Limits...
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 genome of rice-infecting Pseudomonas harbor high level of structural polymorphism.Global comparison of eight rice-infecting Pseudomonas draft genomes using BLASTn. The inner most ring corresponds to the genomic position at IRRI 6609. The second and third rings indicate G+C content and G+C skew, respectively. The rest of the rings indicate presence and absence portions of the eight rice-infecting Pseudomonas draft genomes against IRRI 6609. Solid colors represent genomic regions with hits while white spaced represent gaps. P. fuscovaginae (Pfv) and P. fuscovaginae-like (Pfv-like) strains are depicted. Sequence identity is related to color intensity. Also included are locations of four intact prophage insertions found in Pfv-like IRRI 6609 (S4 Fig). The global alignment was visualized using BRIG [43].
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4589537&req=5

pone.0139256.g003: The genome of rice-infecting Pseudomonas harbor high level of structural polymorphism.Global comparison of eight rice-infecting Pseudomonas draft genomes using BLASTn. The inner most ring corresponds to the genomic position at IRRI 6609. The second and third rings indicate G+C content and G+C skew, respectively. The rest of the rings indicate presence and absence portions of the eight rice-infecting Pseudomonas draft genomes against IRRI 6609. Solid colors represent genomic regions with hits while white spaced represent gaps. P. fuscovaginae (Pfv) and P. fuscovaginae-like (Pfv-like) strains are depicted. Sequence identity is related to color intensity. Also included are locations of four intact prophage insertions found in Pfv-like IRRI 6609 (S4 Fig). The global alignment was visualized using BRIG [43].

Mentions: A significant variation in the genomic composition of Pseudomonas groups has been reported recently [20, 64] and previous studies on Pfv have also found important genetic and biochemical variations among strains from different parts of the world [10, 35]. To understand the genome structure of rice-infecting Pseudomonas pathogens, we performed a comparative genomics analysis on eight draft genome datasets (Table 1). Whole genome alignments showed a high level of polymorphism among strains of Pfv and Pfv-like (Fig 3). Many syntenic blocks were interrupted by insertions, deletions, and rearrangements. A closer comparison of the eight genomes in terms of percentage of nucleotide identity and orthologous genes can be found in Table 2. Although Pfv and Pfv-like genomes appear to have many syntenic regions (Fig 3), our structural and gene content assessments illustrate a large degree of genomic diversity in Pfv-like strains. Loper et al. [20] also found a similar pattern when they analyzed members of the P. fluorescens subgroup that are closely related or belonged to the same taxa.


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 genome of rice-infecting Pseudomonas harbor high level of structural polymorphism.Global comparison of eight rice-infecting Pseudomonas draft genomes using BLASTn. The inner most ring corresponds to the genomic position at IRRI 6609. The second and third rings indicate G+C content and G+C skew, respectively. The rest of the rings indicate presence and absence portions of the eight rice-infecting Pseudomonas draft genomes against IRRI 6609. Solid colors represent genomic regions with hits while white spaced represent gaps. P. fuscovaginae (Pfv) and P. fuscovaginae-like (Pfv-like) strains are depicted. Sequence identity is related to color intensity. Also included are locations of four intact prophage insertions found in Pfv-like IRRI 6609 (S4 Fig). The global alignment was visualized using BRIG [43].
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139256.g003: The genome of rice-infecting Pseudomonas harbor high level of structural polymorphism.Global comparison of eight rice-infecting Pseudomonas draft genomes using BLASTn. The inner most ring corresponds to the genomic position at IRRI 6609. The second and third rings indicate G+C content and G+C skew, respectively. The rest of the rings indicate presence and absence portions of the eight rice-infecting Pseudomonas draft genomes against IRRI 6609. Solid colors represent genomic regions with hits while white spaced represent gaps. P. fuscovaginae (Pfv) and P. fuscovaginae-like (Pfv-like) strains are depicted. Sequence identity is related to color intensity. Also included are locations of four intact prophage insertions found in Pfv-like IRRI 6609 (S4 Fig). The global alignment was visualized using BRIG [43].
Mentions: A significant variation in the genomic composition of Pseudomonas groups has been reported recently [20, 64] and previous studies on Pfv have also found important genetic and biochemical variations among strains from different parts of the world [10, 35]. To understand the genome structure of rice-infecting Pseudomonas pathogens, we performed a comparative genomics analysis on eight draft genome datasets (Table 1). Whole genome alignments showed a high level of polymorphism among strains of Pfv and Pfv-like (Fig 3). Many syntenic blocks were interrupted by insertions, deletions, and rearrangements. A closer comparison of the eight genomes in terms of percentage of nucleotide identity and orthologous genes can be found in Table 2. Although Pfv and Pfv-like genomes appear to have many syntenic regions (Fig 3), our structural and gene content assessments illustrate a large degree of genomic diversity in Pfv-like strains. Loper et al. [20] also found a similar pattern when they analyzed members of the P. fluorescens subgroup that are closely related or belonged to the same taxa.

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