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Chuang SC, Dobhal S, Alvarez AM, Arif M. Three new species, Xanthomonas hawaiiensis sp. nov., Stenotrophomonas aracearum sp. nov., and Stenotrophomonas oahuensis sp. nov., isolated from the Araceae family. Front Microbiol 2024; 15:1356025. [PMID: 38655077 PMCID: PMC11035887 DOI: 10.3389/fmicb.2024.1356025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Xanthomonas and Stenotrophomonas are closely related genera in the family Lysobacteraceae. In our previous study of aroid-associated bacterial strains, most strains isolated from anthurium and other aroids were reclassified as X. phaseoli and other Xanthomonas species. However, two strains isolated from Spathiphyllum and Colocasia were phylogenetically distant from other strains in the Xanthomonas clade and two strains isolated from Anthurium clustered within the Stenotrophomonas clade. Phylogenetic trees based on 16S rRNA and nine housekeeping genes placed the former strains with the type strain of X. sacchari from sugarcane and the latter strains with the type strain of S. bentonitica from bentonite. In pairwise comparisons with type strains, the overall genomic relatedness indices required delineation of new species; digital DNA-DNA hybridization and average nucleotide identity values were lower than 70 and 95%, respectively. Hence, three new species are proposed: S. aracearum sp. nov. and S. oahuensis sp. nov. for two strains from anthurium and X. hawaiiensis sp. nov. for the strains from spathiphyllum and colocasia, respectively. The genome size of X. hawaiiensis sp. nov. is ~4.88 Mbp and higher than S. aracearum sp. nov. (4.33 Mbp) and S. oahuensis sp. nov. (4.68 Mbp). Gene content analysis revealed 425 and 576 core genes present in 40 xanthomonads and 25 stenotrophomonads, respectively. The average number of unique genes in Stenotrophomonas spp. was higher than in Xanthomonas spp., implying higher genetic diversity in Stenotrophomonas.
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Affiliation(s)
| | | | | | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaiʻi at Mānoa, Honolulu, HI, United States
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2
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Pena MM, Bhandari R, Bowers RM, Weis K, Newberry E, Wagner N, Pupko T, Jones JB, Woyke T, Vinatzer BA, Jacques MA, Potnis N. Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas. Genome Biol Evol 2024; 16:evae074. [PMID: 38648506 PMCID: PMC11032200 DOI: 10.1093/gbe/evae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2024] [Indexed: 04/25/2024] Open
Abstract
The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.
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Affiliation(s)
- Michelle M Pena
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
- Present address: Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kylie Weis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric Newberry
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Naama Wagner
- The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel Aviv, Israel
| | - Tal Pupko
- The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel Aviv, Israel
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Life and Environmental Sciences, University of California Merced, Merced, CA, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Marie-Agnès Jacques
- Institut Agro, INRAE, IRHS, SFR QUASAV, University of Angers, Angers F-49000, France
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
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Peduzzi C, Sagia A, Burokienė D, Nagy IK, Fischer-Le Saux M, Portier P, Dereeper A, Cunnac S, Roman-Reyna V, Jacobs JM, Bragard C, Koebnik R. Complete Genome Sequencing of Three Clade-1 Xanthomonads Reveals Genetic Determinants for a Lateral Flagellin and the Biosynthesis of Coronatine-Like Molecules in Xanthomonas. PHYTOPATHOLOGY 2023; 113:1185-1191. [PMID: 36611232 DOI: 10.1094/phyto-10-22-0373-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Evolutionarily, early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, as well as Xanthomonas translucens, which infects small-grain cereals and diverse grasses but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches have indicated that this clade likely contains more, yet-undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean, and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. Furthermore, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
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Affiliation(s)
- Chloé Peduzzi
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Angeliki Sagia
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Daiva Burokienė
- Nature Research Centre, Institute of Botany, Laboratory of Plant Pathology, Vilnius, Lithuania
| | | | | | - Perrine Portier
- Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Alexis Dereeper
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Sébastien Cunnac
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Claude Bragard
- Earth & Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, Cirad, INRAE, Institut Agro, IRD, Montpellier, France
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Miranda RP, Turrini PCG, Bonadio DT, Zerillo MM, Berselli AP, Creste S, Van Sluys MA. Genome Organization of Four Brazilian Xanthomonas albilineans Strains Does Not Correlate with Aggressiveness. Microbiol Spectr 2023; 11:e0280222. [PMID: 37052486 PMCID: PMC10269729 DOI: 10.1128/spectrum.02802-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 03/03/2023] [Indexed: 04/14/2023] Open
Abstract
An integrative approach combining genomics, transcriptomics, and cell biology is presented to address leaf scald disease, a major problem for the sugarcane industry. To gain insight into the biology of the causal agent, the complete genome sequences of four Brazilian Xanthomonas albilineans strains with differing virulence capabilities are presented and compared to the GPEPC73 reference strain and FJ1. Based on the aggressiveness index, different strains were compared: Xa04 and Xa11 are highly aggressive, Xa26 is intermediate, and Xa21 is the least, while, based on genome structure, Xa04 shares most of its genomic features with Xa26, and Xa11 share most of its genomic features with Xa21. In addition to presenting more clustered regularly interspaced short palindromic repeats (CRISPR) clusters, four more novel prophage insertions are present than the previously sequenced GPEPC73 and FJ1 strains. Incorporating the aggressiveness index and in vitro cell biology into these genome features indicates that disease establishment is not a result of a single determinant factor, as in most other Xanthomonas species. The Brazilian strains lack the previously described plasmids but present more prophage regions. In pairs, the most virulent and the least virulent share unique prophages. In vitro transcriptomics shed light on the 54 most highly expressed genes among the 4 strains compared to ribosomal proteins (RPs), of these, 3 outer membrane proteins. Finally, comparative albicidin inhibition rings and in vitro growth curves of the four strains also do not correlate with pathogenicity. In conclusion, the results disclose that leaf scald disease is not associated with a single shared characteristic between the most or the least pathogenic strains. IMPORTANCE An integrative approach is presented which combines genomics, transcriptomics, and cell biology to address leaf scald disease. The results presented here disclose that the disease is not associated with a single shared characteristic between the most pathogenic strains or a unique genomic pattern. Sequence data from four Brazilian strains are presented that differ in pathogenicity index: Xa04 and Xa11 are highly virulent, Xa26 is intermediate, and Xa21 is the least pathogenic strain, while, based on genome structure, Xa04 shares with Xa26, and Xa11 shares with X21 most of the genome features. Other than presenting more CRISPR clusters and prophages than the previously sequenced strains, the integration of aggressiveness and cell biology points out that disease establishment is not a result of a single determinant factor as in other xanthomonads.
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Affiliation(s)
- Raquel P. Miranda
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Paula C. G. Turrini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Dora T. Bonadio
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Marcelo M. Zerillo
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Arthur P. Berselli
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
| | - Silvana Creste
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Campinas, São Paulo, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Butanta, São Paulo, Brazil
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5
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Cardoso JLS, Souza AA, Vieira MLC. Molecular basis for host responses to Xanthomonas infection. PLANTA 2022; 256:84. [PMID: 36114308 DOI: 10.1007/s00425-022-03994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
This review highlights the most relevant and recent updated information available on the defense responses of selected hosts against Xanthomonas spp. Xanthomonas is one of the most important genera of Gram-negative phytopathogenic bacteria, severely affecting the productivity of economically important crops worldwide, colonizing either the vascular system or the mesophyll tissue of the host. Due to its rapid propagation, Xanthomonas poses an enormous challenge to farmers, because it is usually controlled using huge quantities of copper-based chemicals, adversely impacting the environment. Thus, developing new ways of preventing colonization by these bacteria has become essential. Advances in genomic and transcriptomic technologies have significantly elucidated at molecular level interactions between various crops and Xanthomonas species. Understanding how these hosts respond to the infection is crucial if we are to exploit potential approaches for improving crop breeding and cutting productivity losses. This review focuses on our current knowledge of the defense response mechanisms in agricultural crops after Xanthomonas infection. We describe the molecular basis of host-bacterium interactions over a broad spectrum with the aim of improving our fundamental understanding of which genes are involved and how they work in this interaction, providing information that can help to speed up plant breeding programs, namely using gene editing approaches.
