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Philippe Prior - One of the best experts on this subject based on the ideXlab platform.
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Contrasting genetic diversity and structure among Malagasy Ralstonia pseudosolanacearum Phylotype I populations inferred from an optimized Multilocus Variable Number of Tandem Repeat Analysis scheme.
PloS one, 2020Co-Authors: Hasina Rasoamanana, Santatra Ravelomanantsoa, Noura Yahiaoui, Niry Tiana Dianzinga, Emeline Rébert, Miharisoa-mirana Gauche, Yann Pecrix, Laurent Costet, Adrien Rieux, Philippe PriorAbstract:The Ralstonia solanacearum species complex (RSSC), composed of three species and four Phylotypes, are globally distributed soil-borne bacteria with a very broad host range. In 2009, a devastating potato bacterial wilt outbreak was declared in the central highlands of Madagascar, which reduced the production of vegetable crops including potato, eggplant, tomato and pepper. A molecular epidemiology study of Malagasy RSSC strains carried out between 2013 and 2017 identified R. pseudosolanacearum (Phylotypes I and III) and R. solanacearum (Phylotype II). A previously published population biology analysis of Phylotypes II and III using two MultiLocus Variable Number of Tandem Repeats Analysis (MLVA) schemes revealed an emergent epidemic Phylotype II (sequevar 1) group and endemic Phylotype III isolates. We developed an optimized MLVA scheme (RS1-MLVA14) to characterize Phylotype I strains in Madagascar to understand their genetic diversity and structure. The collection included isolates from 16 fields of different Solanaceae species sampled in Analamanga and Itasy regions (highlands) in 2013 (123 strains) and in Atsinanana region (lowlands) in 2006 (25 strains). Thirty-one haplotypes were identified, two of them being particularly prevalent: MT007 (30.14%) and MT004 (16.44%) (sequevar 18). Genetic diversity analysis revealed a significant contrasting level of diversity according to elevation and sampling region. More diverse at low altitude than at high altitude, the Malagasy Phylotype I isolates were structured in two clusters, probably resulting from different historical introductions. Interestingly, the most prevalent Malagasy Phylotype I isolates were genetically distant from regional and worldwide isolates. In this work, we demonstrated that the RS1-MLVA14 scheme can resolve differences from regional to field scales and is thus suited for deciphering the epidemiology of Phylotype I populations.
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TALE-Like Effectors Are an Ancestral Feature of the Ralstonia solanacearum Species Complex and Converge in DNA Targeting Specificity
Frontiers in Plant Science, 2016Co-Authors: Niklas Schandry, Philippe Prior, Orlando De Lange, Thomas LahayeAbstract:Raistonia solanacearum, a species complex of bacterial plant pathogens divided into four monophyletic Phylotypes, causes plant diseases in tropical climates around the world. Some strains exhibit a broad host range on solanaceous hosts, while others are highly host-specific as for example some banana-pathogenic strains. Previous studies showed that transcription activator-like (TAL) effectors from Raistonia, termed RipTALs, are capable of activating reporter genes in planta, if these are preceded by a matching effector binding element (EBE). RipTALs target DNA via their central repeat domain (CRD), where one repeat pairs with one DNA-base of the given EBE. The repeat variable diresidue dictates base repeat specificity in a predictable fashion, known as the TALE code. In this work, we analyze RipTALs across all Phylotypes of the Ralstonia solanacearum species complex. We find that RipTALs are prevalent in Phylotypes I and IV but absent from most Phylotype III and II strains (10/12, 8/14, 1/24, and 1/5 strains contained a RipTAL, respectively). RipTALs originating from strains of the same Phylotype show high levels of sequence similarity (>98%) in the N-terminal and C-terminal regions, while RipTALs isolated from different Phylotypes show 47-91% sequence similarity in those regions, giving rise to four RipTAL classes. We show that, despite sequence divergence, the base preference for guanine, mediated by the N-terminal region, is conserved across RipTALs of all classes. Using the number and order of repeats found in the CRD, we functionally sub-classify RipTALs, introduce a new simple nomenclature, and predict matching EBEs for all seven distinct RipTALs identified. We experimentally study RipTAL EBEs and uncover that some RipTALs are able to target the EBEs of other RipTALs, referred to as cross-reactivity. In particular, RipTALs from strains with a broad host range on solanaceous hosts cross-react on each other's EBEs. Investigation of sequence divergence between RipTAL repeats allows for a reconstruction of repeat array biogenesis, for example through slipped strand mispairing or gene conversion. Using these studies we show how RipTALs of broad host range strains evolved convergently toward a shared target sequence. Finally, we discuss the differences between TALE-likes of plant pathogens in the context of disease ecology.
