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Harrison J, Hussain RMF, Greer SF, Ntoukakis V, Aspin A, Vicente JG, Grant M, Studholme DJ. Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. Access Microbiol 2023; 5:acmi000532.v3. [PMID: 37601434 PMCID: PMC10436009 DOI: 10.1099/acmi.0.000532.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/25/2023] [Indexed: 08/22/2023] Open
Abstract
Here we report draft-quality genome sequences for pathotype strains of eight plant-pathogenic bacterial pathovars: Xanthomonas campestris pv. asclepiadis, X. campestris pv. cannae, X. campestris pv. esculenti, X. campestris pv. nigromaculans, X. campestris pv. parthenii, X. campestris pv. phormiicola, X. campestris pv. zinniae and X. dyei pv. eucalypti (= X. campestris pv. eucalypti). We also sequenced the type strain of species X. melonis and the unclassified Xanthomonas strain NCPPB 1067. These data will be useful for phylogenomic and taxonomic studies, filling some important gaps in sequence coverage of Xanthomonas phylogenetic diversity. We include representatives of previously under-sequenced pathovars and species-level clades. Furthermore, these genome sequences may be useful in elucidating the molecular basis for important phenotypes, such as biosynthesis of coronatine-related toxins and degradation of fungal toxin cercosporin.
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Affiliation(s)
| | - Rana Muhammad Fraz Hussain
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
| | - Shannon F. Greer
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
| | - Vardis Ntoukakis
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Andrew Aspin
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Joana G. Vicente
- Wellesbourne Campus, School of Life Sciences, University of Warwick, Coventry, CV35 9EF, UK
- Fera Science Ltd., York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Murray Grant
- Gibbet Hill Campus, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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2
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Te Molder D, Poncheewin W, Schaap PJ, Koehorst JJ. Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains. BMC Genomics 2021; 22:848. [PMID: 34814827 PMCID: PMC8612006 DOI: 10.1186/s12864-021-08093-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. RESULTS Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. CONCLUSION The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.
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Affiliation(s)
- Dennie Te Molder
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Wasin Poncheewin
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands
- UNLOCK, Wageningen University, Wageningen, the Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, the Netherlands.
- UNLOCK, Wageningen University, Wageningen, the Netherlands.
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3
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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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4
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Li T, Mann R, Sawbridge T, Kaur J, Auer D, Spangenberg G. Novel Xanthomonas Species From the Perennial Ryegrass Seed Microbiome - Assessing the Bioprotection Activity of Non-pathogenic Relatives of Pathogens. Front Microbiol 2020; 11:1991. [PMID: 32983016 PMCID: PMC7479056 DOI: 10.3389/fmicb.2020.01991] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/28/2020] [Indexed: 11/13/2022] Open
Abstract
The productivity of the Australian dairy industry is underpinned by pasture grasses, and importantly perennial ryegrass. The performance of these pasture grasses is supported by the fungal endophyte Epichloë spp. that has bioprotection activities, however, the broader microbiome is not well characterized. In this study, we characterized a novel bioprotectant Xanthomonas species isolated from perennial ryegrass (Lolium perenne L. cv. Alto). In vitro and in planta bioassays against key fungal pathogens of grasses (Sclerotium rolfsii, Drechslera brizae and Microdochium nivale) indicated strong bioprotection activities. A complete circular chromosome of ∼5.2 Mb was generated for three strains of the novel Xanthomonas sp. Based on the 16S ribosomal RNA gene, the strains were closely related to the plant pathogen Xanthomonas translucens, however, comparative genomics of 22 closely related xanthomonad strains indicated that these strains were a novel species. The comparative genomics analysis also identified two unique gene clusters associated with the production of bioprotectant secondary metabolites including one associated with a novel nonribosomal peptide synthetase and another with a siderophore. The analysis also identified genes associated with an endophytic lifestyle (e.g., Type VI secretion system), while no genes associated with pathogenicity were identified (e.g., Type III secretion system and effectors). Overall, these results indicate that these strains represent a novel, bioactive, non-pathogenic species of the genus Xanthomonas. Strain GW was the designated type strain of this novel Xanthomonas sp.
