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Comparative genomics of Pseudomonas syringae pv. syringae strains B301D and HS191 and insights into intrapathovar traits associated with plant pathogenesis.

Ravindran A, Jalan N, Yuan JS, Wang N, Gross DC - Microbiologyopen (2015)

Bottom Line: Differences are observed in the type III effector composition for the three strains that likely influences host range.The HS191 genome had the largest number at 25 of effector genes, and seven effector genes are specific to this monocot strain.Toxin production is another major trait associated with virulence of P. syringae pv. syringae, and HS191 is distinguished by genes for production of syringopeptin SP25 and mangotoxin.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, 77843-2132.

No MeSH data available.


Related in: MedlinePlus

Circular representation of three genome comparisons using the BLAST Ring Image Generator (BRIG) software (Alikhan et al. 2011). The inner scales designate the coordinates in kilobase pairs (kbp). White spaces indicate regions with no identity to the reference genome. The gene clusters absent in B301D are indicated by a red arrow, clusters absent in HS191 are indicated by a green arrow, clusters absent in B728a are indicated by a purple arrow, and clusters absent in both the query genomes are indicated by a black arrow. (A) B728a genome (center) compared against the genomes of B301D (Ring 1 in red) and HS191 (Ring 2 in green). (B) B301D genome (center) compared against the genomes of B3728a (Ring 1 in purple) and HS191 (Ring 2 in green). (C) HS191 genome (center) compared against the genomes of B728a (Ring 1 in purple) and B301D (Ring 2 in red). Relative shading density (from darker to lighter) within each circle represents relative levels of nucleotide homology.
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fig03: Circular representation of three genome comparisons using the BLAST Ring Image Generator (BRIG) software (Alikhan et al. 2011). The inner scales designate the coordinates in kilobase pairs (kbp). White spaces indicate regions with no identity to the reference genome. The gene clusters absent in B301D are indicated by a red arrow, clusters absent in HS191 are indicated by a green arrow, clusters absent in B728a are indicated by a purple arrow, and clusters absent in both the query genomes are indicated by a black arrow. (A) B728a genome (center) compared against the genomes of B301D (Ring 1 in red) and HS191 (Ring 2 in green). (B) B301D genome (center) compared against the genomes of B3728a (Ring 1 in purple) and HS191 (Ring 2 in green). (C) HS191 genome (center) compared against the genomes of B728a (Ring 1 in purple) and B301D (Ring 2 in red). Relative shading density (from darker to lighter) within each circle represents relative levels of nucleotide homology.

Mentions: BRIG analysis was used to compare the genomes of B728a, B301D, and HS191 to identify large genome regions that are absent in one or more of these strains (Fig.3A–C). Seven B728a genomic regions, ranging in size from 8.7 to 81.0 kb, are absent in both strains B301D and HS191 (labeled in Fig.3A as Psyr_0733 to 0750, Psyr_0919 to 0938, Psyr_2623 to 2688, Psyr_3074 to 3090, Psyr_3804 to 3818, Psyr_4509 to 4517, and Psyr_4643 to 4659). Although these regions in B728a primarily carry genes of unknown function, three of the regions carry a type III effector gene (avrRpm1, Psyr_0738; hopAF1, Psyr_3813; hopAB1, Psyr_4659). It was noted, however, that the HS191 genome carries the hopAF1 gene (PsyrH_07325), but lacks the surrounding genes observed in B728a (Psyr_3804 to 3818). In addition, the B301D genome lacks a 109.1 kb B728a region (Psyr_1426 to 1534) and an 85.3 kb HS191 region (PsyrH_22675 to 23150) containing several genes of unknown function, and a few genes associated with type IV secretion. A ∼50 kb region, associated with a temperate phage conserved in B728a (Psyr_2759 to 2823) and B301D (PsyrB_13920 to 14250), is absent in the HS191 genome. HS191 also lacks a second gene cluster of unknown function estimated to be ∼18 kb in strains B728a (Psyr_2546 to 2564) and B301D (PsyrB_12905 to 12990).