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First Report of Ralstonia pseudosolanacearum Phylotype I Causing Bacterial Wilt on Rodrigues Island, Indian Ocean
Plant Disease, 2016Co-Authors: Noura Yahiaoui, Gilles Cellier, Philippe Prior, Jean-jacques Chéron, Rajan Jeetah, Jérôme Félicité, S. Benimadhu, Fabien Guérin, Stephane PoussierAbstract:The Ralstonia solanacearum species complex (Rssc) encompasses strains that are highly destructive on a wide host range, and some are listed as quarantine organisms in Europe, the United States, and many other countries. This soil-borne bacterial plant pathogen invades the roots and colonizes the xylem vessels, causing a bacterial wilt (BW) disease. Strains are distributed into four phylogenetic groups (Phylotypes) linked to their geographical origin of evolution: Phylotype I (Asia), Phylotype II (America), Phylotype III (Africa), and Phylotype IV (Australia - Indonesia - Japan). Phylotypes are subdivided into sequevars, encompassing strains that share high homology on the endoglucanase gene partial sequence (750 bp) (Fegan and Prior 2005). Rodrigues is part of the Mascarene Islands in the Southwest Indian Ocean. In February 2016, a survey was conducted to identify the causal agent of BW, encountered for years on this island. Typical BW disease symptoms, including leaf epinasty and browning vessels, were observed on tomato (Solanum lycopersicum L.) in Terre Rouge and on chili pepper (Capsicum frutescens L.) in Nouvelle Decouverte and Montagne Malgache. Seventy-eight stem sections were collected, surface disinfected with 70% ethanol, and crushed into 2 ml of Tris-buffer, then processed for bacterial isolation by plating 50 µl on SM-1 medium (Granada and Sequeira 1983). Among all of the collected stems, typical Ralstonia pseudosolanacearum colonies grew on the semiselective medium from 51 of the 78 samples. Corresponding strains were subcultured and typed as R. pseudosolanacearum Phylotype I (Safni et al. 2014), based on the PMX-PCR (Fegan and Prior 2005). A subset of six strains, two from each location, was selected for sequevar identification (Fegan et al. 1998). Strains CFBP8472 and CFBP8465 (Terre Rouge) were identified as sequevar I-31 (GenBank KX242311 and KX242312), but strains CFBP8467 and CFBP8468 (Montagne Malgache) along with CFBP8469 and CFBP8466 (Nouvelle Decouverte) were identified as sequevar I-33 (KX242313 to KX242316). This subset of strains was inoculated on five plants per strain by soil drenching on the susceptible tomato cultivar L390 (Lebeau et al. 2011) with 5 ml of a calibrated suspension (108 CFU/ml in Tris-buffer). Plants were grown in a fully controlled environment at day/night temperatures of 30/25°C ± 1°C under high relative humidity (∼90%). Sterile Tris-buffer inoculated negative controls were grown with the same parameters. Typical BW symptoms were observed within 6 days postinoculation and strains were reisolated and characterized using the same protocol as for the strains that were inoculated, fulfilling Koch's postulates. No symptoms were observed and no Rssc strains could be isolated from negative controls. To our knowledge, this is the first report of R. pseudosolanacearum Phylotype I strains causing bacterial wilt on tomato and pepper on Rodrigues. Further studies need to be conducted on the prevalence and diversity of the Rssc strains causing the BW disease, in order to implement adapted control measures, such as the use of local and adapted resistant cultivars. Further surveys on other Southwest Indian Ocean islands such as Mauritius, Reunion, and Seychelles should be achieved to determine the potential origin of the R. pseudosolanacearum Phylotype I strains isolated on Rodrigues island. (Texte integral)
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Evolutionary history of Ralstonia Solanacearum inferred from MLSA
2012Co-Authors: Emmanuel Wicker, Jean-charles De Cambiaire, Christophe Lemaire, Pierre Lefeuvre, Stephane Poussier, Philippe PriorAbstract:We used multilocus sequence analysis (MLSA) on a worldwide collection of the plant pathogenic Ralstonia solanacearum (Betaproteobacteria) to retrace its complex evolutionary history. Using genetic imprints left during Ralstonia solanacearum evolution, we were able to delineate distinct evolutionary complex displaying contrasting dynamics. Among the Phylotypes already described (I, IIA, IIB, III, IV), eight groups of strains with distinct evolutionary patterns, named clades, were identified. From our recombination analysis, we identified 21 recombination events that occurred within and across these lineages. Although appearing the most divergent and ancestral Phylotype, Phylotype IV was inferred as a gene donor for the majority of the recombination events that we detected. Whereas this Phylotype apparently fuelled the species diversity, ongoing diversification was mainly detected within Phylotype I, IIA and III. These three groups presented a recent expanding population structure, a high level of homologous recombination, and evidences of long distance migrations. Factors such as adaptation to a specific host or intense trading of infected crops may have promoted this diversification. Whether Ralstonia solanacearum lineages will eventually evolve in distinct species remains difficult to predict. The intensification of cropping and increase of geographical dispersion may favour situations of Phylotype sympatry and promote higher exchange of key factors for host adaptation from their common genetic pool. (Resume d'auteur)
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Evolutionary history of Ralstonia Solanacearum inferred from MLSA
2012Co-Authors: Emmanuel Wicker, Jean-charles De Cambiaire, Christophe Lemaire, Pierre Lefeuvre, Stephane Poussier, Philippe PriorAbstract:We used multilocus sequence analysis (MLSA) on a worldwide collection of the plant pathogenic Ralstonia solanacearum (Betaproteobacteria) to retrace its complex evolutionary history. Using genetic imprints left during Ralstonia solanacearum evolution, we were able to delineate distinct evolutionary complex displaying contrasting dynamics. Among the Phylotypes already described (I, IIA, IIB, III, IV), eight groups of strains with distinct evolutionary patterns, named clades, were identified. From our recombination analysis, we identified 21 recombination events that occurred within and across these lineages. Although appearing the most divergent and ancestral Phylotype, Phylotype IV was inferred as a gene donor for the majority of the recombination events that we detected. Whereas this Phylotype apparently fuelled the species diversity, ongoing diversification was mainly detected within Phylotype I, IIA and III. These three groups presented a recent expanding population structure, a high level of homologous recombination, and evidences of long distance migrations. Factors such as adaptation to a specific host or intense trading of infected crops may have promoted this diversification. Whether Ralstonia solanacearum lineages will eventually evolve in distinct species remains difficult to predict. The intensification of cropping and increase of geographical dispersion may favour situations of Phylotype sympatry and promote higher exchange of key factors for host adaptation from their common genetic pool. (Résumé d'auteur)
Gilles Cellier - One of the best experts on this subject based on the ideXlab platform.
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Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the Ralstonia solanacearum Species Complex.
Frontiers in plant science, 2018Co-Authors: Santatra Ravelomanantsoa, Gilles Cellier, Stephane Poussier, Laurent Costet, Adrien Rieux, Christian Vernière, Frédéric Chiroleu, Sandrine Arribat, Olivier Pruvost, Isabelle RobèneAbstract:The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step toward control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n = 1224) was assigned to RSSC Phylotypes based on multiplex polymerase chain reaction (PCR). Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with Phylotype IIB sequevar 1 (IIB-1) strains (n = 879). This is the first report of Phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n = 255) were genotyped using the existing MultiLocus Variable-Number Tandem Repeat Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that Phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of Phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of Phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n = 217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy Phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of Phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African Phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.