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Affiliation(s)
- Tongda Li
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Ross Mann
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia
| | - Timothy Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Jatinder Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia
| | - Desmond Auer
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia.,DairyBio, Bundoora, VIC, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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5
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Meline V, Delage W, Brin C, Li‐Marchetti C, Sochard D, Arlat M, Rousseau C, Darrasse A, Briand M, Lebreton G, Portier P, Fischer‐Le Saux M, Durand K, Jacques M, Belin E, Boureau T. Role of the acquisition of a type 3 secretion system in the emergence of novel pathogenic strains of Xanthomonas. MOLECULAR PLANT PATHOLOGY 2019; 20:33-50. [PMID: 30076773 PMCID: PMC6430459 DOI: 10.1111/mpp.12737] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Cases of emergence of novel plant-pathogenic strains are regularly reported that reduce the yields of crops and trees. However, the molecular mechanisms underlying such emergence are still poorly understood. The acquisition by environmental non-pathogenic strains of novel virulence genes by horizontal gene transfer has been suggested as a driver for the emergence of novel pathogenic strains. In this study, we tested such an hypothesis by transferring a plasmid encoding the type 3 secretion system (T3SS) and four associated type 3 secreted proteins (T3SPs) to the non-pathogenic strains of Xanthomonas CFBP 7698 and CFBP 7700, which lack genes encoding T3SS and any previously known T3SPs. The resulting strains were phenotyped on Nicotiana benthamiana using chlorophyll fluorescence imaging and image analysis. Wild-type, non-pathogenic strains induced a hypersensitive response (HR)-like necrosis, whereas strains complemented with T3SS and T3SPs suppressed this response. Such suppression depends on a functional T3SS. Amongst the T3SPs encoded on the plasmid, Hpa2, Hpa1 and, to a lesser extent, XopF1 collectively participate in suppression. Monitoring of the population sizes in planta showed that the sole acquisition of a functional T3SS by non-pathogenic strains impairs growth inside leaf tissues. These results provide functional evidence that the acquisition via horizontal gene transfer of a T3SS and four T3SPs by environmental non-pathogenic strains is not sufficient to make strains pathogenic. In the absence of a canonical effector, the sole acquisition of a T3SS seems to be counter-selective, and further acquisition of type 3 effectors is probably needed to allow the emergence of novel pathogenic strains.
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Affiliation(s)
- Valérian Meline
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Wesley Delage
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Chrystelle Brin
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Camille Li‐Marchetti
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Daniel Sochard
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Matthieu Arlat
- INRAUMR 441, Laboratoire des Interactions Plantes Micro‐organismes (LIPM)F‐31326Castanet‐TolosanFrance
| | - Céline Rousseau
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Armelle Darrasse
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Martial Briand
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Guillaume Lebreton
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Perrine Portier
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
- CIRM‐CFBP French Collection for Plant‐associated BacteriaIRHSUMR 1345INRA‐ACO‐UA42 rue Georges Morel49070Beaucouzé CedexFrance
| | - Marion Fischer‐Le Saux
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
- CIRM‐CFBP French Collection for Plant‐associated BacteriaIRHSUMR 1345INRA‐ACO‐UA42 rue Georges Morel49070Beaucouzé CedexFrance
| | - Karine Durand
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Marie‐Agnès Jacques
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
| | - Etienne Belin
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS)Université d’AngersF‐49000AngersFrance
| | - Tristan Boureau
- IRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
- Platform PHENOTICIRHSINRA, Université d’AngersAgrocampus‐OuestSFR 4207 QuaSav49071BeaucouzéFrance
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6
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Vicente JG, Rothwell S, Holub EB, Studholme DJ. Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida. Int J Syst Evol Microbiol 2017; 67:3645-3654. [PMID: 28840805 DOI: 10.1099/ijsem.0.002189] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe two new species of the genus Xanthomonas, represented by yellow mucoid bacterial strains isolated from diseased leaves of watercress (Nasturtium officinale) produced in Florida, USA. One strain was pathogenic on watercress, but not in other species including a range of brassicas; other strains were not pathogenic in any of the tested plants. Data from Biolog carbon source utilization tests and nucleotide sequence data from 16S and gyrB loci suggested that both pathogenic and non-pathogenic strains were related to, yet distinct from, previously described Xanthomonas species. Multilocus sequence analysis and whole genome-wide comparisons of the average nucleotide identity (ANI) of genomes of two strains from watercress showed that these are distinct and share less than 95 % ANI with all other known species; the non-pathogenic strain WHRI 8848 is close to Xanthomonascassavae (ANI of 93.72 %) whilst the pathogenic strain WHRI 8853 is close to a large clade of species that includes Xanthomonasvesicatoria (ANI ≤90.25 %). Based on these results, we propose that both strains represent new Xanthomonas species named Xanthomonas floridensis sp. nov. (type strain WHRI 8848=ATCC TSD-60=ICMP 21312=LMG 29665=NCPPB 4601) and Xanthomonas nasturtii sp. nov. (type strain WHRI 8853=ATCC TSD-61=ICMP 21313=LMG 29666=NCPPB 4600), respectively. The presence of non-pathogenic Xanthomonas strains in watercress and their interaction with pathogenic strains needs to be further investigated. Although the importance of the new pathogenic species is yet to be determined, the bacterial disease that it causes constitutes a threat to watercress production and its distribution should be monitored.