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Affiliation(s)
- Jéssica L S Cardoso
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Alessandra A Souza
- Citrus Research Center "Sylvio Moreira", Agronomic Institute (IAC), Cordeirópolis, SP, 13490-000, Brazil
| | - Maria Lucia C Vieira
- Genetics Department, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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6
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Kanukollu S, Remus R, Rücker AM, Buchen-Tschiskale C, Hoffmann M, Kolb S. Methanol utilizers of the rhizosphere and phyllosphere of a common grass and forb host species. ENVIRONMENTAL MICROBIOME 2022; 17:35. [PMID: 35794633 PMCID: PMC9258066 DOI: 10.1186/s40793-022-00428-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ozone depletion. The phyllosphere is a favoured habitat of plant-colonizing methanol-utilizing bacteria. These bacteria also occur in the rhizosphere, but their relevance for methanol consumption and ecosystem fluxes is unclear. Methanol utilizers of the plant-associated microbiota are key for the mitigation of methanol emission through consumption. However, information about grassland plant microbiota members, their biodiversity and metabolic traits, and thus key actors in the global methanol budget is largely lacking. RESULTS We investigated the methanol utilization and consumption potentials of two common plant species (Festuca arundinacea and Taraxacum officinale) in a temperate grassland. The selected grassland exhibited methanol formation. The detection of 13C derived from 13C-methanol in 16S rRNA of the plant microbiota by stable isotope probing (SIP) revealed distinct methanol utilizer communities in the phyllosphere, roots and rhizosphere but not between plant host species. The phyllosphere was colonized by members of Gamma- and Betaproteobacteria. In the rhizosphere, 13C-labelled Bacteria were affiliated with Deltaproteobacteria, Gemmatimonadates, and Verrucomicrobiae. Less-abundant 13C-labelled Bacteria were affiliated with well-known methylotrophs of Alpha-, Gamma-, and Betaproteobacteria. Additional metagenome analyses of both plants were consistent with the SIP results and revealed Bacteria with methanol dehydrogenases (e.g., MxaF1 and XoxF1-5) of known but also unusual genera (i.e., Methylomirabilis, Methylooceanibacter, Gemmatimonas, Verminephrobacter). 14C-methanol tracing of alive plant material revealed divergent potential methanol consumption rates in both plant species but similarly high rates in the rhizosphere and phyllosphere. CONCLUSIONS Our study revealed the rhizosphere as an overlooked hotspot for methanol consumption in temperate grasslands. We further identified unusual new but potentially relevant methanol utilizers besides well-known methylotrophs in the phyllosphere and rhizosphere. We did not observe a plant host-specific methanol utilizer community. Our results suggest that our approach using quantitative SIP and metagenomics may be useful in future field studies to link gross methanol consumption rates with the rhizosphere and phyllosphere microbiome.
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Affiliation(s)
- Saranya Kanukollu
- Microbial Biogeochemistry, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Rainer Remus
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | | | - Caroline Buchen-Tschiskale
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Present Address: Johann Heinrich von Thünen-Institut, Institute of Climate-Smart Agriculture, Braunschweig, Germany
| | - Mathias Hoffmann
- Isotope Biogeochemistry and Gas Fluxes, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, RA1 Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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7
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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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8
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Bansal K, Kumar S, Kaur A, Singh A, Patil PB. Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas. Genomics 2021; 113:3989-4003. [PMID: 34610367 DOI: 10.1016/j.ygeno.2021.09.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Genus Xanthomonas is a group of phytopathogens that is phylogenetically related to Xylella, Stenotrophomonas, and Pseudoxanthomonas, having diverse lifestyles. Xylella is a lethal plant pathogen with a highly reduced genome, atypical GC content and is taxonomically related to these three genera. Deep phylo-taxono genomics reveals that Xylella is a variant Xanthomonas lineage that is sandwiched between Xanthomonas clades. Comparative studies suggest the role of unique pigment and exopolysaccharide gene clusters in the emergence of Xanthomonas and Xylella clades. Pan-genome analysis identified a set of unique genes associated with sub-lineages representing plant-associated Xanthomonas clade and nosocomial origin Stenotrophomonas clade. Overall, our study reveals the importance of reconciling classical phenotypic data and genomic findings in reconstituting the taxonomic status of these four genera. SIGNIFICANCE STATEMENT: Xylella fastidiosa is a devastating pathogen of perennial dicots such as grapes, citrus, coffee, and olives. An insect vector transmits the pathogen to its specific host wherein the infection leads to complete wilting of the plants. The genome of X. fastidiosa is significantly reduced both in terms of size (2 Mb) and GC content (50%) when compared with its relatives such as Xanthomonas, Stenotrophomonas, and Pseudoxanthomonas that have higher GC content (65%) and larger genomes (5 Mb). In this study, using systematic and in-depth genome-based taxonomic and phylogenetic criteria and comparative studies, we assert the need to unify Xanthomonas with its relatives (Xylella, Stenotrophomonas and Pseudoxanthomonas). Interestingly, Xylella revealed itself as a minor variant lineage embedded within two major Xanthomonas lineages comprising member species of different hosts.
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Affiliation(s)
- Kanika Bansal
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Amandeep Kaur
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Anu Singh
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.
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9
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Secrete or perish: The role of secretion systems in Xanthomonas biology. Comput Struct Biotechnol J 2020; 19:279-302. [PMID: 33425257 PMCID: PMC7777525 DOI: 10.1016/j.csbj.2020.12.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria of the Xanthomonas genus are mainly phytopathogens of a large variety of crops of economic importance worldwide. Xanthomonas spp. rely on an arsenal of protein effectors, toxins and adhesins to adapt to the environment, compete with other microorganisms and colonize plant hosts, often causing disease. These protein effectors are mainly delivered to their targets by the action of bacterial secretion systems, dedicated multiprotein complexes that translocate proteins to the extracellular environment or directly into eukaryotic and prokaryotic cells. Type I to type VI secretion systems have been identified in Xanthomonas genomes. Recent studies have unravelled the diverse roles played by the distinct types of secretion systems in adaptation and virulence in xanthomonads, unveiling new aspects of their biology. In addition, genome sequence information from a wide range of Xanthomonas species and pathovars have become available recently, uncovering a heterogeneous distribution of the distinct families of secretion systems within the genus. In this review, we describe the architecture and mode of action of bacterial type I to type VI secretion systems and the distribution and functions associated with these important nanoweapons within the Xanthomonas genus.