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Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the Ralstonia solanacearum Species Complex
Frontiers in Plant Science, 2018Co-Authors: Santatra Ravelomanantsoa, Gilles Cellier, Stephane Poussier, Laurent Costet, Adrien Rieux, Christian Vernière, Frédéric Chiroleu, Sandrine Arribat, Olivier Pruvost, Isabelle RobèneAbstract:The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step towards control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n=1224) was assigned to RSSC Phylotypes based on multiplex PCR. Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with Phylotype IIB-1 strains (n=879). This is the first report of Phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n=255) were genotyped using the existing MultiLocus Variable-number TR Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that Phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of Phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of Phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n=217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy Phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of Phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African Phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.
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First Report of Ralstonia pseudosolanacearum Phylotype I Causing Bacterial Wilt on Rodrigues Island, Indian Ocean
Plant Disease, 2016Co-Authors: Noura Yahiaoui, Gilles Cellier, Philippe Prior, Jean-jacques Chéron, Rajan Jeetah, Jérôme Félicité, S. Benimadhu, Fabien Guérin, Stephane PoussierAbstract:The Ralstonia solanacearum species complex (Rssc) encompasses strains that are highly destructive on a wide host range, and some are listed as quarantine organisms in Europe, the United States, and many other countries. This soil-borne bacterial plant pathogen invades the roots and colonizes the xylem vessels, causing a bacterial wilt (BW) disease. Strains are distributed into four phylogenetic groups (Phylotypes) linked to their geographical origin of evolution: Phylotype I (Asia), Phylotype II (America), Phylotype III (Africa), and Phylotype IV (Australia - Indonesia - Japan). Phylotypes are subdivided into sequevars, encompassing strains that share high homology on the endoglucanase gene partial sequence (750 bp) (Fegan and Prior 2005). Rodrigues is part of the Mascarene Islands in the Southwest Indian Ocean. In February 2016, a survey was conducted to identify the causal agent of BW, encountered for years on this island. Typical BW disease symptoms, including leaf epinasty and browning vessels, were observed on tomato (Solanum lycopersicum L.) in Terre Rouge and on chili pepper (Capsicum frutescens L.) in Nouvelle Decouverte and Montagne Malgache. Seventy-eight stem sections were collected, surface disinfected with 70% ethanol, and crushed into 2 ml of Tris-buffer, then processed for bacterial isolation by plating 50 µl on SM-1 medium (Granada and Sequeira 1983). Among all of the collected stems, typical Ralstonia pseudosolanacearum colonies grew on the semiselective medium from 51 of the 78 samples. Corresponding strains were subcultured and typed as R. pseudosolanacearum Phylotype I (Safni et al. 2014), based on the PMX-PCR (Fegan and Prior 2005). A subset of six strains, two from each location, was selected for sequevar identification (Fegan et al. 1998). Strains CFBP8472 and CFBP8465 (Terre Rouge) were identified as sequevar I-31 (GenBank KX242311 and KX242312), but strains CFBP8467 and CFBP8468 (Montagne Malgache) along with CFBP8469 and CFBP8466 (Nouvelle Decouverte) were identified as sequevar I-33 (KX242313 to KX242316). This subset of strains was inoculated on five plants per strain by soil drenching on the susceptible tomato cultivar L390 (Lebeau et al. 2011) with 5 ml of a calibrated suspension (108 CFU/ml in Tris-buffer). Plants were grown in a fully controlled environment at day/night temperatures of 30/25°C ± 1°C under high relative humidity (∼90%). Sterile Tris-buffer inoculated negative controls were grown with the same parameters. Typical BW symptoms were observed within 6 days postinoculation and strains were reisolated and characterized using the same protocol as for the strains that were inoculated, fulfilling Koch's postulates. No symptoms were observed and no Rssc strains could be isolated from negative controls. To our knowledge, this is the first report of R. pseudosolanacearum Phylotype I strains causing bacterial wilt on tomato and pepper on Rodrigues. Further studies need to be conducted on the prevalence and diversity of the Rssc strains causing the BW disease, in order to implement adapted control measures, such as the use of local and adapted resistant cultivars. Further surveys on other Southwest Indian Ocean islands such as Mauritius, Reunion, and Seychelles should be achieved to determine the potential origin of the R. pseudosolanacearum Phylotype I strains isolated on Rodrigues island. (Texte integral)
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Phylogeny and population structure of Brown rot-and Moko disease-causing strains of Ralstonia solanacearum Phylotype II
Applied and environmental microbiology, 2012Co-Authors: Gilles Cellier, Pierre Lefeuvre, Frédéric Chiroleu, Benoit Remenant, Philippe PriorAbstract:The ancient soilborne plant vascular pathogen Ralstonia solanacearum has evolved and adapted to cause severe damage in an unusually wide range of plants. In order to better describe and understand these adaptations, strains with very similar lifestyles and host specializations are grouped into ecotypes. We used comparative genomic hybridization (CGH) to investigate three particular ecotypes in the American Phylotype II group: (i) brown rot strains from Phylotypes IIB-1 and IIB-2, historically known as race 3 biovar 2 and clonal; (ii) new pathogenic variants from Phylotype IIB-4NPB that lack pathogenicity for banana but can infect many other plant species; and (iii) Moko disease-causing strains from Phylotypes IIB-3, IIB-4, and IIA-6, historically known as race 2, that cause wilt on banana, plantain, and Heliconia spp. We compared the genomes of 72 R. solanacearum strains, mainly from the three major ecotypes of Phylotype II, using a newly developed pangenomic microarray to decipher their population structure and gain clues about the epidemiology of these ecotypes. Strain phylogeny and population structure were reconstructed. The results revealed a phylogeographic structure within brown rot strains, allowing us to distinguish European outbreak strains of Andean and African origins. The pangenomic CGH data also demonstrated that Moko ecotype IIB-4 is phylogenetically distinct from the emerging IIB-4NPB strains. These findings improved our understanding of the epidemiology of important ecotypes in Phylotype II and will be useful for evolutionary analyses and the development of new DNA-based diagnostic tools.
