonas arboricola Represent Widespread Epidemic Clones Distinct from Poorly Pathogenic Strains, as Revealed by Multilocus Sequence Typing. Appl Environ Microbiol 2015; 81:4651-68. [PMID: 25934623 PMCID: PMC4551192 DOI: 10.1128/aem.00050-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/25/2015] [Indexed: 12/11/2022] Open
Abstract
Deep and comprehensive knowledge of the genetic structure of pathogenic species is the cornerstone on which the design of precise molecular diagnostic tools is built. Xanthomonas arboricola is divided into pathovars, some of which are classified as quarantine organisms in many countries and are responsible for diseases on nut and stone fruit trees that have emerged worldwide. Recent taxonomic studies of the genus Xanthomonas showed that strains isolated from other hosts should be classified in X. arboricola, extending the host range of the species. To investigate the genetic structure of X. arboricola and the genetic relationships between highly pathogenic strains and strains apparently not relevant to plant health, we conducted multilocus sequence analyses on a collection of strains representative of the known diversity of the species. Most of the pathovars were clustered in separate monophyletic groups. The pathovars pruni, corylina, and juglandis, responsible for pandemics in specific hosts, were highly phylogenetically related and clustered in three distinct clonal complexes. In contrast, strains with no or uncertain pathogenicity were represented by numerous unrelated singletons scattered in the phylogenic tree. Depending on the pathovar, intra- and interspecies recombination played contrasting roles in generating nucleotide polymorphism. This work provides a population genetics framework for molecular epidemiological surveys of emerging plant pathogens within X. arboricola. Based on our results, we propose to reclassify three former pathovars of Xanthomonas campestris as X. arboricola pv. arracaciae comb. nov., X. arboricola pv. guizotiae comb. nov., and X. arboricola pv. zantedeschiae comb. nov. An emended description of X. arboricola Vauterin et al. 1995 is provided.
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Affiliation(s)
- Marion Fischer-Le Saux
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Sophie Bonneau
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Salwa Essakhi
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Charles Manceau
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Marie-Agnès Jacques
- INRA, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Université d'Angers, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France Agrocampus Ouest, UMR1345 IRHS Institut de Recherche en Horticulture et Semences, Beaucouzé, France
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35
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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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Lamichhane JR. Xanthomonas arboricola Diseases of Stone Fruit, Almond, and Walnut Trees: Progress Toward Understanding and Management. PLANT DISEASE 2014; 98:1600-1610. [PMID: 30703892 DOI: 10.1094/pdis-08-14-0831-fe] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Stone fruit (Prunus spp.: apricot, cherry, peach, nectarine, plum, and sloe), almond (Prunus spp.), and walnut (Juglans spp.) crops are among the most economically important tree crops worldwide and are cultivated to a different extent on all continents. The number of countries growing these crops has increased in the last decade with a subsequent increase in acreage globally. Throughout the range of cultivation, Prunus spp. and Juglans spp. are often subjected to pathogen attack. Among them, Xanthomonas arboricola has become markedly important over the last decade. The putative pathovars of X. arboricola, pv. pruni and pv. juglandis, cause bacterial canker and spot and bacterial blight on stone fruits and almond, and on walnut, respectively. In recent years, disease outbreaks caused by X. arboricola on Prunus and on Juglans have increased, as has international concern. The rate at which these outbreaks are occurring suggests the possibility of future epidemics. To address the consequences of such disease emergences, it is important to understand the epidemiology of these diseases, about which little is known to date. The objectives of this review are to provide an overview of X. arboricola diseases of stone fruit, almond, and walnut trees, and to discuss current and future management strategies.