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10
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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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11
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He YW, Cao XQ, Poplawsky AR. Chemical Structure, Biological Roles, Biosynthesis and Regulation of the Yellow Xanthomonadin Pigments in the Phytopathogenic Genus Xanthomonas. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:705-714. [PMID: 32027580 DOI: 10.1094/mpmi-11-19-0326-cr] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Xanthomonadins are membrane-bound yellow pigments that are typically produced by phytopathogenic bacterial Xanthomonas spp., Xylella fastidiosa, and Pseudoxanthomonas spp. They are also produced by a diversity of environmental bacterial species. Considerable research has revealed that they are a unique group of halogenated, aryl-polyene, water-insoluble pigments. Xanthomonadins have been shown to play important roles in epiphytic survival and host-pathogen interactions in the phytopathogen Xanthomonas campestris pv. campestris, which is the causal agent of black rot in crucifers. Here, we review recent advances in the understanding of xanthomonadin chemical structures, physiological roles, biosynthetic pathways, regulatory mechanisms, and crosstalk with other signaling pathways. The aim of the present review is to provide clues for further in-depth research on xanthomonadins from Xanthomonas and other related bacterial species.
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Affiliation(s)
- Ya-Wen He
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Qiang Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Alan R Poplawsky
- Department of Entomology, Plant Pathology and Nematology, University of Idaho, Moscow, ID 83844, U.S.A
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12
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Shah SMA, Haq F, Ma W, Xu X, Wang S, Xu Z, Zou L, Zhu B, Chen G. Tal1 NXtc01 in Xanthomonas translucens pv. cerealis Contributes to Virulence in Bacterial Leaf Streak of Wheat. Front Microbiol 2019; 10:2040. [PMID: 31551976 PMCID: PMC6737349 DOI: 10.3389/fmicb.2019.02040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Xanthomonas translucens pv. cerealis (Xtc) causes bacterial leaf streak (BLS) of important cereal crops, including wheat (Triticum aestivum) and barley (Hordeum vulgare). Transcription activator-like effectors (TALEs) play vital roles in many plant diseases caused by Xanthomonas spp., however, TALEs have not been previously characterized in Xtc. In this study, the whole genome of NXtc01, a virulent strain of Xtc from Xinjiang, China, was sequenced and compared with genomes of other Xanthomonas spp. Xtc NXtc01 consists of a single 4,622,298 bp chromosome that encodes 4,004 genes. Alignment of the NXtc01 sequence with the draft genome of Xtc strain CFBP 2541 (United States) revealed a single giant inversion and differences in the location of two tal genes, which were designated tal1 and tal2. In NXtc01, both tal genes are located on the chromosome, whereas tal2 is plasmid-encoded in CFBP 2541. The repeat variable diresidues (RVDs) at the 12th and 13th sites within Tal2 repeat units were identical in both strains, whereas Tal1 showed differences in the third RVD. Xtc NXtc01 and CFBP 2541 encoded 35 and 33 non-TALE type III effectors (T3Es), respectively. tal1, tal2, and tal-free deletion mutants of Xtc NXtc01 were constructed and evaluated for virulence. The tal1 and tal-free deletion mutants were impaired with respect to symptom development and growth in wheat, suggesting that tal1 is a virulence factor in NXtc01. This was confirmed in gain-of-function experiments that showed the introduction of tal1, but not tal2, restored virulence to the tal-free mutant. Furthermore, we generated a hrcC deletion mutant of NXtc01; the hrcC mutant was non-pathogenic on wheat and unable to elicit a hypersensitive response in the non-host Nicotiana benthamiana. Our data provide a platform for exploring the roles of both TALEs and non-TALEs in promoting BLS on wheat.
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Affiliation(s)
- Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Fazal Haq
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Wenxiu Ma
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Xiameng Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Zhengyin Xu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Lifang Zou
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Bo Zhu
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
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13
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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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14
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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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15
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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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16
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Walitang DI, Kim K, Madhaiyan M, Kim YK, Kang Y, Sa T. Characterizing endophytic competence and plant growth promotion of bacterial endophytes inhabiting the seed endosphere of Rice. BMC Microbiol 2017; 17:209. [PMID: 29073903 PMCID: PMC5658939 DOI: 10.1186/s12866-017-1117-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/18/2017] [Indexed: 12/20/2022] Open
Abstract
Background Rice (Oryza sativa L. ssp. indica) seeds as plant microbiome present both an opportunity and a challenge to colonizing bacterial community living in close association with plants. Nevertheless, the roles and activities of bacterial endophytes remain largely unexplored and insights into plant-microbe interaction are compounded by its complexity. In this study, putative functions or physiological properties associated with bacterial endophytic nature were assessed. Also, endophytic roles in plant growth and germination that may allow them to be selectively chosen by plants were also studied. Results The cultivable seed endophytes were dominated by Proteobacteria particularly class Gammaproteobacteria. Highly identical type strains were isolated from the seed endosphere regardless of the rice host’s physiological tolerance to salinity. Among the type strains, Flavobacterium sp., Microbacterium sp. and Xanthomonas sp. were isolated from the salt-sensitive and salt-tolerant cultivars. PCA-Biplot ordination also showed that specific type strains isolated from different rice cultivars have distinguishing similar characteristics. Flavobacterium sp. strains are phosphate solubilizers and indole-3-acetic acid producers with high tolerance to salinity and osmotic stress. Pseudomonas strains are characterized as high siderophore producers while Microbacterium sp. and Xanthomonas sp. strains have very high pectinase and cellulase activity. Among the physiological traits of the seed endophytes, bacterial pectinase and cellulase activity are positively correlated as well as salt and osmotic tolerance. Overall characterization shows that majority of the isolates could survive in 4–8% salt concentration as well as in 0.6 M and 1.2 M sucrose solution. The activities of catalase, pectinase and cellulase were also observed in almost all of the isolates indicating the importance of these characteristics for survival and colonization into the seed endosphere. Seed bacterial endophytes also showed promising plant growth promoting activities including hormone modulation, nitrogen fixation, siderophore production and phosphate solubilization. Conclusion Though many of the isolates possess similar PGP and endophytic physiological traits, this study shows some prominent and distinguishing traits among bacterial groups indicating key determinants for their success as endophytes in the rice seed endosphere. Rice seeds are also inhabited by bacterial endophytes that promote growth during early seedling development. Electronic supplementary material The online version of this article (10.1186/s12866-017-1117-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Denver I Walitang
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Kiyoon Kim
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Munusamy Madhaiyan
- Temasek Life Sciences Laboratory, Biomaterials and Biocatalyst, National University of Singapore, Singapore, Singapore
| | - Young Kee Kim
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Yeongyeong Kang
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Tongmin Sa
- Department of Environmental and Biological Chemistry, College of Agriculture, Life and Environmental Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
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17
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Merda D, Briand M, Bosis E, Rousseau C, Portier P, Barret M, Jacques MA, Fischer-Le Saux M. Ancestral acquisitions, gene flow and multiple evolutionary trajectories of the type three secretion system and effectors in Xanthomonas plant pathogens. Mol Ecol 2017; 26:5939-5952. [PMID: 28869687 PMCID: PMC7168496 DOI: 10.1111/mec.14343] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 08/03/2017] [Accepted: 08/05/2017] [Indexed: 12/13/2022]
Abstract
Deciphering the evolutionary history and transmission patterns of virulence determinants is necessary to understand the emergence of novel pathogens. The main virulence determinant of most pathogenic proteobacteria is the type three secretion system (T3SS). The Xanthomonas genus includes bacteria responsible for numerous epidemics in agroecosystems worldwide and represents a major threat to plant health. The main virulence factor of Xanthomonas is the Hrp2 family T3SS; however, this system is not conserved in all strains and it has not been previously determined whether the distribution of T3SS in this bacterial genus has resulted from losses or independent acquisitions. Based on comparative genomics of 82 genome sequences representing the diversity of the genus, we have inferred three ancestral acquisitions of the Hrp2 cluster during Xanthomonas evolution followed by subsequent losses in some commensal strains and re‐acquisition in some species. While mutation was the main force driving polymorphism at the gene level, interspecies homologous recombination of large fragments expanding through several genes shaped Hrp2 cluster polymorphism. Horizontal gene transfer of the entire Hrp2 cluster also occurred. A reduced core effectome composed of xopF1, xopM, avrBs2 and xopR was identified that may allow commensal strains overcoming plant basal immunity. In contrast, stepwise accumulation of numerous type 3 effector genes was shown in successful pathogens responsible for epidemics. Our data suggest that capacity to intimately interact with plants through T3SS would be an ancestral trait of xanthomonads. Since its acquisition, T3SS has experienced a highly dynamic evolutionary history characterized by intense gene flux between species that may reflect its role in host adaptation.