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Description des écotypes du Phylotype II dans le complexe d'espèces Ralstonia solanacearum : diversité et évolution
2010Co-Authors: Gilles CellierAbstract:Le modèle étudié est l’agent phytopathogène vasculaire Ralstonia solanacearum, en portant une attention particulière aux souches de Phylotype II. Cette bactérie d’origine tellurique est très diversifiée, tant au plan génétique que phénotypique. Sa classification en constante évolution témoigne d’une volonté de clarifier cette biodiversité inhabituellement forte, tout en cherchant à reconnaître les écotypes structurant ce complexe d’espèces, i.e., des groupes de souches partageant à la fois des traits génotypiques et biologiques spécifiques. Dans le cadre de ce pathosystème modèle, nous nous sommes attachés dans un premier temps à revisiter de façon précise les pathotypes au sein d’écotypes bien décrits dans la littérature, ou à en faire la description (Phylotype III africain). Nous avons observé une forte convergence phénotypique entre les souches de Phylotype III des hauts plateaux africains et les souches Brown rot de Phylotype IIB-1, capables de flétrir la pomme de terre et d’autres Solanacées à température froide. L’adaptation de souches aussi diverses pour la tolérance au froid nous a conduits à dresser un bilan de la situation R. solanacearum en Europe et in extenso dans le bassin méditerranéen. Cette approche a permis d’apprécier les degrés de divergence significative dans le pouvoir pathogène (virulence et agressivité) sur Solanaceae au sein de souches quasi clonales unifiant l’écotype Brown rot, qui s’établissent aussi sous forme d’infections latentes dans les tissus vasculaires de bananiers (Musacées). Dans le même temps, le phénotype de souches pathogènes du bananier, unifiant l’écotype Moko, a aussi été revisité sur Solanaceae qu’elles parviennent à flétrir, y compris des ressources génétiques résistantes au flétrissement bactérien. L’ensemble de ces données expérimentales a permis de dégager les critères de sélection pour le choix de trois nouvelles souches du complexe d’espèces R. solanacearum, dont nous avons obtenu les séquences génomiques. Notre approche en génomique comparative a permis de décrire le premier pangénome chez cet agent pathogène : l’ensemble les gènes repérés de l’espèce. Ces données ont été exploitées par différentes approches bio-informatiques et permettent de concevoir une refonte pertinente du complexe d’espèces R. solanacearum en trois nouvelles espèces génomiques, regroupant les souches de Phylotypes I (Asie) et III (Afrique) d’une part, puis les souches de Phylotype II (Amérique), et enfin les souches de Phylotype IV (Indonésie) d’autre part. Ce pangénome a ensuite été exploité en concevant et développant une puce à ADN, un outil permettant l’exploration à haut débit d’une grande quantité de souches. La densité des données expérimentales accumulées permet une démarche vers l’écologie moléculaire et de reconstituer certains pans du passé évolutif des souches de Phylotype II chez R. solanacearum. Par ailleurs, l’analyse approfondie de ces données de génomique, associant phylogéographie et structuration des populations de l’écotype Brown rot, montre une double situation épidémiologique en Europe, recoupant des influences andines et africaines. De la même façon, l’écotype Moko présente trois structures génétiques distinctes. Ces données ont été analysées de manière à retracer les principaux flux de gènes dans les états ancestraux des Phylotypes et de dégager la forte contribution de la partie mobile du génome, des gènes relatifs à l’adaptation environnementale et à la pathogénie, comme moteurs dans l’évolution de cet important organisme phytopathogène.
Emmanuel Wicker - One of the best experts on this subject based on the ideXlab platform.
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Eggplant Resistance to the Ralstonia solanacearum Species Complex Involves Both Broad-Spectrum and Strain-Specific Quantitative Trait Loci
Frontiers in Plant Science, 2017Co-Authors: Sylvia Salgon, Emmanuel Wicker, Cyril Jourda, Christopher Sauvage, Marie-christine Brand-daunay, Bernard Reynaud, Jacques DintingerAbstract:Bacterial wilt (BW) is a major disease of solanaceous crops caused by the Ralstonia solanacearum species complex (RSSC). Strains are grouped into five Phylotypes (I, IIA, IIB, III, and IV). Varietal resistance is the most sustainable strategy for managing BW. Nevertheless, breeding to improve cultivar resistance has been limited by the pathogen's extensive genetic diversity. Identifying the genetic bases of specific and non-specific resistance is a prerequisite to breed improvement. A major gene (ERs1) was previously mapped in eggplant (Solanum melongena L.) using an intraspecific population of recombinant inbred lines derived from the cross of susceptible MM738 (S) x resistant AG91-25 (R). ERs1 was originally found to control three strains from Phylotype I, while being totally ineffective against a virulent strain from the same Phylotype. We tested this population against four additional RSSC strains, representing Phylotypes I, IIA, IIB, and III in order to clarify the action spectrum of ERs1. We recorded wilting symptoms and bacterial stem colonization under controlled artificial inoculation. We constructed a high-density genetic map of the population using single nucleotide polymorphisms (SNPs) developed from genotyping-by-sequencing and added 168 molecular markers [amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and sequence-related amplified polymorphisms (SRAPs)] developed previously. The new linkage map based on a total of 1,035 markers was anchored on eggplant, tomato, and potato genomes. Quantitative trait locus (QTL) mapping for resistance against a total of eight RSSC strains resulted in the detection of one major Phylotype-specific QTL and two broad-spectrum QTLs. The major QTL, which specifically controls three Phylotype I strains, was located at the bottom of chromosome 9 and corresponded to the previously identified major gene ERs1. Five candidate R-genes were underlying this QTL, with different alleles between the parents. The two other QTLs detected on chromosomes 2 and 5 were found to be associated with partial resistance to strains of Phylotypes I, IIA, III and strains of Phylotypes IIA and III, respectively. Markers closely linked to these three QTLs will be crucial for breeding eggplant with broad-spectrum resistance to BW. Furthermore, our study provides an important contribution to the molecular characterization of ERs1, which was initially considered to be a major resistance gene.