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Affiliation(s)
- Jay Ram Lamichhane
- French National Institute for Agricultural Research (INRA), UAR 1240 Eco-Innov Research Unit, 78850 Thiverval-Grignon, France
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Scientific Opinion on the pest categorisation ofXanthomonas axonopodispv.phaseoliandXanthomonas fuscanssubsp.fuscans. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3856] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Harrison J, Studholme DJ. Draft genome sequence of Xanthomonas axonopodis pathovar vasculorum NCPPB 900. FEMS Microbiol Lett 2014; 360:113-6. [PMID: 25263632 DOI: 10.1111/1574-6968.12607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/28/2022] Open
Abstract
Xanthomonas axonopodis pathovar vasculorum strain NCPPB 900 was isolated from sugarcane on Reunion island in 1960. Consistent with its belonging to fatty-acid type D, multi-locus sequence analysis confirmed that NCPPB 900 falls within the species X. axonopodis. This genome harbours sequences similar to plasmids pXCV183 from X. campestris pv. vesicatoria 85-10 and pPHB194 from Burkholderia pseudomallei. Its repertoire of predicted effectors includes homologues of XopAA, XopAD, XopAE, XopB, XopD, XopV, XopZ, XopC and XopI and transcriptional activator-like effectors and it is predicted to encode a novel phosphonate natural product also encoded by the genome of the phylogenetically distant X. vasicola pv. vasculorum. Availability of this novel genome sequence may facilitate the study of interactions between xanthomonads and sugarcane, a host-pathogen system that appears to have evolved several times independently within the genus Xanthomonas and may also provide a source of target sequences for molecular detection and diagnostics
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Wasukira A, Coulter M, Al-Sowayeh N, Thwaites R, Paszkiewicz K, Kubiriba J, Smith J, Grant M, Studholme DJ. Genome Sequencing of Xanthomonas vasicola Pathovar vasculorum Reveals Variation in Plasmids and Genes Encoding Lipopolysaccharide Synthesis, Type-IV Pilus and Type-III Secretion Effectors. Pathogens 2014; 3:211-37. [PMID: 25437615 PMCID: PMC4235730 DOI: 10.3390/pathogens3010211] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/10/2014] [Accepted: 03/03/2014] [Indexed: 01/01/2023] Open
Abstract
Xanthomonas vasicola pathovar vasculorum (Xvv) is the bacterial agent causing gumming disease in sugarcane. Here, we compare complete genome sequences for five isolates of Xvv originating from sugarcane and one from maize. This identified two distinct types of lipopolysaccharide synthesis gene clusters among Xvv isolates: one is similar to that of Xanthomonas axonopodis pathovar citri (Xac) and is probably the ancestral type, while the other is similar to those of the sugarcane-inhabiting species, Xanthomonas sacchari. Four of six Xvv isolates harboured sequences similar to the Xac plasmid, pXAC47, and showed a distinct Type-IV pilus (T4P) sequence type, whereas the T4P locus of the other two isolates resembled that of the closely related banana pathogen, Xanthomonas campestris pathovar musacearum (Xcm). The Xvv isolate from maize has lost a gene encoding a homologue of the virulence effector, xopAF, which was present in all five of the sugarcane isolates, while xopL contained a premature stop codon in four out of six isolates. These findings shed new light on evolutionary events since the divergence of Xvv and Xcm, as well as further elucidating the relationships between the two closely related pathogens.
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Affiliation(s)
- Arthur Wasukira
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
| | - Max Coulter
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
| | - Noorah Al-Sowayeh
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
| | - Richard Thwaites
- The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, UK.
| | - Konrad Paszkiewicz
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
| | - Jerome Kubiriba
- National Crops Resources Research Institute (NaCRRI), Kampala 7084, Uganda.
| | - Julian Smith
- The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, UK.
| | - Murray Grant
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
| | - David J Studholme
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
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Cesbron S, Pothier J, Gironde S, Jacques MA, Manceau C. Development of multilocus variable-number tandem repeat analysis (MLVA) for Xanthomonas arboricola pathovars. J Microbiol Methods 2014; 100:84-90. [PMID: 24631558 DOI: 10.1016/j.mimet.2014.02.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/27/2014] [Accepted: 02/28/2014] [Indexed: 11/19/2022]
Abstract
Xanthomonas arboricola is an important bacterial species, the pathovars of which are responsible for bacterial blight diseases on stone fruit, hazelnut, Persian walnut, poplar, strawberry, poinsettia and banana. In this study, we evaluated variable number tandem repeats (VNTR) as a molecular typing tool for assessing the genetic diversity within pathovars of X. arboricola. Screening of the X. arboricola pv. pruni genome sequence (CFBP5530 strain) predicted 51 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 51 loci were designed, and their discriminatory power was initially evaluated with a core collection of 8 X. arboricola strains representative of the different pathovars. Next, the 26 polymorphic VNTR loci present in all strains were used for genotyping a collection of 61 strains. MLVA is a typing method that clearly differentiates X. arboricola strains. The MLVA scheme described in this study is a rapid and reliable molecular typing tool that can be used for further epidemiological studies of bacterial diseases caused by X. arboricola pathovars.
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Affiliation(s)
- Sophie Cesbron
- INRA, UMR1345 IRHS, F-49071 Beaucouzé, France; AGROCAMPUS OUEST, UMR1345 IRHS, F-49071 Beaucouzé, France; Université d'Angers, UMR1345 IRHS, SFR 4207 QUASAV, PRES L'UNAM, F-49071 Beaucouzé, France.