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Affiliation(s)
- Déborah Merda
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Martial Briand
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College, Karmiel, Israel
| | - Céline Rousseau
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Perrine Portier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Matthieu Barret
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
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18
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Falahi Charkhabi N, Booher NJ, Peng Z, Wang L, Rahimian H, Shams-Bakhsh M, Liu Z, Liu S, White FF, Bogdanove AJ. Complete Genome Sequencing and Targeted Mutagenesis Reveal Virulence Contributions of Tal2 and Tal4b of Xanthomonas translucens pv. undulosa ICMP11055 in Bacterial Leaf Streak of Wheat. Front Microbiol 2017; 8:1488. [PMID: 28848509 PMCID: PMC5554336 DOI: 10.3389/fmicb.2017.01488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022] Open
Abstract
Bacterial leaf streak caused by Xanthomonas translucens pv. undulosa (Xtu) is an important disease of wheat (Triticum aestivum) and barley (Hordeum vulgare) worldwide. Transcription activator-like effectors (TALEs) play determinative roles in many of the plant diseases caused by the different species and pathovars of Xanthomonas, but their role in this disease has not been characterized. ICMP11055 is a highly virulent Xtu strain from Iran. The aim of this study was to better understand genetic diversity of Xtu and to assess the role of TALEs in bacterial leaf streak of wheat by comparing the genome of this strain to the recently completely sequenced genome of a U.S. Xtu strain, and to several other draft X. translucens genomes, and by carrying out mutational analyses of the TALE (tal) genes the Iranian strain might harbor. The ICMP11055 genome, including its repeat-rich tal genes, was completely sequenced using single molecule, real-time technology (Pacific Biosciences). It consists of a single circular chromosome of 4,561,583 bp, containing 3,953 genes. Whole genome alignment with the genome of the United States Xtu strain XT4699 showed two major re-arrangements, nine genomic regions unique to ICMP11055, and one region unique to XT4699. ICMP110055 harbors 26 non-TALE type III effector genes and seven tal genes, compared to 25 and eight for XT4699. The tal genes occur singly or in pairs across five scattered loci. Four are identical to tal genes in XT4699. In addition to common repeat-variable diresidues (RVDs), the tal genes of ICMP11055, like those of XT4699, encode several RVDs rarely observed in Xanthomonas, including KG, NF, Y∗, YD, and YK. Insertion and deletion mutagenesis of ICMP11055 tal genes followed by genetic complementation analysis in wheat cv. Chinese Spring revealed that Tal2 and Tal4b of ICMP11055 each contribute individually to the extent of disease caused by this strain. A largely conserved ortholog of tal2 is present in XT4699, but for tal4b, only a gene with partial, fragmented RVD sequence similarity can be found. Our results lay the foundation for identification of important host genes activated by Xtu TALEs as targets for the development of disease resistant varieties.
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Affiliation(s)
- Nargues Falahi Charkhabi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States.,Department of Plant Pathology, Tarbiat Modares UniversityTehran, Iran
| | - Nicholas J Booher
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Zhao Peng
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States.,Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
| | - Heshmat Rahimian
- Department of Plant Protection, Sari Agricultural Science and Natural Resources UniversitySari, Iran
| | | | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, FargoND, United States
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States
| | - Frank F White
- Department of Plant Pathology, Kansas State University, ManhattanKS, United States.,Department of Plant Pathology, University of Florida, GainesvilleFL, United States
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, IthacaNY, United States
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Pesce C, Jacobs JM, Berthelot E, Perret M, Vancheva T, Bragard C, Koebnik R. Comparative Genomics Identifies a Novel Conserved Protein, HpaT, in Proteobacterial Type III Secretion Systems that Do Not Possess the Putative Translocon Protein HrpF. Front Microbiol 2017; 8:1177. [PMID: 28694803 PMCID: PMC5483457 DOI: 10.3389/fmicb.2017.01177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 06/09/2017] [Indexed: 01/09/2023] Open
Abstract
Xanthomonas translucens is the causal agent of bacterial leaf streak, the most common bacterial disease of wheat and barley. To cause disease, most xanthomonads depend on a highly conserved type III secretion system, which translocates type III effectors into host plant cells. Mutagenesis of the conserved type III secretion gene hrcT confirmed that the X. translucens type III secretion system is required to cause disease on the host plant barley and to trigger a non-host hypersensitive response (HR) in pepper leaves. Type III effectors are delivered to the host cell by a surface appendage, the Hrp pilus, and a translocon protein complex that inserts into the plant cell plasma membrane. Homologs of the Xanthomonas HrpF protein, including PopF from Ralstonia solanacearum and NolX from rhizobia, are thought to act as a translocon protein. Comparative genomics revealed that X. translucens strains harbor a noncanonical hrp gene cluster, which rather shares features with type III secretion systems from Ralstonia solanacearum, Paraburkholderia andropogonis, Collimonas fungivorans, and Uliginosibacterium gangwonense than other Xanthomonas spp. Surprisingly, none of these bacteria, except R. solanacearum, encode a homolog of the HrpF translocon. Here, we aimed at identifying a candidate translocon from X. translucens. Notably, genomes from strains that lacked hrpF/popF/nolX instead encode another gene, called hpaT, adjacent to and co-regulated with the type III secretion system gene cluster. An insertional mutant in the X. translucens hpaT gene, which is the first gene of a two-gene operon, hpaT-hpaH, was non-pathogenic on barley and did not cause the HR or programmed cell death in non-host pepper similar to the hrcT mutant. The hpaT mutant phenotypes were partially complemented by either hpaT or the downstream gene, hpaH, which has been described as a facilitator of translocation in Xanthomonas oryzae. Interestingly, the hpaT mutant was also complemented by the hrpF gene from Xanthomonas euvesicatoria. These findings reveal that both HpaT and HpaH contribute to the injection of type III effectors into plant cells.
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Affiliation(s)
- Céline Pesce
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Jonathan M. Jacobs
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Edwige Berthelot
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
| | - Marion Perret
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
| | - Taca Vancheva
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Claude Bragard
- Applied Microbiology Phytopathology, Earth and Life Institute, Université catholique de LouvainLouvain-la-Neuve, Belgium
| | - Ralf Koebnik
- UMR 186 IRD-Cirad-Université Montpellier IPMEMontpellier, France
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20
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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: 118] [Impact Index Per Article: 14.8] [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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Harrison J, Grant MR, Studholme DJ. Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants. GENOME ANNOUNCEMENTS 2016; 4:e01705-15. [PMID: 26868395 PMCID: PMC4751319 DOI: 10.1128/genomea.01705-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 12/21/2015] [Indexed: 12/02/2022]
Abstract
We report here the annotated draft genome sequences of strains Xanthomonas arboricola pv. celebensis NCPPB 1832 and NCPPB 1630 (NCPPB, National Collection of Plant Pathogenic Bacteria), both isolated from Musa species in New Zealand. This will allow the comparison of genomes between phylogenetically distant xanthomonads that have independently converged with the ability to colonize banana plants.