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Suivi de l'évolution d'une population parcellaire de #Ralstonia solanacearum# sous pression de sélection variétale à l'aide de schémas MLVA : Session 5- Dynamique, épidémiologie et génétique des populations bactériennes
2014Co-Authors: Jérémy Guinard, Stephane Poussier, Fabien Guérin, Anne Latreille, Anaïs Damour, Sujeen Lakshmi, Emmanuel WickerAbstract:Le flétrissement bactérien causé par Ralstonia solanacearum (Rs), une bétaproteobactérie vasculaire d'origine tellurique, est considéré comme j'une des phytobactérioses majeures au niveau mondial. Rs est considérée comme un complexe d'espèces subdivisé en 4 Phylotypes dont le Phylotype 1 a le plus fort potentiel évolutif et une prévalence mondialea. La résistance variétale, stratégie de lutte la plus prometteuse, reste cependant difficile du fait de l'extrême plasticité génomique et phénotypique de la bactérie. Les plus hauts ni veaux de résistance ont été identifiés chez l'aubergine mais la question de leur durabilité reste ouverte. Ainsi nous proposons d'étudier la durabilité de la résistance de l'aubergine AG9 125, portant le gène majeur Ers/ u, à travers le suivi évolutif de la structure génétique d'une population parcellaire de Rs Phylotype 1 soumise à des cultures répétées de cette accession. Dans cette parcelle, ont été implantés un cycle de culture de tomate sensible suivi de trois cycles de culture d'accessions d'aubergine résistante (AG9 1-25) et sensible (MM738). L'incidence de la maladie a été suivi puis des bactéries ont été isolées et analysées avec un premier schéma MLVAc (MultiLocus VNTR Analysis) mais celui-ci s'est révélé trop peu résolutif. Nous avons alors développé un nouveau schéma MLVA après criblage in silico de trois génomes (deux de Phylotype 1 et un de Phylotype III ). Ce schéma à 8 loci minisatellites, spécifiques au Phylotype l, est plus discriminant que le schéma précédent sur des populations parcellaires ou régionales. Cet outil a révélé une faible diversité génétique (O,215<H,<O,33 8) des 1285 souches de Rs collectées. Une réduction de la diversité génétique et haplotypique est observable associée à une hausse de l'incidence de la maladie entre les cycles culturaux. Les premiers résultats suggèrent une sélection des haplotypes par l'hôte résistant ainsi qu'une adaptation à l'aubergine sensible. (Résumé d'auteur)
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Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot
Journal of Microbiological Methods, 2013Co-Authors: Carine A. N'guessan, Stephane Poussier, Sylvain Brisse, Anne-claire Le Roux-nio, Daouda Koné, Emmanuel WickerAbstract:Ralstonia solanacearum is an important soil borne bacterial plant pathogen causing bacterial wilt on many important crops. To better monitor epidemics, efficient tools that can identify and discriminate populations are needed. In this study, we assessed variable number of tandem repeats (VNTR) genotyping as a new tool for epidemiological surveillance of R. solanacearum Phylotypes, and more specifically for the monitoring of the monomorphic ecotypes "Moko" (banana-pathogenic) and "brown rot" (potato-pathogenic under cool conditions). Screening of six R. solanacearum genome sequences lead to select 36 VNTR loci that were preliminarily amplified on 24 strains. From this step, 26 single-locus primer pairs were multiplexed, and applied to a worldwide collection of 337 strains encompassing the whole phylogenetic diversity, with revelation on a capillary-electrophoresis genotype. Four loci were monomorphic within all Phylotypes and were not retained; the other loci were highly polymorphic but displayed a clear Phylotype-specificity. Phylotypespecific MLVA schemes were thus defined, based on 13 loci for Phylotype I, 12 loci for Phylotype II, 11 loci for Phylotype III and 6 for Phylotype IV. MLVA typing was significantly more discriminative than egl-based sequevar typing, particularly on monomorphic "brown rot" ecotype (Phylotype IIB/sequevar 1) and "Moko disease" clade 4 (Phylotype IIB/sequevar 4). Our results raise promising prospects for studies of population genetic structures and epidemiological monitoring. (Résumé d'auteur)
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Evolutionary history of Ralstonia Solanacearum inferred from MLSA
2012Co-Authors: Emmanuel Wicker, Jean-charles De Cambiaire, Christophe Lemaire, Pierre Lefeuvre, Stephane Poussier, Philippe PriorAbstract:We used multilocus sequence analysis (MLSA) on a worldwide collection of the plant pathogenic Ralstonia solanacearum (Betaproteobacteria) to retrace its complex evolutionary history. Using genetic imprints left during Ralstonia solanacearum evolution, we were able to delineate distinct evolutionary complex displaying contrasting dynamics. Among the Phylotypes already described (I, IIA, IIB, III, IV), eight groups of strains with distinct evolutionary patterns, named clades, were identified. From our recombination analysis, we identified 21 recombination events that occurred within and across these lineages. Although appearing the most divergent and ancestral Phylotype, Phylotype IV was inferred as a gene donor for the majority of the recombination events that we detected. Whereas this Phylotype apparently fuelled the species diversity, ongoing diversification was mainly detected within Phylotype I, IIA and III. These three groups presented a recent expanding population structure, a high level of homologous recombination, and evidences of long distance migrations. Factors such as adaptation to a specific host or intense trading of infected crops may have promoted this diversification. Whether Ralstonia solanacearum lineages will eventually evolve in distinct species remains difficult to predict. The intensification of cropping and increase of geographical dispersion may favour situations of Phylotype sympatry and promote higher exchange of key factors for host adaptation from their common genetic pool. (Resume d'auteur)
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Evolutionary history of Ralstonia Solanacearum inferred from MLSA
2012Co-Authors: Emmanuel Wicker, Jean-charles De Cambiaire, Christophe Lemaire, Pierre Lefeuvre, Stephane Poussier, Philippe PriorAbstract:We used multilocus sequence analysis (MLSA) on a worldwide collection of the plant pathogenic Ralstonia solanacearum (Betaproteobacteria) to retrace its complex evolutionary history. Using genetic imprints left during Ralstonia solanacearum evolution, we were able to delineate distinct evolutionary complex displaying contrasting dynamics. Among the Phylotypes already described (I, IIA, IIB, III, IV), eight groups of strains with distinct evolutionary patterns, named clades, were identified. From our recombination analysis, we identified 21 recombination events that occurred within and across these lineages. Although appearing the most divergent and ancestral Phylotype, Phylotype IV was inferred as a gene donor for the majority of the recombination events that we detected. Whereas this Phylotype apparently fuelled the species diversity, ongoing diversification was mainly detected within Phylotype I, IIA and III. These three groups presented a recent expanding population structure, a high level of homologous recombination, and evidences of long distance migrations. Factors such as adaptation to a specific host or intense trading of infected crops may have promoted this diversification. Whether Ralstonia solanacearum lineages will eventually evolve in distinct species remains difficult to predict. The intensification of cropping and increase of geographical dispersion may favour situations of Phylotype sympatry and promote higher exchange of key factors for host adaptation from their common genetic pool. (Résumé d'auteur)
Stephane Poussier - One of the best experts on this subject based on the ideXlab platform.
