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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

Phylogenetic relationships of the genomes of strains B301D and HS191 to other Pseudomonas species and pathovars. The maximum likelihood tree was constructed using concatenated alignments of 10 housekeeping genes: acsA, aroE, dnaE, guaA, gyrB, mutL, ppsA, pyrC, recA, and rpoB. The MrBayes package (Ronquist and Huelsenbeck 2003) was used to calculate the clade credibility values shown as values within interior nodes. Strains of Pseudomonas syringae in genomospecies 1 are indicated by the outside bracket and the strains originating from monocot and dicot hosts are as indicated by two inside brackets. Strains B301D and HS191 that were sequenced in this study are shown in red, enlarged lettering. The outgroup genome sequence used was Escherichia coli K-12 substrain MG1655.
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fig01: Phylogenetic relationships of the genomes of strains B301D and HS191 to other Pseudomonas species and pathovars. The maximum likelihood tree was constructed using concatenated alignments of 10 housekeeping genes: acsA, aroE, dnaE, guaA, gyrB, mutL, ppsA, pyrC, recA, and rpoB. The MrBayes package (Ronquist and Huelsenbeck 2003) was used to calculate the clade credibility values shown as values within interior nodes. Strains of Pseudomonas syringae in genomospecies 1 are indicated by the outside bracket and the strains originating from monocot and dicot hosts are as indicated by two inside brackets. Strains B301D and HS191 that were sequenced in this study are shown in red, enlarged lettering. The outgroup genome sequence used was Escherichia coli K-12 substrain MG1655.

Mentions: The evolutionary position of P. syringae pv. syringae strains B301D and HS191 relative to other pathovars and species of Pseudomonas was determined by multi-locus sequence analysis (MLSA) using methods described previously (Loper et al. 2012). Several strains selected for phylogenetic analysis were available as draft genome sequences, but they contained the full housekeeping gene sequences necessary for MLSA. Genomospecies 1 was represented by P. syringae pv. syringae strains SM, B64, BRIP 34876, BRIP 34881, and BRIP 39023 (Gardiner et al. 2013; Dudnik and Dudler 2014b) in addition to B728a (Feil et al. 2005). The other Pseudomonas strains used in the analysis are listed in Figure1. The MLSA data is based on phylogenetic analysis of the DNA sequences of 10 housekeeping genes (i.e., acsA, aroE, dnaE, guaA, gyrB, mutL, ppsA, pyrC, recA, and rpoB) obtained in this study or available at the NCBI GenBank database. DNA sequences were aligned by concatenation using the MEGA5 program (Tamura et al. 2011) with default settings. Maximum Likelihood analysis was performed for 1000 bootstrap replications using the equally weighted heuristic search option in PAUP v4.0 (Swofford 2002). A general time-reversible model with variable sites and discrete gamma distribution (GTR+I+G) as a best-fit model was selected by Akaike Information Criterion (AIC) in MrModeltest v2.3 (Nylander 2004). Bayesian analyses were run for 3,500,000 generations for housekeeping genes, performed in MrBayes v3.1.2 (Ronquist and Huelsenbeck 2003). Posterior probability (PP) values were subsequently calculated. Every 100th tree after stabilization (burn-in) was sampled to calculate a 50% majority rule consensus tree. The final phylogenetic tree was constructed using the program FigTree v1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/).


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)

Phylogenetic relationships of the genomes of strains B301D and HS191 to other Pseudomonas species and pathovars. The maximum likelihood tree was constructed using concatenated alignments of 10 housekeeping genes: acsA, aroE, dnaE, guaA, gyrB, mutL, ppsA, pyrC, recA, and rpoB. The MrBayes package (Ronquist and Huelsenbeck 2003) was used to calculate the clade credibility values shown as values within interior nodes. Strains of Pseudomonas syringae in genomospecies 1 are indicated by the outside bracket and the strains originating from monocot and dicot hosts are as indicated by two inside brackets. Strains B301D and HS191 that were sequenced in this study are shown in red, enlarged lettering. The outgroup genome sequence used was Escherichia coli K-12 substrain MG1655.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig01: Phylogenetic relationships of the genomes of strains B301D and HS191 to other Pseudomonas species and pathovars. The maximum likelihood tree was constructed using concatenated alignments of 10 housekeeping genes: acsA, aroE, dnaE, guaA, gyrB, mutL, ppsA, pyrC, recA, and rpoB. The MrBayes package (Ronquist and Huelsenbeck 2003) was used to calculate the clade credibility values shown as values within interior nodes. Strains of Pseudomonas syringae in genomospecies 1 are indicated by the outside bracket and the strains originating from monocot and dicot hosts are as indicated by two inside brackets. Strains B301D and HS191 that were sequenced in this study are shown in red, enlarged lettering. The outgroup genome sequence used was Escherichia coli K-12 substrain MG1655.
Mentions: The evolutionary position of P. syringae pv. syringae strains B301D and HS191 relative to other pathovars and species of Pseudomonas was determined by multi-locus sequence analysis (MLSA) using methods described previously (Loper et al. 2012). Several strains selected for phylogenetic analysis were available as draft genome sequences, but they contained the full housekeeping gene sequences necessary for MLSA. Genomospecies 1 was represented by P. syringae pv. syringae strains SM, B64, BRIP 34876, BRIP 34881, and BRIP 39023 (Gardiner et al. 2013; Dudnik and Dudler 2014b) in addition to B728a (Feil et al. 2005). The other Pseudomonas strains used in the analysis are listed in Figure1. The MLSA data is based on phylogenetic analysis of the DNA sequences of 10 housekeeping genes (i.e., acsA, aroE, dnaE, guaA, gyrB, mutL, ppsA, pyrC, recA, and rpoB) obtained in this study or available at the NCBI GenBank database. DNA sequences were aligned by concatenation using the MEGA5 program (Tamura et al. 2011) with default settings. Maximum Likelihood analysis was performed for 1000 bootstrap replications using the equally weighted heuristic search option in PAUP v4.0 (Swofford 2002). A general time-reversible model with variable sites and discrete gamma distribution (GTR+I+G) as a best-fit model was selected by Akaike Information Criterion (AIC) in MrModeltest v2.3 (Nylander 2004). Bayesian analyses were run for 3,500,000 generations for housekeeping genes, performed in MrBayes v3.1.2 (Ronquist and Huelsenbeck 2003). Posterior probability (PP) values were subsequently calculated. Every 100th tree after stabilization (burn-in) was sampled to calculate a 50% majority rule consensus tree. The final phylogenetic tree was constructed using the program FigTree v1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/).

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