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A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage.

Pruvost O, Magne M, Boyer K, Leduc A, Tourterel C, Drevet C, Ravigné V, Gagnevin L, Guérin F, Chiroleu F, Koebnik R, Verdier V, Vernière C - PLoS ONE (2014)

Bottom Line: A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31.MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies.MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing.

View Article: PubMed Central - PubMed

Affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.

ABSTRACT
MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).

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Plot describing the discriminatory power (expressed as G/N, the ratio between the number of haplotypes and the number of strains) in relation to the number of TR loci assayed.Black dashes represent the range of G/N ratios. Red dashes indicate 2.5 and 97.5% quantiles. Red dots indicate the median G/N values.
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pone-0098129-g002: Plot describing the discriminatory power (expressed as G/N, the ratio between the number of haplotypes and the number of strains) in relation to the number of TR loci assayed.Black dashes represent the range of G/N ratios. Red dashes indicate 2.5 and 97.5% quantiles. Red dots indicate the median G/N values.

Mentions: Based on the sequential approach, a minimum of 14 TR loci was required to discriminate all haplotypes. Permutation tests were performed in order to assess how the ratio between the number of haplotypes and the number of strains (G/N) was influenced by the number of TR loci (Fig. 2). This suggested that a limited number of carefully selected markers could be used for routine analyses. A balanced selection of PCA-uncorrelated, highly polymorphic markers (as suggested by Nei's genetic diversity and their involvement in SLV and DLV in the minimum spanning tree) and markers differentiating genetic lineages (e.g. Xcc3522 and Xcc4424) was made. A genotyping scheme based on 12 TR loci (MLVA-12) (Table 1) that resolved 89% of the total diversity and produced a tree structure consistent with the MLVA-31-based DAPC clustering (Fig. S1) is proposed for routine epidemiological investigations.


A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage.

Pruvost O, Magne M, Boyer K, Leduc A, Tourterel C, Drevet C, Ravigné V, Gagnevin L, Guérin F, Chiroleu F, Koebnik R, Verdier V, Vernière C - PLoS ONE (2014)

Plot describing the discriminatory power (expressed as G/N, the ratio between the number of haplotypes and the number of strains) in relation to the number of TR loci assayed.Black dashes represent the range of G/N ratios. Red dashes indicate 2.5 and 97.5% quantiles. Red dots indicate the median G/N values.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4045669&req=5

pone-0098129-g002: Plot describing the discriminatory power (expressed as G/N, the ratio between the number of haplotypes and the number of strains) in relation to the number of TR loci assayed.Black dashes represent the range of G/N ratios. Red dashes indicate 2.5 and 97.5% quantiles. Red dots indicate the median G/N values.
Mentions: Based on the sequential approach, a minimum of 14 TR loci was required to discriminate all haplotypes. Permutation tests were performed in order to assess how the ratio between the number of haplotypes and the number of strains (G/N) was influenced by the number of TR loci (Fig. 2). This suggested that a limited number of carefully selected markers could be used for routine analyses. A balanced selection of PCA-uncorrelated, highly polymorphic markers (as suggested by Nei's genetic diversity and their involvement in SLV and DLV in the minimum spanning tree) and markers differentiating genetic lineages (e.g. Xcc3522 and Xcc4424) was made. A genotyping scheme based on 12 TR loci (MLVA-12) (Table 1) that resolved 89% of the total diversity and produced a tree structure consistent with the MLVA-31-based DAPC clustering (Fig. S1) is proposed for routine epidemiological investigations.

Bottom Line: A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31.MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies.MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing.

View Article: PubMed Central - PubMed

Affiliation: UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint Pierre, La Réunion, France.

ABSTRACT
MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria, but not on bacterial plant pathogens of agricultural importance albeit such tools would improve our understanding of their epidemiology, as well as of the history of epidemics on a global scale. Xanthomonas citri pv. citri is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of Xanthomonas citri pv. citri strain IAPAR 306 and of phylogenetically related xanthomonads for tandem repeats. From these in silico data, an optimized MLVA scheme was developed to assess the global diversity of this monomorphic bacterium. Thirty-one minisatellite loci (MLVA-31) were selected to assess the genetic structure of 129 strains representative of the worldwide pathological and genetic diversity of X. citri pv. citri. Based on Discriminant Analysis of Principal Components (DAPC), four pathotype-specific clusters were defined. DAPC cluster 1 comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. A subset of 12 loci (MLVA-12) resolved 89% of the total diversity and matched the genetic structure revealed by MLVA-31. MLVA-12 is proposed for routine epidemiological identification of X. citri pv. citri, whereas MLVA-31 is proposed for phylogenetic and population genetics studies. MLVA-31 represents an opportunity for international X. citri pv. citri genotyping and data sharing. The MLVA-31 data generated in this study was deposited in the Xanthomonas citri genotyping database (http://www.biopred.net/MLVA/).

Show MeSH
Related in: MedlinePlus