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Affiliation(s)
- James Harrison
- School of Biosciences, University of Exeter, Devon, United Kingdom
| | - Murray R Grant
- School of Biosciences, University of Exeter, Devon, United Kingdom
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Adriko J, Aritua V, Mortensen CN, Tushemereirwe WK, Mulondo AL, Kubiriba J, Lund OS. Biochemical and molecular tools reveal two diverse Xanthomonas groups in bananas. Microbiol Res 2015; 183:109-16. [PMID: 26805624 DOI: 10.1016/j.micres.2015.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/23/2015] [Accepted: 12/06/2015] [Indexed: 11/27/2022]
Abstract
Xanthomonas campestris pv. musacearum (Xcm) causing the banana Xanthomonas wilt (BXW) disease has been the main xanthomonad associated with bananas in East and Central Africa based on phenotypic and biochemical characteristics. However, biochemical methods cannot effectively distinguish between pathogenic and non-pathogenic xanthomonads. In this study, gram-negative and yellow-pigmented mucoid bacteria were isolated from BXW symptomatic and symptomless bananas collected from different parts of Uganda. Biolog, Xcm-specific (GspDm), Xanthomonas vasicola species-specific (NZ085) and Xanthomonas genus-specific (X1623) primers in PCR, and sequencing of ITS region were used to identify and characterize the isolates. Biolog tests revealed several isolates as xanthomonads. The GspDm and NZ085 primers accurately identified three isolates from diseased bananas as Xcm and these were pathogenic when re-inoculated into bananas. DNA from more isolates than those amplified by GspDm and NZ085 primers were amplified by the X1623 primers implying they are xanthomonads, these were however non-pathogenic on bananas. In the 16-23 ITS sequence based phylogeny, the pathogenic bacteria clustered together with the Xcm reference strain, while the non-pathogenic xanthomonads isolated from both BXW symptomatic and symptomless bananas clustered with group I xanthomonads. The findings reveal dynamic Xanthomonas populations in bananas, which can easily be misrepresented by only using phenotyping and biochemical tests. A combination of tools provides the most accurate identity and characterization of these plant associated bacteria. The interactions between the pathogenic and non-pathogenic xanthomonads in bananas may pave way to understanding effect of microbial interactions on BXW disease development and offer clues to biocontrol of Xcm.
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Affiliation(s)
- J Adriko
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Hoejbakkegaard Allé 3, 2630 Taastrup, Denmark; National Agricultural Research Laboratories, P. O. Box 7065, Kampala, Uganda.
| | - V Aritua
- International Center for Tropical Agriculture (CIAT), P. O. Box 6247, Kampala, Uganda
| | - C N Mortensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Hoejbakkegaard Allé 3, 2630 Taastrup, Denmark
| | - W K Tushemereirwe
- National Agricultural Research Laboratories, P. O. Box 7065, Kampala, Uganda
| | - A L Mulondo
- National Agricultural Research Laboratories, P. O. Box 7065, Kampala, Uganda
| | - J Kubiriba
- National Agricultural Research Laboratories, P. O. Box 7065, Kampala, Uganda
| | - O S Lund
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Hoejbakkegaard Allé 3, 2630 Taastrup, Denmark
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Pieretti I, Cociancich S, Bolot S, Carrère S, Morisset A, Rott P, Royer M. Full Genome Sequence Analysis of Two Isolates Reveals a Novel Xanthomonas Species Close to the Sugarcane Pathogen Xanthomonas albilineans. Genes (Basel) 2015; 6:714-33. [PMID: 26213974 PMCID: PMC4584326 DOI: 10.3390/genes6030714] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/03/2015] [Accepted: 07/14/2015] [Indexed: 12/28/2022] Open
Abstract
Xanthomonas albilineans is the bacterium responsible for leaf scald, a lethal disease of sugarcane. Within the Xanthomonas genus, X. albilineans exhibits distinctive genomic characteristics including the presence of significant genome erosion, a non-ribosomal peptide synthesis (NRPS) locus involved in albicidin biosynthesis, and a type 3 secretion system (T3SS) of the Salmonella pathogenicity island-1 (SPI-1) family. We sequenced two X. albilineans-like strains isolated from unusual environments, i.e., from dew droplets on sugarcane leaves and from the wild grass Paspalum dilatatum, and compared these genomes sequences with those of two strains of X. albilineans and three of Xanthomonas sacchari. Average nucleotide identity (ANI) and multi-locus sequence analysis (MLSA) showed that both X. albilineans-like strains belong to a new species close to X. albilineans that we have named "Xanthomonas pseudalbilineans". X. albilineans and "X. pseudalbilineans" share many genomic features including (i) the lack of genes encoding a hypersensitive response and pathogenicity type 3 secretion system (Hrp-T3SS), and (ii) genome erosion that probably occurred in a common progenitor of both species. Our comparative analyses also revealed specific genomic features that may help X. albilineans interact with sugarcane, e.g., a PglA endoglucanase, three TonB-dependent transporters and a glycogen metabolism gene cluster. Other specific genomic features found in the "X. pseudalbilineans" genome may contribute to its fitness and specific ecological niche.
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Affiliation(s)
- Isabelle Pieretti
- CIRAD UMR BGPI, TA A-54/K, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France.
| | - Stéphane Cociancich
- CIRAD UMR BGPI, TA A-54/K, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France.
| | - Stéphanie Bolot
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, 24 Chemin de Borde Rouge-Auzeville CS52627, F-31326 Castanet Tolosan Cedex, France.
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, 24 Chemin de Borde Rouge-Auzeville CS52627, F-31326 Castanet Tolosan Cedex, France.
| | - Sébastien Carrère
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, 24 Chemin de Borde Rouge-Auzeville CS52627, F-31326 Castanet Tolosan Cedex, France.
- CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, 24 Chemin de Borde Rouge-Auzeville CS52627, F-31326 Castanet Tolosan Cedex, France.
| | - Alexandre Morisset
- CIRAD UMR BGPI, TA A-54/K, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France.
| | - Philippe Rott
- CIRAD UMR BGPI, TA A-54/K, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France.
| | - Monique Royer
- CIRAD UMR BGPI, TA A-54/K, Campus International de Baillarguet, F-34398 Montpellier Cedex 5, France.