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Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the Ralstonia solanacearum Species Complex.
Frontiers in plant science, 2018Co-Authors: Santatra Ravelomanantsoa, Gilles Cellier, Stephane Poussier, Laurent Costet, Adrien Rieux, Christian Vernière, Frédéric Chiroleu, Sandrine Arribat, Olivier Pruvost, Isabelle RobèneAbstract:The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step toward control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n = 1224) was assigned to RSSC Phylotypes based on multiplex polymerase chain reaction (PCR). Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with Phylotype IIB sequevar 1 (IIB-1) strains (n = 879). This is the first report of Phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n = 255) were genotyped using the existing MultiLocus Variable-Number Tandem Repeat Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that Phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of Phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of Phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n = 217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy Phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of Phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African Phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.
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Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the Ralstonia solanacearum Species Complex
Frontiers in Plant Science, 2018Co-Authors: Santatra Ravelomanantsoa, Gilles Cellier, Stephane Poussier, Laurent Costet, Adrien Rieux, Christian Vernière, Frédéric Chiroleu, Sandrine Arribat, Olivier Pruvost, Isabelle RobèneAbstract:The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step towards control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n=1224) was assigned to RSSC Phylotypes based on multiplex PCR. Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with Phylotype IIB-1 strains (n=879). This is the first report of Phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n=255) were genotyped using the existing MultiLocus Variable-number TR Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that Phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of Phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of Phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n=217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy Phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of Phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African Phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.
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First Report of Ralstonia pseudosolanacearum Phylotype I Causing Bacterial Wilt on Rodrigues Island, Indian Ocean
Plant Disease, 2016Co-Authors: Noura Yahiaoui, Gilles Cellier, Philippe Prior, Jean-jacques Chéron, Rajan Jeetah, Jérôme Félicité, S. Benimadhu, Fabien Guérin, Stephane PoussierAbstract:The Ralstonia solanacearum species complex (Rssc) encompasses strains that are highly destructive on a wide host range, and some are listed as quarantine organisms in Europe, the United States, and many other countries. This soil-borne bacterial plant pathogen invades the roots and colonizes the xylem vessels, causing a bacterial wilt (BW) disease. Strains are distributed into four phylogenetic groups (Phylotypes) linked to their geographical origin of evolution: Phylotype I (Asia), Phylotype II (America), Phylotype III (Africa), and Phylotype IV (Australia - Indonesia - Japan). Phylotypes are subdivided into sequevars, encompassing strains that share high homology on the endoglucanase gene partial sequence (750 bp) (Fegan and Prior 2005). Rodrigues is part of the Mascarene Islands in the Southwest Indian Ocean. In February 2016, a survey was conducted to identify the causal agent of BW, encountered for years on this island. Typical BW disease symptoms, including leaf epinasty and browning vessels, were observed on tomato (Solanum lycopersicum L.) in Terre Rouge and on chili pepper (Capsicum frutescens L.) in Nouvelle Decouverte and Montagne Malgache. Seventy-eight stem sections were collected, surface disinfected with 70% ethanol, and crushed into 2 ml of Tris-buffer, then processed for bacterial isolation by plating 50 µl on SM-1 medium (Granada and Sequeira 1983). Among all of the collected stems, typical Ralstonia pseudosolanacearum colonies grew on the semiselective medium from 51 of the 78 samples. Corresponding strains were subcultured and typed as R. pseudosolanacearum Phylotype I (Safni et al. 2014), based on the PMX-PCR (Fegan and Prior 2005). A subset of six strains, two from each location, was selected for sequevar identification (Fegan et al. 1998). Strains CFBP8472 and CFBP8465 (Terre Rouge) were identified as sequevar I-31 (GenBank KX242311 and KX242312), but strains CFBP8467 and CFBP8468 (Montagne Malgache) along with CFBP8469 and CFBP8466 (Nouvelle Decouverte) were identified as sequevar I-33 (KX242313 to KX242316). This subset of strains was inoculated on five plants per strain by soil drenching on the susceptible tomato cultivar L390 (Lebeau et al. 2011) with 5 ml of a calibrated suspension (108 CFU/ml in Tris-buffer). Plants were grown in a fully controlled environment at day/night temperatures of 30/25°C ± 1°C under high relative humidity (∼90%). Sterile Tris-buffer inoculated negative controls were grown with the same parameters. Typical BW symptoms were observed within 6 days postinoculation and strains were reisolated and characterized using the same protocol as for the strains that were inoculated, fulfilling Koch's postulates. No symptoms were observed and no Rssc strains could be isolated from negative controls. To our knowledge, this is the first report of R. pseudosolanacearum Phylotype I strains causing bacterial wilt on tomato and pepper on Rodrigues. Further studies need to be conducted on the prevalence and diversity of the Rssc strains causing the BW disease, in order to implement adapted control measures, such as the use of local and adapted resistant cultivars. Further surveys on other Southwest Indian Ocean islands such as Mauritius, Reunion, and Seychelles should be achieved to determine the potential origin of the R. pseudosolanacearum Phylotype I strains isolated on Rodrigues island. (Texte integral)
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Suivi de l'évolution d'une population parcellaire de #Ralstonia solanacearum# sous pression de sélection variétale à l'aide de schémas MLVA : Session 5- Dynamique, épidémiologie et génétique des populations bactériennes
