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Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

Quibod IL, Grande G, Oreiro EG, Borja FN, Dossa GS, Mauleon R, Cruz CV, Oliva R - PLoS ONE (2015)

Bottom Line: Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world.Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism.The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

View Article: PubMed Central - PubMed

Affiliation: Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.

ABSTRACT
Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

No MeSH data available.


Related in: MedlinePlus

The core secretome of rice-infecting Pseudomonas has signatures of positive selection.Distribution of Ka/Ks ratio for 123 protein-coding genes, calculated with Yn00 [59] method on rice-infecting Pseudomonas-all (black, P-all, n = 8), P. fuscovaginae (blue, Pfv, n = 5), and P. fuscovaginae-like (orange, Pfv-like, n = 3) datasets. All secreted protein selected on this graph have p-values ≤ 0.01.
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pone.0139256.g008: The core secretome of rice-infecting Pseudomonas has signatures of positive selection.Distribution of Ka/Ks ratio for 123 protein-coding genes, calculated with Yn00 [59] method on rice-infecting Pseudomonas-all (black, P-all, n = 8), P. fuscovaginae (blue, Pfv, n = 5), and P. fuscovaginae-like (orange, Pfv-like, n = 3) datasets. All secreted protein selected on this graph have p-values ≤ 0.01.

Mentions: A common feature of effector genes from plant pathogenic microbes is the strong signature of positive selection [84–86]. To characterize the selection pressures underlying the Pfv and Pfv-like core secretome and to identify candidate effector genes, we calculated Ka/Ks ratio using Yn00 [59] on alignments of 123 orthologous loci across the eight genomes. Using a cutoff p-value of 95%, we found that Ka value was greater than Ks (ω = Ka/Ks > 1) in 75 of 123 genes (Fig 8). We obtained ω values ranging from 0.45 to 4.0 (average of 2.4). When we analyzed each group separately, Pfv secretome ω values ranged from 0.37 to 3.76 (average of 1.65) while Pfv-like ranged from 0.14 to 0.8 (average of 0.48) (Fig 8). Among the 75 selected genes, we found high ω values in 3 out of 13 genes that were specific to rice-infecting Pseudomonas (Fig 8). This result shows significant differences in the number of genes under selection between Pfv and Pfv-like. Whether this difference is due to variation in selection pressure or sampling bias between groups is still unknown. Collectively, our findings point out that natural selection is continuously shaping the secreted repertoire of the rice-infecting Pseudomonas, which is a common pattern for other Pseudomonas pathogens [85, 87].


Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot.

Quibod IL, Grande G, Oreiro EG, Borja FN, Dossa GS, Mauleon R, Cruz CV, Oliva R - PLoS ONE (2015)

The core secretome of rice-infecting Pseudomonas has signatures of positive selection.Distribution of Ka/Ks ratio for 123 protein-coding genes, calculated with Yn00 [59] method on rice-infecting Pseudomonas-all (black, P-all, n = 8), P. fuscovaginae (blue, Pfv, n = 5), and P. fuscovaginae-like (orange, Pfv-like, n = 3) datasets. All secreted protein selected on this graph have p-values ≤ 0.01.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4589537&req=5

pone.0139256.g008: The core secretome of rice-infecting Pseudomonas has signatures of positive selection.Distribution of Ka/Ks ratio for 123 protein-coding genes, calculated with Yn00 [59] method on rice-infecting Pseudomonas-all (black, P-all, n = 8), P. fuscovaginae (blue, Pfv, n = 5), and P. fuscovaginae-like (orange, Pfv-like, n = 3) datasets. All secreted protein selected on this graph have p-values ≤ 0.01.
Mentions: A common feature of effector genes from plant pathogenic microbes is the strong signature of positive selection [84–86]. To characterize the selection pressures underlying the Pfv and Pfv-like core secretome and to identify candidate effector genes, we calculated Ka/Ks ratio using Yn00 [59] on alignments of 123 orthologous loci across the eight genomes. Using a cutoff p-value of 95%, we found that Ka value was greater than Ks (ω = Ka/Ks > 1) in 75 of 123 genes (Fig 8). We obtained ω values ranging from 0.45 to 4.0 (average of 2.4). When we analyzed each group separately, Pfv secretome ω values ranged from 0.37 to 3.76 (average of 1.65) while Pfv-like ranged from 0.14 to 0.8 (average of 0.48) (Fig 8). Among the 75 selected genes, we found high ω values in 3 out of 13 genes that were specific to rice-infecting Pseudomonas (Fig 8). This result shows significant differences in the number of genes under selection between Pfv and Pfv-like. Whether this difference is due to variation in selection pressure or sampling bias between groups is still unknown. Collectively, our findings point out that natural selection is continuously shaping the secreted repertoire of the rice-infecting Pseudomonas, which is a common pattern for other Pseudomonas pathogens [85, 87].

Bottom Line: Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world.Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism.The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

View Article: PubMed Central - PubMed

Affiliation: Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines.

ABSTRACT
Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

No MeSH data available.


Related in: MedlinePlus