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Ravelomanantsoa S.,BIOS UMR PVBMT | Ravelomanantsoa S.,University of Reunion Island | Ravelomanantsoa S.,University of Antananarivo | Robene I.,BIOS UMR PVBMT | And 6 more authors.
PeerJ | Year: 2016

Background. Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of the Ralstonia solanacearum species complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III. Methods. We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used. Results and Discussion. Sixteen polymorphic TR loci, which included seven microsatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more discriminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC phylotype III. © 2016 Ravelomanantsoa et al.


Leduc A.,UMR PVBMT | Traore Y.N.,Institute Polytechnique Rural | Boyer K.,UMR PVBMT | Magne M.,UMR PVBMT | And 9 more authors.
Environmental Microbiology | Year: 2015

Molecular epidemiology studies further our understanding of migrations of phytopathogenic bacteria, the major determining factor in their emergence. Asiatic citrus canker, caused by Xanthomonas citri pv.citri, was recently reported in Mali and Burkina Faso, a region remote from other contaminated areas. To identify the origin and pathways of these emergences, we used two sets of markers, minisatellites and microsatellites, for investigating different evolutionary scales. Minisatellite typing suggested the introduction of two groups of strains in Mali (DAPC1 and DAPC2), consistent with microsatellite typing. DAPC2 was restricted to Bamako district, whereas DAPC1 strains were found much more invasive. The latter strains formed a major clonal complex based on microsatellite data with the primary and secondary founders detected in commercial citrus nurseries and orchards. This suggests that human activities played a major role in the spread of DAPC1 strains via the movement of contaminated propagative material, further supported by the frequent lack of differentiation between populations from geographically distant nurseries and orchards. Approximate Bayesian Computation analyses supported the hypothesis that strains from Burkina Faso resulted from a bridgehead invasion from Mali. Multi-locus variable number of tandem repeat analysis and Approximate Bayesian Computation are useful for understanding invasion routes and pathways of monomorphic bacterial pathogens. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.


Verniere C.,UMR PVBMT | Bui Thi Ngoc L.,UMR PVBMT | Jarne P.,French National Center for Scientific Research | Ravigne V.,CIRAD - Agricultural Research for Development | And 5 more authors.
Environmental Microbiology | Year: 2014

Investigating the population biology of plant pathogens in their native areas is essential to understand the factors that shape their population structure and favour their spread. Monomorphic pathogens dispatch extremely low genetic diversity in invaded areas, and native areas constitute a major reservoir for future emerging strains. One of these, the gammaproteobacterium Xanthomonas citri pv. citri, causes Asiatic canker and is a considerable threat to citrus worldwide. We studied its population genetic structure by genotyping 555 strains from 12 Vietnam provinces at 14 tandem repeat loci and insertion sequences. Discriminant analysis of principal components identified six clusters. Five of them were composed of endemic strains distributed heterogeneously across sampled provinces. A sixth cluster, VN6, displayed a much lower diversity and a clonal expansion structure, suggesting recent epidemic spread. No differences in aggressiveness on citrus or resistance to bactericides were detected between VN6 and other strains. VN6 likely represents a case of bioinvasion following introduction in a native area likely through contaminated plant propagative material. Highly polymorphic markers are useful for revealing migration patterns of recently introduced populations of a monomorphic bacterial plant pathogen. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.


Escalon A.,UMR PVBMT | Javegny S.,UMR PVBMT | Verniere C.,UMR PVBMT | Noel L.D.,French National Institute for Agricultural Research | And 9 more authors.
Molecular Plant Pathology | Year: 2013

The mechanisms determining the host range of Xanthomonas are still undeciphered, despite much interest in their potential roles in the evolution and emergence of plant pathogenic bacteria. Xanthomonas citri pv. citri (Xci) is an interesting model of host specialization because of its pathogenic variants: pathotype A strains infect a wide range of Rutaceous species, whereas pathotype A*/AW strains have a host range restricted to Mexican lime (Citrus aurantifolia) and alemow (Citrus macrophylla). Based on a collection of 55 strains representative of Xci worldwide diversity assessed by amplified fragment length polymorphism (AFLP), we investigated the distribution of type III effectors (T3Es) in relation to host range. We examined the presence of 66 T3Es from xanthomonads in Xci and identified a repertoire of 28 effectors, 26 of which were shared by all Xci strains, whereas two (xopAG and xopC1) were present only in some A*/AW strains. We found that xopAG (=avrGf1) was present in all AW strains, but also in three A* strains genetically distant from AW, and that all xopAG-containing strains induced the hypersensitive response (HR) on grapefruit and sweet orange. The analysis of xopAD and xopAG suggested horizontal transfer between X. citri pv. bilvae, another citrus pathogen, and some Xci strains. A strains were genetically less diverse, induced identical phenotypic responses and possessed indistinguishable T3E repertoires. Conversely, A*/AW strains exhibited a wider genetic diversity in which clades correlated with geographical origin and T3E repertoire, but not with pathogenicity, according to T3E deletion experiments. Our data outline the importance of taking into account the heterogeneity of XciA*/AW strains when analysing the mechanisms of host specialization. © 2013 BSPP AND JOHN WILEY & SONS LTD.


Fartek B.,UMR PVBMT | Fartek B.,University of Reunion Island | Nibouche S.,UMR PVBMT | Atiama-Nurbel T.,UMR PVBMT | And 2 more authors.
Plant Breeding | Year: 2014

The objective of this study was to analyse the genotypic variability of sugarcane resistance to the main aphid vector of the Sugarcane yellow leaf virus (ScYLV) (Polerovirus, Luteoviridae), Melanaphis sacchari. We assessed the incidence of aphids in a field trial comparing 181 sugarcane cultivars. Based on the percentage of infested leaves, aphid incidence was scored every two weeks during three cropping seasons. Analysis of variance revealed highly significant genotype, and genotype × year variance, and high broad sense heritability. Using semivariograms, we showed that the alpha lattice design used in the field trial was able to cope with spatial correlation issues caused by the patchy nature of aphid infestations. Twenty-two aphid resistant cultivars were identified. A laboratory study of the development of M. sacchari on four of these 22 resistant cultivars confirmed the resistant status of three of them. We observed modest positive phenotypic and genetic correlations between the aphid incidence and the incidence of ScYLV. The 22 cultivars resistant to M. sacchari showed twofold lower mean virus incidence than the remaining 159 cultivars. © 2014 Blackwell Verlag GmbH.

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