2014Co-Authors: Jérémy Guinard, Stephane Poussier, Fabien Guérin, Anne Latreille, Anaïs Damour, Sujeen Lakshmi, Emmanuel WickerAbstract:Le flétrissement bactérien causé par Ralstonia solanacearum (Rs), une bétaproteobactérie vasculaire d'origine tellurique, est considéré comme j'une des phytobactérioses majeures au niveau mondial. Rs est considérée comme un complexe d'espèces subdivisé en 4 Phylotypes dont le Phylotype 1 a le plus fort potentiel évolutif et une prévalence mondialea. La résistance variétale, stratégie de lutte la plus prometteuse, reste cependant difficile du fait de l'extrême plasticité génomique et phénotypique de la bactérie. Les plus hauts ni veaux de résistance ont été identifiés chez l'aubergine mais la question de leur durabilité reste ouverte. Ainsi nous proposons d'étudier la durabilité de la résistance de l'aubergine AG9 125, portant le gène majeur Ers/ u, à travers le suivi évolutif de la structure génétique d'une population parcellaire de Rs Phylotype 1 soumise à des cultures répétées de cette accession. Dans cette parcelle, ont été implantés un cycle de culture de tomate sensible suivi de trois cycles de culture d'accessions d'aubergine résistante (AG9 1-25) et sensible (MM738). L'incidence de la maladie a été suivi puis des bactéries ont été isolées et analysées avec un premier schéma MLVAc (MultiLocus VNTR Analysis) mais celui-ci s'est révélé trop peu résolutif. Nous avons alors développé un nouveau schéma MLVA après criblage in silico de trois génomes (deux de Phylotype 1 et un de Phylotype III ). Ce schéma à 8 loci minisatellites, spécifiques au Phylotype l, est plus discriminant que le schéma précédent sur des populations parcellaires ou régionales. Cet outil a révélé une faible diversité génétique (O,215<H,<O,33 8) des 1285 souches de Rs collectées. Une réduction de la diversité génétique et haplotypique est observable associée à une hausse de l'incidence de la maladie entre les cycles culturaux. Les premiers résultats suggèrent une sélection des haplotypes par l'hôte résistant ainsi qu'une adaptation à l'aubergine sensible. (Résumé d'auteur)
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Development of variable number of tandem repeats typing schemes for Ralstonia solanacearum, the agent of bacterial wilt, banana Moko disease and potato brown rot
Journal of Microbiological Methods, 2013Co-Authors: Carine A. N'guessan, Stephane Poussier, Sylvain Brisse, Anne-claire Le Roux-nio, Daouda Koné, Emmanuel WickerAbstract:Ralstonia solanacearum is an important soil borne bacterial plant pathogen causing bacterial wilt on many important crops. To better monitor epidemics, efficient tools that can identify and discriminate populations are needed. In this study, we assessed variable number of tandem repeats (VNTR) genotyping as a new tool for epidemiological surveillance of R. solanacearum Phylotypes, and more specifically for the monitoring of the monomorphic ecotypes "Moko" (banana-pathogenic) and "brown rot" (potato-pathogenic under cool conditions). Screening of six R. solanacearum genome sequences lead to select 36 VNTR loci that were preliminarily amplified on 24 strains. From this step, 26 single-locus primer pairs were multiplexed, and applied to a worldwide collection of 337 strains encompassing the whole phylogenetic diversity, with revelation on a capillary-electrophoresis genotype. Four loci were monomorphic within all Phylotypes and were not retained; the other loci were highly polymorphic but displayed a clear Phylotype-specificity. Phylotypespecific MLVA schemes were thus defined, based on 13 loci for Phylotype I, 12 loci for Phylotype II, 11 loci for Phylotype III and 6 for Phylotype IV. MLVA typing was significantly more discriminative than egl-based sequevar typing, particularly on monomorphic "brown rot" ecotype (Phylotype IIB/sequevar 1) and "Moko disease" clade 4 (Phylotype IIB/sequevar 4). Our results raise promising prospects for studies of population genetic structures and epidemiological monitoring. (Résumé d'auteur)
Santatra Ravelomanantsoa - One of the best experts on this subject based on the ideXlab platform.
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Contrasting genetic diversity and structure among Malagasy Ralstonia pseudosolanacearum Phylotype I populations inferred from an optimized Multilocus Variable Number of Tandem Repeat Analysis scheme.
PloS one, 2020Co-Authors: Hasina Rasoamanana, Santatra Ravelomanantsoa, Noura Yahiaoui, Niry Tiana Dianzinga, Emeline Rébert, Miharisoa-mirana Gauche, Yann Pecrix, Laurent Costet, Adrien Rieux, Philippe PriorAbstract:The Ralstonia solanacearum species complex (RSSC), composed of three species and four Phylotypes, are globally distributed soil-borne bacteria with a very broad host range. In 2009, a devastating potato bacterial wilt outbreak was declared in the central highlands of Madagascar, which reduced the production of vegetable crops including potato, eggplant, tomato and pepper. A molecular epidemiology study of Malagasy RSSC strains carried out between 2013 and 2017 identified R. pseudosolanacearum (Phylotypes I and III) and R. solanacearum (Phylotype II). A previously published population biology analysis of Phylotypes II and III using two MultiLocus Variable Number of Tandem Repeats Analysis (MLVA) schemes revealed an emergent epidemic Phylotype II (sequevar 1) group and endemic Phylotype III isolates. We developed an optimized MLVA scheme (RS1-MLVA14) to characterize Phylotype I strains in Madagascar to understand their genetic diversity and structure. The collection included isolates from 16 fields of different Solanaceae species sampled in Analamanga and Itasy regions (highlands) in 2013 (123 strains) and in Atsinanana region (lowlands) in 2006 (25 strains). Thirty-one haplotypes were identified, two of them being particularly prevalent: MT007 (30.14%) and MT004 (16.44%) (sequevar 18). Genetic diversity analysis revealed a significant contrasting level of diversity according to elevation and sampling region. More diverse at low altitude than at high altitude, the Malagasy Phylotype I isolates were structured in two clusters, probably resulting from different historical introductions. Interestingly, the most prevalent Malagasy Phylotype I isolates were genetically distant from regional and worldwide isolates. In this work, we demonstrated that the RS1-MLVA14 scheme can resolve differences from regional to field scales and is thus suited for deciphering the epidemiology of Phylotype I populations.