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24
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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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25
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Hodgetts J, Karamura G, Johnson G, Hall J, Perkins K, Beed F, Nakato V, Grant M, Studholme DJ, Boonham N, Smith J. Development of a lateral flow device for in-field detection and evaluation of PCR-based diagnostic methods for Xanthomonas campestris pv. musacearum, the causal agent of banana xanthomonas wilt. PLANT PATHOLOGY 2015; 64:559-567. [PMID: 32313307 PMCID: PMC7159137 DOI: 10.1111/ppa.12289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Xanthomonas campestris pv. musacearum (Xcm) is the causal agent of banana xanthomonas wilt, a major threat to banana production in eastern and central Africa. The pathogen is present in very high levels within infected plants and can be transmitted by a broad range of mechanisms; therefore early specific detection is vital for effective disease management. In this study, a polyclonal antibody (pAb) was developed and deployed in a lateral flow device (LFD) format to allow rapid in-field detection of Xcm. Published Xcm PCR assays were also independently assessed: only two assays gave specific amplification of Xcm, whilst others cross-reacted with non-target Xanthomonas species. Pure cultures of Xcm were used to immunize a rabbit, the IgG antibodies purified from the serum and the resulting polyclonal antibodies tested using ELISA and LFD. Testing against a wide range of bacterial species showed the pAb detected all strains of Xcm, representing isolates from seven countries and the known genetic diversity of Xcm. The pAb also detected the closely related Xanthomonas axonopodis pv. vasculorum (Xav), primarily a sugarcane pathogen. Detection was successful in both naturally and experimentally infected banana plants, and the LFD limit of detection was 105 cells mL-1. Whilst the pAb is not fully specific for Xcm, Xav has never been found in banana. Therefore the LFD can be used as a first-line screening tool to detect Xcm in the field. Testing by LFD requires no equipment, can be performed by non-scientists and is cost-effective. Therefore this LFD provides a vital tool to aid in the management and control of Xcm.
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Affiliation(s)
- J Hodgetts
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - G Karamura
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter Devon EX4 4QD UK
- National Agricultural Research Laboratories PO Box 7064 Kampala Uganda
| | - G Johnson
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - J Hall
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - K Perkins
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - F Beed
- International Institute of Tropical Agriculture - Tanzania PO Box 34441 Dar es Salaam Tanzania
| | - V Nakato
- International Institute of Tropical Agriculture - Uganda PO Box 7878 Kampala Uganda
| | - M Grant
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter Devon EX4 4QD UK
| | - D J Studholme
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter Devon EX4 4QD UK
| | - N Boonham
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - J Smith
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
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26
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Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed. J Biotechnol 2015; 206:77-8. [PMID: 25931193 DOI: 10.1016/j.jbiotec.2015.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 04/20/2015] [Indexed: 11/24/2022]
Abstract
Xanthomonas sacchari, was first identified as a pathogenic bacterium isolated from diseased sugarcane in Guadeloupe. In this study, R1 was first isolated from rice seed samples from Philippines in 2002. The antagonistic ability against several rice pathogens raises our attention. The genomic feature of this strain was described in this paper. The total genome size of X. sacchari R1 is 5,000,479 bp with 4315 coding sequences (CDS), 59 tRNAs, 2rRNAs and one plasmid.
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27
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Pieretti I, Pesic A, Petras D, Royer M, Süssmuth RD, Cociancich S. What makes Xanthomonas albilineans unique amongst xanthomonads? FRONTIERS IN PLANT SCIENCE 2015; 6:289. [PMID: 25964795 PMCID: PMC4408752 DOI: 10.3389/fpls.2015.00289] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/09/2015] [Indexed: 06/04/2023]
Abstract
Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. Compared to other species of Xanthomonas, X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy. Its genome, which has experienced significant erosion, has unique genomic features. It lacks two loci required for pathogenicity in other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis and the Hrp-T3SS (hypersensitive response and pathogenicity-type three secretion system) gene clusters. Instead, X. albilineans harbors in its genome an SPI-1 (Salmonella pathogenicity island-1) T3SS gene cluster usually found in animal pathogens. X. albilineans produces a potent DNA gyrase inhibitor called albicidin, which blocks chloroplast differentiation, resulting in the characteristic white foliar stripe symptoms. The antibacterial activity of albicidin also confers on X. albilineans a competitive advantage against rival bacteria during sugarcane colonization. Recent chemical studies have uncovered the unique structure of albicidin and allowed us to partially elucidate its fascinating biosynthesis apparatus, which involves an enigmatic hybrid PKS/NRPS (polyketide synthase/non-ribosomal peptide synthetase) machinery.
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Affiliation(s)
| | - Alexander Pesic
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Daniel Petras
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
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28
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Pieretti I, Bolot S, Carrère S, Barbe V, Cociancich S, Rott P, Royer M. Draft Genome Sequence of Xanthomonas sacchari Strain LMG 476. GENOME ANNOUNCEMENTS 2015; 3:e00146-15. [PMID: 25792064 PMCID: PMC4395056 DOI: 10.1128/genomea.00146-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 02/10/2015] [Indexed: 11/20/2022]
Abstract
We report the high-quality draft genome sequence of Xanthomonas sacchari strain LMG 476, isolated from sugarcane. The genome comparison of this strain with a previously sequenced X. sacchari strain isolated from a distinct environmental source should provide further insights into the adaptation of this species to different habitats and its evolution.
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Affiliation(s)
| | | | - Sébastien Carrère
- INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
| | - Valérie Barbe
- CEA, DSV/IG/Genoscope, Centre National de Séquençage, Evry, 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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Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE, Gupta RS. A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie van Leeuwenhoek 2014; 107:467-85. [DOI: 10.1007/s10482-014-0344-8] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/28/2014] [Indexed: 01/10/2023]
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Tripathi JN, Lorenzen J, Bahar O, Ronald P, Tripathi L. Transgenic expression of the rice Xa21 pattern-recognition receptor in banana (Musa sp.) confers resistance to Xanthomonas campestris pv. musacearum. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:663-73. [PMID: 24612254 PMCID: PMC4110157 DOI: 10.1111/pbi.12170] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/20/2013] [Accepted: 01/09/2014] [Indexed: 05/04/2023]
Abstract
Banana Xanthomonas wilt (BXW), caused by the bacterium Xanthomonas campestris pv. musacearum (Xcm), is the most devastating disease of banana in east and central Africa. The spread of BXW threatens the livelihood of millions of African farmers who depend on banana for food security and income. There are no commercial chemicals, biocontrol agents or resistant cultivars available to control BXW. Here, we take advantage of the robust resistance conferred by the rice pattern-recognition receptor (PRR), XA21, to the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo). We identified a set of genes required for activation of Xa21-mediated immunity (rax) that were conserved in both Xoo and Xcm. Based on the conservation, we hypothesized that intergeneric transfer of Xa21 would confer resistance to Xcm. We evaluated 25 transgenic lines of the banana cultivar 'Gonja manjaya' (AAB) using a rapid bioassay and 12 transgenic lines in the glasshouse for resistance against Xcm. About 50% of the transgenic lines showed complete resistance to Xcm in both assays. In contrast, all of the nontransgenic control plants showed severe symptoms that progressed to complete wilting. These results indicate that the constitutive expression of the rice Xa21 gene in banana results in enhanced resistance against Xcm. Furthermore, this work demonstrates the feasibility of PRR gene transfer between monocotyledonous species and provides a valuable new tool for controlling the BXW pandemic of banana, a staple food for 100 million people in east Africa.
