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Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits.

Marcelletti S, Scortichini M - PLoS ONE (2015)

Bottom Line: Between these two clusters, no recombination event was found.Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae.By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin.

View Article: PubMed Central - PubMed

Affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (C.R.A.)-Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, I-00134, Roma, Italy.

ABSTRACT
The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches.

No MeSH data available.


Related in: MedlinePlus

Split consensus network obtained from 2.812 trees for the nine pseudomonad strains infecting Corylus avellana.A. The tree has a cut-off value of 0.19. The scale bar indicates the number of substitutions per nucleotide position. Strain legend is shown in Table 1. No reticulation was observed between the Pseudomonas avellanae and P. syringae pathovar strains. B. Neighbor-net tree obtained from 2.812 core gene sequence alignments. The dendrogram (i.e., a total of 1.977.984 nucleotides) regards the nine pseudomonad strains infecting Corylus avellana trees. The scale bar indicates the number of substitutions per nucleotide position. Bootstrap values are shown at the main nodes. No reticulation was observed between the Pseudomonas avellanae and P. syringae pathovar strains. In both trees, P. cannabina pv. alisalensis Pcal BS91 was included in the analysis as outgroup. Strain legend is shown in Table 1.
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pone.0131112.g002: Split consensus network obtained from 2.812 trees for the nine pseudomonad strains infecting Corylus avellana.A. The tree has a cut-off value of 0.19. The scale bar indicates the number of substitutions per nucleotide position. Strain legend is shown in Table 1. No reticulation was observed between the Pseudomonas avellanae and P. syringae pathovar strains. B. Neighbor-net tree obtained from 2.812 core gene sequence alignments. The dendrogram (i.e., a total of 1.977.984 nucleotides) regards the nine pseudomonad strains infecting Corylus avellana trees. The scale bar indicates the number of substitutions per nucleotide position. Bootstrap values are shown at the main nodes. No reticulation was observed between the Pseudomonas avellanae and P. syringae pathovar strains. In both trees, P. cannabina pv. alisalensis Pcal BS91 was included in the analysis as outgroup. Strain legend is shown in Table 1.

Mentions: The five newly sequenced genomes, together with those of the four other draft genomes of the pseudomonads infecting C. avellana trees, were cross-compared to determine their sequence similarity. The ANI value calculations, based on the MUMmer alignment of each sequence pair and the TETRA analysis are shown in Tables 2 and 3. The P. avellanae strains showed reciprocal ANI values ranging from 99.84% to 99.98%, whereas the P. syringae pathovar strains exhibited reciprocal values from 96.32% to 98.21%. When the draft genomes of the two groups were compared the reciprocal ANI values never exceeded 88% which was remarkably lower than the 95–96% used to determine a species boundary. The ML dendrogram referring to MLSA (Fig 1) and the neighbor-net network (S2 Fig), both performed with four concatenated housekeeping genes and a total of 6.846 nucleotides, indicated that the four P. avellanae strains clustered separately from the P. syringae pathovar strains as well as from the P. cannabina pv. alisalensis BS91 strain used as an outgroup. The P. avellanae strains clustered in a single clade, whereas each P. syringae pathovar strain exhibited a distinctive nucleotide profile. The consensus network with a cut-off value of 0,19 and based on 2.812 trees (Fig 2A) and the neighbor-net network based on 1.977.984 nucleotides (Fig 2B) also revealed that the two groups of strains clearly clustered separately with P. avellanae falling into one clade and the P. syringae pathovars exhibiting a separate bifurcation with no sign of reticulation. Collectively, these data strongly support the robust demarcation of the two groups of pseudomonads into two distinct clusters.


Comparative Genomic Analyses of Multiple Pseudomonas Strains Infecting Corylus avellana Trees Reveal the Occurrence of Two Genetic Clusters with Both Common and Distinctive Virulence and Fitness Traits.