Comparative genomics of Pseudomonas syringae pv. syringae strains B301D and HS191 and insights into intrapathovar traits associated with plant pathogenesis.

Ravindran A, Jalan N, Yuan JS, Wang N, Gross DC - Microbiologyopen (2015)

Circular representation of three genome comparisons using the BLAST Ring Image Generator (BRIG) software (Alikhan et al. 2011). The inner scales designate the coordinates in kilobase pairs (kbp). White spaces indicate regions with no identity to the reference genome. The gene clusters absent in B301D are indicated by a red arrow, clusters absent in HS191 are indicated by a green arrow, clusters absent in B728a are indicated by a purple arrow, and clusters absent in both the query genomes are indicated by a black arrow. (A) B728a genome (center) compared against the genomes of B301D (Ring 1 in red) and HS191 (Ring 2 in green). (B) B301D genome (center) compared against the genomes of B3728a (Ring 1 in purple) and HS191 (Ring 2 in green). (C) HS191 genome (center) compared against the genomes of B728a (Ring 1 in purple) and B301D (Ring 2 in red). Relative shading density (from darker to lighter) within each circle represents relative levels of nucleotide homology.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4554452&req=5

fig03: Circular representation of three genome comparisons using the BLAST Ring Image Generator (BRIG) software (Alikhan et al. 2011). The inner scales designate the coordinates in kilobase pairs (kbp). White spaces indicate regions with no identity to the reference genome. The gene clusters absent in B301D are indicated by a red arrow, clusters absent in HS191 are indicated by a green arrow, clusters absent in B728a are indicated by a purple arrow, and clusters absent in both the query genomes are indicated by a black arrow. (A) B728a genome (center) compared against the genomes of B301D (Ring 1 in red) and HS191 (Ring 2 in green). (B) B301D genome (center) compared against the genomes of B3728a (Ring 1 in purple) and HS191 (Ring 2 in green). (C) HS191 genome (center) compared against the genomes of B728a (Ring 1 in purple) and B301D (Ring 2 in red). Relative shading density (from darker to lighter) within each circle represents relative levels of nucleotide homology.
Mentions: BRIG analysis was used to compare the genomes of B728a, B301D, and HS191 to identify large genome regions that are absent in one or more of these strains (Fig.3A–C). Seven B728a genomic regions, ranging in size from 8.7 to 81.0 kb, are absent in both strains B301D and HS191 (labeled in Fig.3A as Psyr_0733 to 0750, Psyr_0919 to 0938, Psyr_2623 to 2688, Psyr_3074 to 3090, Psyr_3804 to 3818, Psyr_4509 to 4517, and Psyr_4643 to 4659). Although these regions in B728a primarily carry genes of unknown function, three of the regions carry a type III effector gene (avrRpm1, Psyr_0738; hopAF1, Psyr_3813; hopAB1, Psyr_4659). It was noted, however, that the HS191 genome carries the hopAF1 gene (PsyrH_07325), but lacks the surrounding genes observed in B728a (Psyr_3804 to 3818). In addition, the B301D genome lacks a 109.1 kb B728a region (Psyr_1426 to 1534) and an 85.3 kb HS191 region (PsyrH_22675 to 23150) containing several genes of unknown function, and a few genes associated with type IV secretion. A ∼50 kb region, associated with a temperate phage conserved in B728a (Psyr_2759 to 2823) and B301D (PsyrB_13920 to 14250), is absent in the HS191 genome. HS191 also lacks a second gene cluster of unknown function estimated to be ∼18 kb in strains B728a (Psyr_2546 to 2564) and B301D (PsyrB_12905 to 12990).

Bottom Line: Differences are observed in the type III effector composition for the three strains that likely influences host range.The HS191 genome had the largest number at 25 of effector genes, and seven effector genes are specific to this monocot strain.Toxin production is another major trait associated with virulence of P. syringae pv. syringae, and HS191 is distinguished by genes for production of syringopeptin SP25 and mangotoxin.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, 77843-2132.

No MeSH data available.


Related in: MedlinePlus