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Affiliation(s)
| | - Jim Lorenzen
- International Institute of Tropical Agriculture (IITA), Arusha, Tanzania
| | - Ofir Bahar
- Department of Pathology and the Genome Center, University of California, Davis, USA
| | - Pamela Ronald
- Department of Pathology and the Genome Center, University of California, Davis, USA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
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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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Mensi I, Vernerey MS, Gargani D, Nicole M, Rott P. Breaking dogmas: the plant vascular pathogen Xanthomonas albilineans is able to invade non-vascular tissues despite its reduced genome. Open Biol 2014; 4:130116. [PMID: 24522883 PMCID: PMC3938051 DOI: 10.1098/rsob.130116] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 01/20/2014] [Indexed: 12/13/2022] Open
Abstract
Xanthomonas albilineans, the causal agent of sugarcane leaf scald, is missing the Hrp type III secretion system that is used by many Gram-negative bacteria to colonize their host. Until now, this pathogen was considered as strictly limited to the xylem of sugarcane. We used confocal laser scanning microscopy, immunocytochemistry and transmission electron microscopy (TEM) to investigate the localization of X. albilineans in diseased sugarcane. Sugarcane plants were inoculated with strains of the pathogen labelled with a green fluorescent protein. Confocal microscopy observations of symptomatic leaves confirmed the presence of the pathogen in the protoxylem and metaxylem; however, X. albilineans was also observed in phloem, parenchyma and bulliform cells of the infected leaves. Similarly, vascular bundles of infected sugarcane stalks were invaded by X. albilineans. Surprisingly, the pathogen was also observed in apparently intact storage cells of the stalk and in intercellular spaces between these cells. Most of these observations made by confocal microscopy were confirmed by TEM. The pathogen exits the xylem following cell wall and middle lamellae degradation, thus creating openings to reach parenchyma cells. This is the first description of a plant pathogenic vascular bacterium invading apparently intact non-vascular plant tissues and multiplying in parenchyma cells.
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Affiliation(s)
- Imène Mensi
- CIRAD, UMR BGPI, TA A-54/K, Montpellier Cedex 5 34398, France
| | | | - Daniel Gargani
- CIRAD, UMR BGPI, TA A-54/K, Montpellier Cedex 5 34398, France
| | - Michel Nicole
- IRD, UMR RPB, BP 64501, Montpellier Cedex 5 34394, France
| | - Philippe Rott
- CIRAD, UMR BGPI, TA A-54/K, Montpellier Cedex 5 34398, France
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Genomic analysis of Xanthomonas translucens pathogenic on wheat and barley reveals cross-kingdom gene transfer events and diverse protein delivery systems. PLoS One 2014; 9:e84995. [PMID: 24416331 PMCID: PMC3887016 DOI: 10.1371/journal.pone.0084995] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 11/25/2013] [Indexed: 01/09/2023] Open
Abstract
In comparison to dicot-infecting bacteria, only limited numbers of genome sequences are available for monocot-infecting and in particular cereal-infecting bacteria. Herein we report the characterisation and genome sequence of Xanthomonas translucens isolate DAR61454 pathogenic on wheat and barley. Based on phylogenetic analysis of the ATP synthase beta subunit (atpD) gene, DAR61454 is most closely related to other X. translucens strains and the sugarcane- and banana- infecting Xanthomonas strains, but shares a type III secretion system (T3SS) with X. translucens pv. graminis and more distantly related xanthomonads. Assays with an adenylate cyclase reporter protein demonstrate that DAR61454's T3SS is functional in delivering proteins to wheat cells. X. translucens DAR61454 also encodes two type VI secretion systems with one most closely related to those found in some strains of the rice infecting strain X. oryzae pv. oryzae but not other xanthomonads. Comparative analysis of 18 different Xanthomonas isolates revealed 84 proteins unique to cereal (i.e. rice) infecting isolates and the wheat/barley infecting DAR61454. Genes encoding 60 of these proteins are found in gene clusters in the X. translucens DAR61454 genome, suggesting cereal-specific pathogenicity islands. However, none of the cereal pathogen specific proteins were homologous to known Xanthomonas spp. effectors. Comparative analysis outside of the bacterial kingdom revealed a nucleoside triphosphate pyrophosphohydrolase encoding gene in DAR61454 also present in other bacteria as well as a number of pathogenic Fusarium species, suggesting that this gene may have been transmitted horizontally from bacteria to the Fusarium lineage of pathogenic fungi. This example further highlights the importance of horizontal gene acquisition from bacteria in the evolution of fungi.
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Royer M, Koebnik R, Marguerettaz M, Barbe V, Robin GP, Brin C, Carrere S, Gomez C, Hügelland M, Völler GH, Noëll J, Pieretti I, Rausch S, Verdier V, Poussier S, Rott P, Süssmuth RD, Cociancich S. Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides. BMC Genomics 2013; 14:658. [PMID: 24069909 PMCID: PMC3849588 DOI: 10.1186/1471-2164-14-658] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 09/22/2013] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Various bacteria can use non-ribosomal peptide synthesis (NRPS) to produce peptides or other small molecules. Conserved features within the NRPS machinery allow the type, and sometimes even the structure, of the synthesized polypeptide to be predicted. Thus, bacterial genome mining via in silico analyses of NRPS genes offers an attractive opportunity to uncover new bioactive non-ribosomally synthesized peptides. Xanthomonas is a large genus of Gram-negative bacteria that cause disease in hundreds of plant species. To date, the only known small molecule synthesized by NRPS in this genus is albicidin produced by Xanthomonas albilineans. This study aims to estimate the biosynthetic potential of Xanthomonas spp. by in silico analyses of NRPS genes with unknown function recently identified in the sequenced genomes of X. albilineans and related species of Xanthomonas. RESULTS We performed in silico analyses of NRPS genes present in all published genome sequences of Xanthomonas spp., as well as in unpublished draft genome sequences of Xanthomonas oryzae pv. oryzae strain BAI3 and Xanthomonas spp. strain XaS3. These two latter strains, together with X. albilineans strain GPE PC73 and X. oryzae pv. oryzae strains X8-1A and X11-5A, possess novel NRPS gene clusters and share related NRPS-associated genes such as those required for the biosynthesis of non-proteinogenic amino acids or the secretion of peptides. In silico prediction of peptide structures according to NRPS architecture suggests eight different peptides, each specific to its producing strain. Interestingly, these eight peptides cannot be assigned to any known gene cluster or related to known compounds from natural product databases. PCR screening of a collection of 94 plant pathogenic bacteria indicates that these novel NRPS gene clusters are specific to the genus Xanthomonas and are also present in Xanthomonas translucens and X. oryzae pv. oryzicola. Further genome mining revealed other novel NRPS genes specific to X. oryzae pv. oryzicola or Xanthomonas sacchari. CONCLUSIONS This study revealed the significant potential of the genus Xanthomonas to produce new non-ribosomally synthesized peptides. Interestingly, this biosynthetic potential seems to be specific to strains of Xanthomonas associated with monocotyledonous plants, suggesting a putative involvement of non-ribosomally synthesized peptides in plant-bacteria interactions.
