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Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas -specific and rpo D genes

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ABSTRACT

Phylogenetic relationship of 22 FLPs was revealed on the basis of polymorphism in three genes namely 16S rDNA, Pseudomonas-specific and rpoD gene regions. The primers for 16S rDNA, Pseudomonas-specific region and rpoD gene region were amplifying a region of 1492, 990 and 760 bp, respectively, from all the isolates investigated. The RFLP analysis of the PCR products resulted in a classification of these fluorescent pseudomonads which was best answered by rpoD-based RFLP analysis. The 22 FLPs were placed in two major clusters and seven subclusters suggesting that these were genotypically heterogenous and might belong to several species within Pseudomonas sensu stricto. Sequence analysis of these three genes for three selected isolates AS5, AS7 and AS15 showed 16S rDNA and Pseudomonas-specific gene region phylogenies were generally similar, but rpoD gene phylogeny was somewhat different from these two genes. These results were also congruent with the results of RFLP of these three genes. rpoD provided comparable phylogenetic resolution to that of the 16S rRNA and Pseudomonas-specific genes at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoD could complement and better justify the information provided by the 16S rRNA gene. Hence rpoD can be used further as an evolutionary chronometer for species-level identification.

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Neighbour-joining phylogenetic tree based on rpoD gene sequences (736 nt) Pseudomonas aeruginosa strain AS5 KM593260, