Limits...
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

Recombination networks regarding four housekeeping genes of the nine pseudomonad strains infecting Corylus avellana trees.The networks were built using gapA, gltA, gyrB, rpoD genes. Strain legend is shown in Table 1. The scale bar indicates the number of substitutions per nucleotide position. Strong signal of recombination are present solely between the Pseudomonas syringae pathovars. P. cannabina pv. alisalensis Pcal BS91 was included in the analysis as outgroup.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131112.g003: Recombination networks regarding four housekeeping genes of the nine pseudomonad strains infecting Corylus avellana trees.The networks were built using gapA, gltA, gyrB, rpoD genes. Strain legend is shown in Table 1. The scale bar indicates the number of substitutions per nucleotide position. Strong signal of recombination are present solely between the Pseudomonas syringae pathovars. P. cannabina pv. alisalensis Pcal BS91 was included in the analysis as outgroup.

Mentions: Neither the consensus nor the neighbor-net networks built with 2.812 trees and 1.977.984 nucleotides, respectively, revealed any reticulation between the strains belonging to the P. avellanae and P. syringae clusters (Fig 2A and 2B and S2 Fig). Additionally, the recombination networks performed with the four housekeeping genes using the Split Tree 4 software did not identify any reticulation between the two groups. By contrast, signs of recombination events were evident in each of the housekeeping genes assessed here from the P. syringae pathovars avellanae, coryli and syringae strains infecting C. avellana (Fig 3). GARD analysis confirmed the absence of recombination between the P. avellanae and P. syringae strains. The coalescent tree obtained from the Clonal Frame (S3 Fig) revealed the same clustering as that observed with MLSA. In fact, the P. avellanae strains clustered separately from the P. syringae pathovar strains, thus revealing two distinct clonal complexes. According to the Clonal Frame analysis, the four P. avellanae strains coalesced at the same time (coalescent unit of 2.88), whereas the P syringae pathovars strains showed different coalescent times, with a species coalescent unit of 2.60. No recent common ancestor was found for the two clusters. The gene flow measured using the fixation index (FST) and calculated with the four housekeeping genes ranged from 0.882 to 0.907. These high values confirmed the distinctiveness of the two groups. Additionally, the McDonald-Kreitman (MK) tests for adaptive divergence between P. avellanae and the P. syringae pathovars avellanae, coryli and syringae strains run on the four housekeeping genes did not reveal any evidence of positive selection.


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)

Recombination networks regarding four housekeeping genes of the nine pseudomonad strains infecting Corylus avellana trees.The networks were built using gapA, gltA, gyrB, rpoD genes. Strain legend is shown in Table 1. The scale bar indicates the number of substitutions per nucleotide position. Strong signal of recombination are present solely between the Pseudomonas syringae pathovars. P. cannabina pv. alisalensis Pcal BS91 was included in the analysis as outgroup.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492584&req=5

pone.0131112.g003: Recombination networks regarding four housekeeping genes of the nine pseudomonad strains infecting Corylus avellana trees.The networks were built using gapA, gltA, gyrB, rpoD genes. Strain legend is shown in Table 1. The scale bar indicates the number of substitutions per nucleotide position. Strong signal of recombination are present solely between the Pseudomonas syringae pathovars. P. cannabina pv. alisalensis Pcal BS91 was included in the analysis as outgroup.
Mentions: Neither the consensus nor the neighbor-net networks built with 2.812 trees and 1.977.984 nucleotides, respectively, revealed any reticulation between the strains belonging to the P. avellanae and P. syringae clusters (Fig 2A and 2B and S2 Fig). Additionally, the recombination networks performed with the four housekeeping genes using the Split Tree 4 software did not identify any reticulation between the two groups. By contrast, signs of recombination events were evident in each of the housekeeping genes assessed here from the P. syringae pathovars avellanae, coryli and syringae strains infecting C. avellana (Fig 3). GARD analysis confirmed the absence of recombination between the P. avellanae and P. syringae strains. The coalescent tree obtained from the Clonal Frame (S3 Fig) revealed the same clustering as that observed with MLSA. In fact, the P. avellanae strains clustered separately from the P. syringae pathovar strains, thus revealing two distinct clonal complexes. According to the Clonal Frame analysis, the four P. avellanae strains coalesced at the same time (coalescent unit of 2.88), whereas the P syringae pathovars strains showed different coalescent times, with a species coalescent unit of 2.60. No recent common ancestor was found for the two clusters. The gene flow measured using the fixation index (FST) and calculated with the four housekeeping genes ranged from 0.882 to 0.907. These high values confirmed the distinctiveness of the two groups. Additionally, the McDonald-Kreitman (MK) tests for adaptive divergence between P. avellanae and the P. syringae pathovars avellanae, coryli and syringae strains run on the four housekeeping genes did not reveal any evidence of positive selection.

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