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Affiliation(s)
- Joana G Vicente
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
| | - Steve Rothwell
- Vitacress Ltd, Lower Link Farm, St. Mary Bourne, Andover, Hampshire SP11 6DB, UK
| | - Eric B Holub
- School of Life Sciences, The University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
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7
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Jacques MA, Arlat M, Boulanger A, Boureau T, Carrère S, Cesbron S, Chen NWG, Cociancich S, Darrasse A, Denancé N, Fischer-Le Saux M, Gagnevin L, Koebnik R, Lauber E, Noël LD, Pieretti I, Portier P, Pruvost O, Rieux A, Robène I, Royer M, Szurek B, Verdier V, Vernière C. Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:163-87. [PMID: 27296145 DOI: 10.1146/annurev-phyto-080615-100147] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strains usually cause disease on only a few plant species and are highly adapted to their hosts, making them pertinent models to study host specificity. This review summarizes our current understanding of the molecular basis of host specificity in the Xanthomonas genus, with a particular focus on the ecology, physiology, and pathogenicity of the bacterium. Despite our limited understanding of the basis of host specificity, type III effectors, microbe-associated molecular patterns, lipopolysaccharides, transcriptional regulators, and chemotactic sensors emerge as key determinants for shaping host specificity.
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Affiliation(s)
- Marie-Agnès Jacques
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Matthieu Arlat
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, F-31062 Toulouse, France
| | - Alice Boulanger
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
- Université de Toulouse, Université Paul Sabatier, F-31062 Toulouse, France
| | - Tristan Boureau
- Université Angers, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France;
| | - Sébastien Carrère
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
| | - Sophie Cesbron
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Nicolas W G Chen
- Agrocampus Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France;
| | - Stéphane Cociancich
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Armelle Darrasse
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Nicolas Denancé
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Marion Fischer-Le Saux
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Lionel Gagnevin
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Ralf Koebnik
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Emmanuelle Lauber
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
| | - Laurent D Noël
- INRA, UMR 441 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France; , , , ,
- CNRS, UMR 2594 Laboratoire des Interactions Plantes Micro-organismes (LIPM), F-31326 Castanet-Tolosan, France
| | - Isabelle Pieretti
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Perrine Portier
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences (IRHS), F-49071 Beaucouzé, France; , , , , ,
| | - Olivier Pruvost
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Adrien Rieux
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Isabelle Robène
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), F-97410 Saint-Pierre, La Réunion, France; , ,
| | - Monique Royer
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
| | - Boris Szurek
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Valérie Verdier
- IRD, CIRAD, University of Montpellier, Interactions Plantes Micro-organismes Environnement (IPME), F-34394 Montpellier, France; , , ,
| | - Christian Vernière
- CIRAD, UMR Biologie et Génétique des Interactions Plante-Parasite (BGPI), F-34398 Montpellier, France; , , ,
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8
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Jacobs JM, Pesce C, Lefeuvre P, Koebnik R. Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. FRONTIERS IN PLANT SCIENCE 2015; 6:431. [PMID: 26136759 DOI: 10.3389/fpls.2015.00431.ecollection2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/27/2015] [Indexed: 05/24/2023]
Abstract
Pathogenic bacteria in the genus Xanthomonas cause diseases on over 350 plant species, including cannabis (Cannabis sativa L.). Because of regulatory limitations, the biology of the Xanthomonas-cannabis pathosystem remains largely unexplored. To gain insight into the evolution of Xanthomonas strains pathogenic to cannabis, we sequenced the genomes of two geographically distinct Xanthomonas strains, NCPPB 3753 and NCPPB 2877, which were previously isolated from symptomatic plant tissue in Japan and Romania. Comparative multilocus sequence analysis of housekeeping genes revealed that they belong to Group 2, which comprises most of the described species of Xanthomonas. Interestingly, both strains lack the Hrp Type III secretion system and do not contain any of the known Type III effectors. Yet their genomes notably encode two key Hrp pathogenicity regulators HrpG and HrpX, and hrpG and hrpX are in the same genetic organization as in the other Group 2 xanthomonads. Promoter prediction of HrpX-regulated genes suggests the induction of an aminopeptidase, a lipase and two polygalacturonases upon plant colonization, similar to other plant-pathogenic xanthomonads. Genome analysis of the distantly related Xanthomonas maliensis strain 97M, which was isolated from a rice leaf in Mali, similarly demonstrated the presence of HrpG, HrpX, and a HrpX-regulated polygalacturonase, and the absence of the Hrp Type III secretion system and known Type III effectors. Given the observation that some Xanthomonas strains across distinct taxa do not contain hrpG and hrpX, we speculate a stepwise evolution of pathogenicity, which involves (i) acquisition of key regulatory genes and cell wall-degrading enzymes, followed by (ii) acquisition of the Hrp Type III secretion system, which is ultimately accompanied by (iii) successive acquisition of Type III effectors.
