New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations

Guinard, Jérémy; Latreille, Anne; Guérin, Fabien; Poussier, Stéphane; Wicker, Emmanuel

doi:10.1128/aem.03095-16

Cited by 15 publications

(13 citation statements)

References 73 publications

(102 reference statements)

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“…This study represents an important starting point for regional breeding programmes for bacterial wilt resistance and deployment strategies not only in Mayotte but also in neighboring southwest Indian Ocean islands and African countries, where the I-31 sequevar is widespread. To understand the epidemiological and evolutionary relationships associated with this genetic lineage, population structure studies must be conducted using methods such as multilocus sequence typing (MLST) and multilocus variable number tandem repeat analysis (MLVA), which have been developed to study RSSC populations on different scales (from cropping areas to continents) (Wicker et al, 2012 ; N'Guessan et al, 2013 ; Parkinson et al, 2013 ; Ravelomanantsoa et al, 2016 ; Guinard et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Sequevar Diversity and Virulence of Ralstonia solanacearum Phylotype I on Mayotte Island (Indian Ocean)

Chesneau

Maignien²,

Boyer

et al. 2018

Front. Plant Sci.

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The genetic and phenotypic diversity of the Ralstonia solanacearum species complex, which causes bacterial wilt to Solanacae, was assessed in 140 strains sampled from the main vegetable production areas of the Mayotte island. Only phylotype I strains were identified in the five surveyed areas. The strains were distributed into the following 4 sequevars: I-31 (85.7%), I-18 (5.0%), I-15 (5.7%), and I-46 (3.6%). The central area of Mayotte was the most diverse region, harboring 4 sequevars representing 47.1% of the collected strains. Virulence tests were performed under field and controlled conditions on a set of 10 tomato breeding line accessions and two commercial hybrid tomato cultivars. The strains belonging to sequevar I-31 showed the highest virulence on the tomatoes (pathotypes T-2 and T-3), whereas sequevars I-18, I-15, and I-46 were grouped into the weakly T-1 pathotype. When the tomato accessions were challenged in the field and growth chambers, the highest level of resistance were observed from the genetically related accessions Hawaii 7996, R3034, TML46, and CLN1463. These accessions were considered moderately to highly resistant to representative strains of the most virulent and prevalent sequevar (I-31). Interestingly, the Platinum F1 cultivar, which was recently commercialized in Mayotte for bacterial wilt resistance, was highly or moderately resistant to all strains. This study represents the first step in the rationalization of resistance deployment strategies against bacterial wilt-causing strains in Mayotte.

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Section: Discussionmentioning

confidence: 99%

Sequevar Diversity and Virulence of Ralstonia solanacearum Phylotype I on Mayotte Island (Indian Ocean)

Chesneau

Maignien²,

Boyer

et al. 2018

Front. Plant Sci.

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“…Further population genetic studies on different scales are also necessary to reconstruct the evolutionary history of this lineage and to decipher the epidemiological relationships between the SWIO and African populations. Such studies could be conducted with more conclusive methods such as the multilocus variable number tandem repeat analysis (MLVA), which was developed to study RSSC populations from cropping areas to continents (N'guessan et al, 2013 ; Parkinson et al, 2013 ; Ravelomanantsoa et al, 2016 ; Guinard et al, 2017 ). All of the MLST sequences generated by this study will be deposited soon in an open-access database dedicated to RSSC useful for BW epidemiosurveillance.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity of the Ralstonia solanacearum Species Complex in the Southwest Indian Ocean Islands

et al. 2017

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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) including SWIO isolates, four CCs being geographically restricted to the SWIO, and four CCs being widespread beyond the SWIO. This work, which highlights notable genetic links between African and SWIO strains, provides a basis for the epidemiological surveillance of RSSC and will contribute to BW management in the SWIO.

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“…In a first step, we worked with VNTR loci that had previously been identified throughout the genomes of RSSC isolates belonging to different phylotypes [ 19 , 20 , 22 , 38 ]. By using the Muscle algorithm in Geneious v10.0.9 [ 39 ], these VNTR, flanked by their primers, were searched and aligned with the reference genome of phylotype I (GMI1000) [ 40 ] and nine draft genome sequences of phylotype I isolates: CFBP7058 (sequevar 13), CIR011-208 (sequevar 17), RD13.01 (sequevar 31), TD13.01 (sequevar 31), CIV23 (sequevar 31), TF31.08 (sequevar 31), PSS04 (sequevar 15), TO10 (sequevar 47) and Y45 (sequevar 44) [ 41 , 42 ].…”

Section: Methodsmentioning

confidence: 99%

“…musacearum [16], Xanthomonas citri pv. viticola [17], and the Ralstonia solanacearum species complex [18][19][20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Contrasting genetic diversity and structure among Malagasy Ralstonia pseudosolanacearum phylotype I populations inferred from an optimized Multilocus Variable Number of Tandem Repeat Analysis scheme

Rasoamanana¹,

Ravelomanantsoa²,

Yahiaoui³

et al. 2020

PLoS ONE

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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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New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations

Cited by 15 publications

References 73 publications

Sequevar Diversity and Virulence of Ralstonia solanacearum Phylotype I on Mayotte Island (Indian Ocean)

Sequevar Diversity and Virulence of Ralstonia solanacearum Phylotype I on Mayotte Island (Indian Ocean)

Genetic Diversity of the Ralstonia solanacearum Species Complex in the Southwest Indian Ocean Islands

Contrasting genetic diversity and structure among Malagasy Ralstonia pseudosolanacearum phylotype I populations inferred from an optimized Multilocus Variable Number of Tandem Repeat Analysis scheme

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