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Some strains that have converged to infect Prunus spp. trees are members of distinct Pseudomonas syringae genomospecies and ecotypes as revealed by in silico genomic comparison

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Abstract

A complementary taxonomic and population genetic study was performed to delineate genetically and ecologically distinct species within the Pseudomonas syringae complex by assessing 16 strains including pathovar strains that have converged to infect Prunus spp. trees, and two outgroups. Both average nucleotide identity and genome-to-genome distance comparison methods revealed the occurrence of distinct genomospecies, namely 1, 2, 3 and 8 (sensu Gardan et al.), with the latter two being closely related. Strains classified as P. s. pv. morsprunorum clustered into two distinct genomospecies, namely 2 and 8. Both the AdaptML and hierarchical Bayesian analysis of population structure methods highlighted the presence of three ecotypes, and the taxonomically related genomospecies 3 and 8 strains were members of the same ecotype. The distribution of pathogenic and virulence-associated genetic traits among Pseudomonas strains did not reveal any distinct type III secretion system effector or phytotoxin distribution pattern that characterized single genomospecies and strains that infect Prunus spp. The complete WHOP (Woody HOst and Pseudomonas spp.) genomic region and the entire β-ketoadipate gene cluster, including the catBCA operon, were found only in the members of genomospecies 2 and in the two P. s. pv. morsprunorum strains of genomospecies 8. A reduced gene flow between the three ecotypes suggested that point mutations played a larger role during the evolution of the strains than recombination. Our data support the idea that Prunus trees can be infected by different strains of distinct Pseudomonas genomospecies/ecotypes through diverse mechanisms of host colonization and infection. Such strains may represent particular lineages that emerged from environments other than that of the infected plant upon acquiring genetic traits that gave them the ability to cause plant diseases. The complementary assessment of bacterial strains using both taxonomic approaches and methods that reveal ecologically homogeneous populations has proven useful in confirming the cohesion of bacterial clusters.

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Acknowledgements

The study was funded by the ordinary budget of Council for Agricultural Research and Analysis of Agricultural Economics (CREA)−Research Centre for Olive, Fruit Trees and Citrus.

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  1. Council for Agricultural Research and Analysis of Agricultural Economics (CREA), Research Centre for Olive, Fruit Trees and Citrus, Via di Fioranello, 52, 00134, Rome, Italy

    Simone Marcelletti & Marco Scortichini

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  1. Simone Marcelletti
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  2. Marco Scortichini
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Correspondence to Marco Scortichini.

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Communicated by Yusuf Akhter.

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203_2018_1573_MOESM1_ESM.tif

Supplementary Figure 1. Genome-wide ML phylogeny of 16 Pseudomonas strains, including the strain that infect Prunus spp. trees (in red). Numbers at the node indicate the number of CDSs shared by the strain in the cluster. Horizontal bar colours: blue: core proteins of the 16 strains; red: genomospecies proteins, green: strain unique proteins. The genomospecies distribution (G) sensu Gardan et al. (1999) and Marcelletti and Scortichini (2014) is reported on the right. Table 1 provides the strain code. (TIF 98 KB)

203_2018_1573_MOESM2_ESM.tif

Supplementary Figure 2. Hierarchical BAPS clustering performed with 16 Pseudomonas strains assessed using ANIb and GGDC methods. Each colour represents an ecotype based on the genome sites not showing recombinant ancestry. G: genomospecies numbering according to Gardan et al. (1999) and Marcelletti and Scortichini (2014). (TIF 14 KB)

203_2018_1573_MOESM3_ESM.tif

Supplementary Figure 3. Distribution of the gene clusters involved in chitinase, β-ketoadipate and nitric oxide metabolism across 14 Pseudomonas strains. The strains that infect Prunus spp. trees are in red. Black box indicates presence. Table 1 provides the strain code. (TIF 157 KB)

203_2018_1573_MOESM4_ESM.tif

Supplementary Figure 4. Recombination network trees generated using SplitsTree4 from the alignment of 14 publicly available norR sequences of Pseudomonas strains (a) and from the eight Pseudomonas strains that infect Prunus spp. trees (b). The scale bar indicates the number of substitutions per nucleotide position. Table 1 provides the strain code. (TIF 3500 KB)

203_2018_1573_MOESM5_ESM.tif

Supplementary Figure 5. Recombination network trees generated using SplitsTree4 from the alignment of 14 publicly available xylA2 sequences of Pseudomonas strains (a) and from the eight Pseudomonas strains that infect Prunus spp. trees (b). The scale bar indicates the number of substitutions per nucleotide position. Table 1 provides the strain code. (TIF 3233 KB)

203_2018_1573_MOESM6_ESM.xls

Supplementary Table 1. Tetranucleotide frequency correlation coefficients (TETRA) values calculated between genomes of 16 Pseudomonas strains belonging to genomospecies 1, 2, 3, 6, 8 and 9. P. viridiflava UASWS0038 and P. cannabina pv. alisalensis BS91 were used as outgroups. (XLS 24 KB)

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Marcelletti, S., Scortichini, M. Some strains that have converged to infect Prunus spp. trees are members of distinct Pseudomonas syringae genomospecies and ecotypes as revealed by in silico genomic comparison. Arch Microbiol 201, 67–80 (2019). https://doi.org/10.1007/s00203-018-1573-4

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