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Affiliation(s)
- Monique Royer
- CIRAD, UMR BGPI, Montpellier Cedex 5, F-34398, France
| | | | | | - Valérie Barbe
- CEA/DSV/IG/Genoscope, Centre National de Séquençage, Evry Cedex F-91057, France
| | | | | | | | - Camila Gomez
- CIRAD, UMR BGPI, Montpellier Cedex 5, F-34398, France
| | - Manuela Hügelland
- Institut für Chemie, Technische Universität Berlin, Berlin D-10623, Germany
| | - Ginka H Völler
- Institut für Chemie, Technische Universität Berlin, Berlin D-10623, Germany
| | - Julie Noëll
- CIRAD, UMR BGPI, Montpellier Cedex 5, F-34398, France
| | | | - Saskia Rausch
- Institut für Chemie, Technische Universität Berlin, Berlin D-10623, Germany
| | | | - Stéphane Poussier
- UMR PVBMT, Université de la Réunion, Saint-Denis, La Réunion F-97715, France
| | - Philippe Rott
- CIRAD, UMR BGPI, Montpellier Cedex 5, F-34398, France
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Wichmann F, Vorhölter FJ, Hersemann L, Widmer F, Blom J, Niehaus K, Reinhard S, Conradin C, Kölliker R. The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection. MOLECULAR PLANT PATHOLOGY 2013; 14:576-88. [PMID: 23578314 PMCID: PMC6638798 DOI: 10.1111/mpp.12030] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Xanthomonas translucens pv. graminis (Xtg) is a gammaproteobacterium that causes bacterial wilt on a wide range of forage grasses. To gain insight into the host-pathogen interaction and to identify the virulence factors of Xtg, we compared a draft genome sequence of one isolate (Xtg29) with other Xanthomonas spp. with sequenced genomes. The type III secretion system (T3SS) encoding a protein transport system for type III effector (T3E) proteins represents one of the most important virulence factors of Xanthomonas spp. In contrast with other Xanthomonas spp. assigned to clade 1 on the basis of phylogenetic analyses, we identified an hrp (hypersensitive response and pathogenicity) gene cluster encoding T3SS components and a representative set of 35 genes encoding putative T3Es in the genome of Xtg29. The T3SS was shown to be divergent from the hrp gene clusters of other sequenced Xanthomonas spp. Xtg mutants deficient in T3SS regulating and structural genes were constructed to clarify the role of the T3SS in forage grass colonization. Italian ryegrass infection with these mutants led to significantly reduced symptoms (P < 0.05) relative to plants infected with the wild-type strain. This showed that the T3SS is required for symptom evocation. In planta multiplication of the T3SS mutants was not impaired significantly relative to the wild-type, indicating that the T3SS is not required for survival until 14 days post-infection. This study represents the first major step to understanding the bacterial colonization strategies deployed by Xtg and may assist in the identification of resistance (R) genes in forage grasses.
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Affiliation(s)
- Fabienne Wichmann
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, 8046 Zurich, Switzerland
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Pieretti I, Royer M, Barbe V, Carrere S, Koebnik R, Couloux A, Darrasse A, Gouzy J, Jacques MA, Lauber E, Manceau C, Mangenot S, Poussier S, Segurens B, Szurek B, Verdier V, Arlat M, Gabriel DW, Rott P, Cociancich S. Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels. BMC Genomics 2012; 13:658. [PMID: 23171051 PMCID: PMC3542200 DOI: 10.1186/1471-2164-13-658] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 11/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. X. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of Xanthomonas. For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenic X. albilineans strain GPE PC73 focused exclusively on distinctive genomic features shared with Xylella fastidiosa-another xylem-limited Xanthomonadaceae. The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features of X. albilineans, and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity. RESULTS Comparative genomic analyses showed that most of the known pathogenicity factors from other Xanthomonas species are conserved in X. albilineans, with the notable absence of two major determinants of the "artillery" of other plant pathogenic species of Xanthomonas: the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity). Genomic features specific to X. albilineans that may contribute to specific adaptation of this pathogen to sugarcane xylem vessels were also revealed. SSH experiments led to the identification of 20 genes common to three highly pathogenic strains but missing in a less pathogenic strain. These 20 genes, which include four ABC transporter genes, a methyl-accepting chemotaxis protein gene and an oxidoreductase gene, could play a key role in pathogenicity. With the exception of hypothetical proteins revealed by our comparative genomic analyses and SSH experiments, no genes potentially involved in any offensive or counter-defensive mechanism specific to X. albilineans were identified, supposing that X. albilineans has a reduced artillery compared to other pathogenic Xanthomonas species. Particular attention has therefore been given to genomic features specific to X. albilineans making it more capable of evading sugarcane surveillance systems or resisting sugarcane defense systems. CONCLUSIONS This study confirms that X. albilineans is a highly distinctive species within the genus Xanthomonas, and opens new perpectives towards a greater understanding of the pathogenicity of this destructive sugarcane pathogen.
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Affiliation(s)
| | - Monique Royer
- CIRAD, UMR BGPI, F-34398 Montpellier Cedex 5, France
| | - Valérie Barbe
- CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France
| | | | - Ralf Koebnik
- IRD, UMR RPB, F-34394 Montpellier Cedex 5, France
| | - Arnaud Couloux
- CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France
| | | | - Jérôme Gouzy
- INRA, UMR LIPM, F-31326 Castanet-Tolosan Cedex France
| | | | | | | | - Sophie Mangenot
- CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France
| | - Stéphane Poussier
- Université de la Réunion, UMR PVBMT, F-97715 Saint-Denis La Réunion, France
| | - Béatrice Segurens
- CEA/DSV/IG/Génoscope, Centre National de Séquençage, F-91057 Evry Cedex France
| | - Boris Szurek
- IRD, UMR RPB, F-34394 Montpellier Cedex 5, France
| | | | - Matthieu Arlat
- Université Paul Sabatier, UMR LIPM, F-31326 Castanet-Tolosan Cedex France
| | - Dean W Gabriel
- University of Florida, Plant Pathology Department, Gainesville FL 32605 USA
| | - Philippe Rott
- CIRAD, UMR BGPI, F-34398 Montpellier Cedex 5, France
| | - Stéphane Cociancich
- CIRAD, UMR BGPI, F-34398 Montpellier Cedex 5, France
- UMR BGPI, Campus International de Baillarguet, TA A-54/K, F-34398 Montpellier Cedex 5, France
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Wasukira A, Tayebwa J, Thwaites R, Paszkiewicz K, Aritua V, Kubiriba J, Smith J, Grant M, Studholme DJ. Genome-wide sequencing reveals two major sub-lineages in the genetically monomorphic pathogen xanthomonas campestris pathovar musacearum. Genes (Basel) 2012; 3:361-77. [PMID: 24704974 PMCID: PMC3902798 DOI: 10.3390/genes3030361] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 06/24/2012] [Accepted: 06/26/2012] [Indexed: 11/18/2022] Open
Abstract
The bacterium Xanthomonas campestris pathovar musacearum (Xcm) is the causal agent of banana Xanthomonas wilt (BXW). This disease has devastated economies based on banana and plantain crops (Musa species) in East Africa. Here we use genome-wide sequencing to discover a set of single-nucleotide polymorphisms (SNPs) among East African isolates of Xcm. These SNPs have potential as molecular markers for phylogeographic studies of the epidemiology and spread of the pathogen. Our analysis reveals two major sub-lineages of the pathogen, suggesting that the current outbreaks of BXW on Musa species in the region may have more than one introductory event, perhaps from Ethiopia. Also, based on comparisons of genome-wide sequence data from multiple isolates of Xcm and multiple strains of X. vasicola pathovar vasculorum, we identify genes specific to Xcm that could be used to specifically detect Xcm by PCR-based methods.
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Affiliation(s)
- Arthur Wasukira
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK.
| | - Johnbosco Tayebwa
- 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.
| | - Valente Aritua
- National Crops Resources Research Institute (NaCRRI), Kampala 7084, Uganda.
| | - 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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Studholme DJ, Wasukira A, Paszkiewicz K, Aritua V, Thwaites R, Smith J, Grant M. Correction: Studholme et al., Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 clade. Genes 2011, 2, 1050-1065. Genes (Basel) 2012; 3:88-9. [PMID: 26791659 PMCID: PMC3902796 DOI: 10.3390/genes3010088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 01/10/2012] [Indexed: 11/21/2022] Open
Affiliation(s)
- David J Studholme
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Arthur Wasukira
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
- National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda.
| | - Konrad Paszkiewicz
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Valente Aritua
- National Crops Resources Research Institute (NaCRRI), P.O. Box 7084, Kampala, Uganda.
- The Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK.
| | - Richard Thwaites
- The Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK.
| | - 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.
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