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Affiliation(s)
- Jonathan M Jacobs
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France
| | - Céline Pesce
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France ; Department of Applied Microbiology, Earth and Life Institute, Université Catholique de Louvain Louvain-la-Neuve, Belgium
| | - Pierre Lefeuvre
- Pôle de Protection des Plantes, Cirad, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical Saint-Pierre, Ile de la Réunion, France
| | - Ralf Koebnik
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France
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Jacobs JM, Pesce C, Lefeuvre P, Koebnik R. Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. FRONTIERS IN PLANT SCIENCE 2015; 6:431. [PMID: 26136759 PMCID: PMC4468381 DOI: 10.3389/fpls.2015.00431] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/27/2015] [Indexed: 05/05/2023]
Abstract
Pathogenic bacteria in the genus Xanthomonas cause diseases on over 350 plant species, including cannabis (Cannabis sativa L.). Because of regulatory limitations, the biology of the Xanthomonas-cannabis pathosystem remains largely unexplored. To gain insight into the evolution of Xanthomonas strains pathogenic to cannabis, we sequenced the genomes of two geographically distinct Xanthomonas strains, NCPPB 3753 and NCPPB 2877, which were previously isolated from symptomatic plant tissue in Japan and Romania. Comparative multilocus sequence analysis of housekeeping genes revealed that they belong to Group 2, which comprises most of the described species of Xanthomonas. Interestingly, both strains lack the Hrp Type III secretion system and do not contain any of the known Type III effectors. Yet their genomes notably encode two key Hrp pathogenicity regulators HrpG and HrpX, and hrpG and hrpX are in the same genetic organization as in the other Group 2 xanthomonads. Promoter prediction of HrpX-regulated genes suggests the induction of an aminopeptidase, a lipase and two polygalacturonases upon plant colonization, similar to other plant-pathogenic xanthomonads. Genome analysis of the distantly related Xanthomonas maliensis strain 97M, which was isolated from a rice leaf in Mali, similarly demonstrated the presence of HrpG, HrpX, and a HrpX-regulated polygalacturonase, and the absence of the Hrp Type III secretion system and known Type III effectors. Given the observation that some Xanthomonas strains across distinct taxa do not contain hrpG and hrpX, we speculate a stepwise evolution of pathogenicity, which involves (i) acquisition of key regulatory genes and cell wall-degrading enzymes, followed by (ii) acquisition of the Hrp Type III secretion system, which is ultimately accompanied by (iii) successive acquisition of Type III effectors.
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Affiliation(s)
- Jonathan M. Jacobs
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
| | - Céline Pesce
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
- Department of Applied Microbiology, Earth and Life Institute, Université Catholique de LouvainLouvain-la-Neuve, Belgium
| | - Pierre Lefeuvre
- Pôle de Protection des Plantes, Cirad, UMR Peuplements Végétaux et Bioagresseurs en Milieu TropicalSaint-Pierre, Ile de la Réunion, France
| | - Ralf Koebnik
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
- *Correspondence: Ralf Koebnik, Institut de Recherche pour le Développement, UMR Interactions – Plantes – Microorganismes – Environnement, Génomique et Transcriptomique des Interactions Plantes-Procaryotes, 921 avenue Agropolis, 34394 Montpellier, France
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