| | - Joel Pothier
- Agroscope Changins-Wädenswil Research Station ACW, Plant Protection Division, Schloss 1, CH-8820 Wädenswil, Switzerland
| | - Sophie Gironde
- INRA, UMR1345 IRHS, F-49071 Beaucouzé, France; AGROCAMPUS OUEST, UMR1345 IRHS, F-49071 Beaucouzé, France; Université d'Angers, UMR1345 IRHS, SFR 4207 QUASAV, PRES L'UNAM, F-49071 Beaucouzé, France
| | - Marie-Agnès Jacques
- INRA, UMR1345 IRHS, F-49071 Beaucouzé, France; AGROCAMPUS OUEST, UMR1345 IRHS, F-49071 Beaucouzé, France; Université d'Angers, UMR1345 IRHS, SFR 4207 QUASAV, PRES L'UNAM, F-49071 Beaucouzé, France
| | - Charles Manceau
- INRA, UMR1345 IRHS, F-49071 Beaucouzé, France; AGROCAMPUS OUEST, UMR1345 IRHS, F-49071 Beaucouzé, France; Université d'Angers, UMR1345 IRHS, SFR 4207 QUASAV, PRES L'UNAM, F-49071 Beaucouzé, France
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Characterization of the pyrophosphate-dependent 6-phosphofructokinase from Xanthomonas campestris pv. campestris. Arch Biochem Biophys 2014; 546:53-63. [DOI: 10.1016/j.abb.2014.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 01/23/2014] [Accepted: 01/26/2014] [Indexed: 01/01/2023]
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42
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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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43
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Arrieta-Ortiz ML, Rodríguez-R LM, Pérez-Quintero ÁL, Poulin L, Díaz AC, Arias Rojas N, Trujillo C, Restrepo Benavides M, Bart R, Boch J, Boureau T, Darrasse A, David P, Dugé de Bernonville T, Fontanilla P, Gagnevin L, Guérin F, Jacques MA, Lauber E, Lefeuvre P, Medina C, Medina E, Montenegro N, Muñoz Bodnar A, Noël LD, Ortiz Quiñones JF, Osorio D, Pardo C, Patil PB, Poussier S, Pruvost O, Robène-Soustrade I, Ryan RP, Tabima J, Urrego Morales OG, Vernière C, Carrere S, Verdier V, Szurek B, Restrepo S, López C, Koebnik R, Bernal A. Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151. PLoS One 2013; 8:e79704. [PMID: 24278159 PMCID: PMC3838355 DOI: 10.1371/journal.pone.0079704] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/24/2013] [Indexed: 11/24/2022] Open
Abstract
Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.
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Affiliation(s)
- Mario L. Arrieta-Ortiz
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Luis M. Rodríguez-R
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | | | - Lucie Poulin
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Ana C. Díaz
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Nathalia Arias Rojas
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Cesar Trujillo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | | | - Rebecca Bart
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Jens Boch
- Department of Genetics, Martin Luther University, Halle-Wittenberg, Germany
| | - Tristan Boureau
- Institut National de la Recherche Agronomique, UMR45 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, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Armelle Darrasse
- Institut National de la Recherche Agronomique, UMR45 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, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Perrine David
- Institut National de la Recherche Agronomique, UMR45 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, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Thomas Dugé de Bernonville
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Paula Fontanilla
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Lionel Gagnevin
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Fabien Guérin
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Marie-Agnès Jacques
- Institut National de la Recherche Agronomique, UMR45 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, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Emmanuelle Lauber
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Pierre Lefeuvre
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Cesar Medina
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Edgar Medina
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Nathaly Montenegro
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Alejandra Muñoz Bodnar
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Laurent D. Noël
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Juan F. Ortiz Quiñones
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniela Osorio
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Carolina Pardo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Prabhu B. Patil
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Stéphane Poussier
- Institut National de la Recherche Agronomique, UMR45 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, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
| | - Olivier Pruvost
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Isabelle Robène-Soustrade
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Robert P. Ryan
- College of Life Sciences, University of Dundee, Dundee, Scotland
| | - Javier Tabima
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Oscar G. Urrego Morales
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Christian Vernière
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Sébastien Carrere
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Valérie Verdier
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, United States of America
| | - Boris Szurek
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Camilo López
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Ralf Koebnik
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Adriana Bernal
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- * E-mail:
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Darrasse A, Carrère S, Barbe V, Boureau T, Arrieta-Ortiz ML, Bonneau S, Briand M, Brin C, Cociancich S, Durand K, Fouteau S, Gagnevin L, Guérin F, Guy E, Indiana A, Koebnik R, Lauber E, Munoz A, Noël LD, Pieretti I, Poussier S, Pruvost O, Robène-Soustrade I, Rott P, Royer M, Serres-Giardi L, Szurek B, van Sluys MA, Verdier V, Vernière C, Arlat M, Manceau C, Jacques MA. Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads. BMC Genomics 2013; 14:761. [PMID: 24195767 PMCID: PMC3826837 DOI: 10.1186/1471-2164-14-761] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. RESULTS Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. CONCLUSIONS This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.