Marcelletti S, Scortichini M - PLoS ONE (2015)

Split consensus network obtained from 2.812 trees for the nine pseudomonad strains infecting Corylus avellana.A. The tree has a cut-off value of 0.19. The scale bar indicates the number of substitutions per nucleotide position. Strain legend is shown in Table 1. No reticulation was observed between the Pseudomonas avellanae and P. syringae pathovar strains. B. Neighbor-net tree obtained from 2.812 core gene sequence alignments. The dendrogram (i.e., a total of 1.977.984 nucleotides) regards the nine pseudomonad strains infecting Corylus avellana trees. The scale bar indicates the number of substitutions per nucleotide position. Bootstrap values are shown at the main nodes. No reticulation was observed between the Pseudomonas avellanae and P. syringae pathovar strains. In both trees, P. cannabina pv. alisalensis Pcal BS91 was included in the analysis as outgroup. Strain legend is shown in Table 1.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4492584&req=5

pone.0131112.g002: Split consensus network obtained from 2.812 trees for the nine pseudomonad strains infecting Corylus avellana.A. The tree has a cut-off value of 0.19. The scale bar indicates the number of substitutions per nucleotide position. Strain legend is shown in Table 1. No reticulation was observed between the Pseudomonas avellanae and P. syringae pathovar strains. B. Neighbor-net tree obtained from 2.812 core gene sequence alignments. The dendrogram (i.e., a total of 1.977.984 nucleotides) regards the nine pseudomonad strains infecting Corylus avellana trees. The scale bar indicates the number of substitutions per nucleotide position. Bootstrap values are shown at the main nodes. No reticulation was observed between the Pseudomonas avellanae and P. syringae pathovar strains. In both trees, P. cannabina pv. alisalensis Pcal BS91 was included in the analysis as outgroup. Strain legend is shown in Table 1.
Mentions: The five newly sequenced genomes, together with those of the four other draft genomes of the pseudomonads infecting C. avellana trees, were cross-compared to determine their sequence similarity. The ANI value calculations, based on the MUMmer alignment of each sequence pair and the TETRA analysis are shown in Tables 2 and 3. The P. avellanae strains showed reciprocal ANI values ranging from 99.84% to 99.98%, whereas the P. syringae pathovar strains exhibited reciprocal values from 96.32% to 98.21%. When the draft genomes of the two groups were compared the reciprocal ANI values never exceeded 88% which was remarkably lower than the 95–96% used to determine a species boundary. The ML dendrogram referring to MLSA (Fig 1) and the neighbor-net network (S2 Fig), both performed with four concatenated housekeeping genes and a total of 6.846 nucleotides, indicated that the four P. avellanae strains clustered separately from the P. syringae pathovar strains as well as from the P. cannabina pv. alisalensis BS91 strain used as an outgroup. The P. avellanae strains clustered in a single clade, whereas each P. syringae pathovar strain exhibited a distinctive nucleotide profile. The consensus network with a cut-off value of 0,19 and based on 2.812 trees (Fig 2A) and the neighbor-net network based on 1.977.984 nucleotides (Fig 2B) also revealed that the two groups of strains clearly clustered separately with P. avellanae falling into one clade and the P. syringae pathovars exhibiting a separate bifurcation with no sign of reticulation. Collectively, these data strongly support the robust demarcation of the two groups of pseudomonads into two distinct clusters.

Bottom Line: Between these two clusters, no recombination event was found.Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae.By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin.

View Article: PubMed Central - PubMed

Affiliation: Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (C.R.A.)-Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, I-00134, Roma, Italy.

ABSTRACT
The European hazelnut (Corylus avellana) is threatened in Europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. A comparison of the draft genomes of nine Pseudomonas strains isolated from symptomatic C. avellana trees was performed to identify common and distinctive genomic traits. The thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: P. avellanae and P. syringae. The latter including the pathovars avellanae, coryli and syringae. Between these two clusters, no recombination event was found. A genomic island of approximately 20 kb, containing the hrp/hrc type III secretion system gene cluster, was found to be present without any genomic difference in all nine pseudomonads. The type III secretion system effector repertoires were remarkably different in the two groups, with P. avellanae showing a higher number of effectors. Homologue genes of the antimetabolite mangotoxin and ice nucleation activity clusters were found solely in all P. syringae pathovar strains, whereas the siderophore yersiniabactin was only present in P. avellanae. All nine strains have genes coding for pectic enzymes and sucrose metabolism. By contrast, they do not have genes coding for indolacetic acid and anti-insect toxin. Collectively, this study reveals that genomically different Pseudomonas can converge on the same host plant by suppressing the host defence mechanisms with the use of different virulence weapons. The integration into their genomes of a horizontally acquired genomic island could play a fundamental role in their evolution, perhaps giving them the ability to exploit new ecological niches.

No MeSH data available.


Related in: MedlinePlus