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Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the Ralstonia solanacearum Species Complex.
Frontiers in plant science, 2018Co-Authors: Santatra Ravelomanantsoa, Gilles Cellier, Stephane Poussier, Laurent Costet, Adrien Rieux, Christian Vernière, Frédéric Chiroleu, Sandrine Arribat, Olivier Pruvost, Isabelle RobèneAbstract:The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step toward control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n = 1224) was assigned to RSSC Phylotypes based on multiplex polymerase chain reaction (PCR). Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with Phylotype IIB sequevar 1 (IIB-1) strains (n = 879). This is the first report of Phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n = 255) were genotyped using the existing MultiLocus Variable-Number Tandem Repeat Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that Phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of Phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of Phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n = 217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy Phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of Phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African Phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.
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Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the Ralstonia solanacearum Species Complex
Frontiers in Plant Science, 2018Co-Authors: Santatra Ravelomanantsoa, Gilles Cellier, Stephane Poussier, Laurent Costet, Adrien Rieux, Christian Vernière, Frédéric Chiroleu, Sandrine Arribat, Olivier Pruvost, Isabelle RobèneAbstract:The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step towards control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n=1224) was assigned to RSSC Phylotypes based on multiplex PCR. Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with Phylotype IIB-1 strains (n=879). This is the first report of Phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n=255) were genotyped using the existing MultiLocus Variable-number TR Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that Phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of Phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of Phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n=217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy Phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of Phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African Phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.
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Genetic Diversity of the Ralstonia solanacearum Species Complex in the Southwest Indian Ocean Islands
Frontiers in Plant Science, 2017Co-Authors: Noura Yahiaoui, Santatra Ravelomanantsoa, Jean-jacques Chéron, Azali Hamza, Bobb Petrousse, Rajan Jeetah, Yasmina Jaufeerally-fakim, Jérôme Félicité, Jacques Fillâtre, Bruno HostachyAbstract:Epidemiological surveillance of plant pathogens based on genotyping methods is mandatory to improve disease management strategies. In the Southwest Indian Ocean (SWIO) islands, bacterial wilt (BW) caused by the Ralstonia solanacearum species complex (RSSC) is hampering the production of many sustainable and cash crops. To thoroughly analyze the genetic diversity of the RSSC in the SWIO, we performed a wide sampling survey (in Comoros, Mauritius, Reunion, Rodrigues, and Seychelles) that yielded 1,704 isolates from 129 plots, mainly from solanaceous crops. Classification of the isolates to the four major RSSC phylogenetic groups, named Phylotypes, showed that 87% were Phylotype I, representing the most prevalent strain in each of the SWIO islands. Additionally, 9.7% were Phylotype II, and 3.3% were Phylotype III; however, these isolates were found only in Reunion. Phylotype IV (2 isolates), known to be restricted to Indonesia-Australia-Japan, was reported in Mauritius, representing the first report of this group in the SWIO. Partial endoglucanase (egl) sequencing, based on the selection of 145 isolates covering the geographic and host diversity in the SWIO (also including strains from Mayotte and Madagascar), revealed 14 sequevars with Reunion and Mauritius displaying the highest sequevar diversity. Through a multilocus sequence analysis (MLSA) scheme based on the partial sequencing of 6 housekeeping genes (gdhA, gyrB, rplB, leuS, adk, and mutS) and 1 virulence-associated gene (egl), we inferred the phylogenetic relationships between these 145 SWIO isolates and 90 worldwide RSSC reference strains. Phylotype I was the most recombinogenic, although recombination events were detected among all Phylotypes. A multilocus sequence typing (MLST) scheme identified 29 sequence types (STs) with variable geographic distributions in the SWIO. The outstanding epidemiologic feature was STI-13 (sequevar I-31), which was overrepresented in the SWIO and obviously reflected a lineage strongly adapted to the SWIO environment. A goeBURST analysis identified eight clonal complexes (CCs)
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Epidemiology of potato bacterial wilt in Madagascar: genetic diversity and population structure of the #Ralstonia solanacearum# species complex (Rssc#)
2016Co-Authors: Santatra Ravelomanantsoa, Laurent Costet, Christian Vernière, Frédéric Chiroleu, Jean-jacques Chéron, Karine Boyer, Stéphanie Javegny, Harinjaka Raveloson, Virginie Ravigné, Olivier PruvostAbstract:The Rssc encompasses strains that are highly destructive worldwide causing bacterial wilt (BW) on a wide plant host range. BW was alread y described in Madagascar (Phylotype I and III) but potato production was hampered by severe outbreaks. Controlling this disease is crucial for Malagasy potato producers. Knowledge of the genetic diversity and population structure of the pathogen was inves tigated, in fine to evaluate resistance of different potato cultivars. We characterized a large collection of strains (n=1224; 74 sites) surveyed from potato areas in 2013, by using different molecular tools. Phylotypes I, II and III were identified and most potato outbreaks were shown to be associated with brown rot strains IIB - 1, whereas members of Phylotype I and III caused few. Along with reference strains, epidemic IIB - 1 strains (n=290) were genotyped through a MLVA scheme ( RS2 - MLVA10), which showed a single clonal complex distributed in wide agro - ecological areas, and genetically related to worldwide genotypes. This suggests this IIB - 1 lineage is busting potato production in Madagascar after being introduced (not cryptic) and spread through release of infected potato - seeds. To assess the population structure of long time recognized Phylotype III strains, 251 strains were analyzed through the newly developed and highly discriminatory typing scheme RS3 - MLVA16. Malagasy population of Phylotype III strains showed a broad genetic basis made of 132 haplotypes in at least 7 clonal complexes; and furthermore distinct from African strains, suggesting its endemic character. At an agro - ecological scale, two major clonal complexes were unified by haplotypes shared between individual areas and the remainder made of haplotypes derived from a unique genotype. This large - scale epidemiological study and the generated sets of data are reference models to further studies of Rssc population in Madagascar and the SWIO* , including evaluation of pathogen aggressiveness and host resistance. (Résumé d'auteur)