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Affiliation(s)
- Armelle Darrasse
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Sébastien Carrère
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
| | - Valérie Barbe
- CEA, Genoscope, Centre National de Séquençage, F-91057, Evry Cedex, France
| | - Tristan Boureau
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Mario L Arrieta-Ortiz
- Universidad de Los Andes, Laboratorio de Micología y Fitopatología Uniandes, Bogotá, Colombia
- current address: Department of Biology, Center for Genomics and Systems Biology, New York University, 10003, New York, NY, USA
| | - Sophie Bonneau
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Martial Briand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Chrystelle Brin
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | | | - Karine Durand
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Stéphanie Fouteau
- CEA, Genoscope, Centre National de Séquençage, F-91057, Evry Cedex, France
| | - Lionel Gagnevin
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Fabien Guérin
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Endrick Guy
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
| | - Arnaud Indiana
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Ralf Koebnik
- IRD, UMR RPB, F-34394, Montpellier Cedex 5, France
| | - Emmanuelle Lauber
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
| | - Alejandra Munoz
- Universidad de Los Andes, Laboratorio de Micología y Fitopatología Uniandes, Bogotá, Colombia
| | - Laurent D Noël
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
| | | | - Stéphane Poussier
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Isabelle Robène-Soustrade
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Philippe Rott
- CIRAD, UMR BGPI, F-34398, Montpellier Cedex 5, France
| | - Monique Royer
- CIRAD, UMR BGPI, F-34398, Montpellier Cedex 5, France
| | - Laurana Serres-Giardi
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
| | - Boris Szurek
- IRD, UMR RPB, F-34394, Montpellier Cedex 5, France
| | | | | | - Christian Vernière
- CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France
- Université de la Réunion, UMR PVBMT, F-97715, Saint-Denis, La Réunion, France
| | - Matthieu Arlat
- INRA, LIPM UMR 441, F-31326, Castanet-Tolosan, France
- CNRS, LIPM UMR 2594, F-31326, Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, UMR LIPM, F-31326, Castanet-Tolosan Cedex, France
| | - Charles Manceau
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
- current address: ANSES, Laboratoire de Santé des végétaux, F-49044, Angers, France
| | - Marie-Agnès Jacques
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, F-49071, Beaucouzé, France
- AGROCAMPUS OUEST, UMR1345 Institut de Recherche en Horticulture et Semences, F-49045, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, F-49045, Angers, France
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45
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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: 6] [Impact Index Per Article: 0.5] [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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46
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High-Quality Draft Genome Sequences of Two Xanthomonas citri pv. malvacearum Strains. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00674-13. [PMID: 23990578 PMCID: PMC3757453 DOI: 10.1128/genomea.00674-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report high-quality draft genome sequences of two strains (race 18 and 20) of Xanthomonas citri pv. malvacearum, the causal agent of bacterial blight of cotton. Comparative genomics will help to decipher mechanisms provoking disease and triggering defense responses and to develop new molecular tools for epidemiological surveillance.
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47
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Chiesa MA, Siciliano MF, Ornella L, Roeschlin RA, Favaro MA, Delgado NP, Sendín LN, Orce IG, Ploper LD, Vojnov AA, Vacas JG, Filippone MP, Castagnaro AP, Marano MR. Characterization of a variant of Xanthomonas citri subsp. citri that triggers a host-specific defense response. PHYTOPATHOLOGY 2013; 103:555-564. [PMID: 23268580 DOI: 10.1094/phyto-11-12-0287-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Citrus is an economically important fruit crop that is severely afflicted by Asiatic citrus bacterial canker (CBC), a disease caused by the phytopathogen Xanthomonas citri subsp. citri (X. citri). To gain insight into the molecular epidemiology of CBC, 42 Xanthomonas isolates were collected from a range of Citrus spp. across 17 different orchards in Tucumán, Argentina and subjected to molecular, biochemical, and pathogenicity tests. Analysis of genome-specific X. citri markers and DNA polymorphisms based on repetitive elements-based polymerase chain reaction showed that all 42 isolates belonged to X. citri. Interestingly, pathogenicity tests showed that one isolate, which shares >90% genetic similarity to the reference strain X. citri T, has host range specificity. This new variant of X. citri subsp. citri, named X. citri A(T), which is deficient in xanthan production, induces an atypical, noncankerous chlorotic phenotype in Citrus limon and C. paradisi and weak cankerous lesions in C. aurantifolia and C. clementina leaves. In C. limon, suppression of canker development is concomitant with an oxidative burst; xanthan is not implicated in the phenotype induced by this interaction, suggesting that other bacterial factors would be involved in triggering the defense response.
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Affiliation(s)
- María A Chiesa
- Instituto de Biología Molecular y Celular de Rosario (IBR)–Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Área Virología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 590, S2002LRK Rosario, Argentina
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48
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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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49
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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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50
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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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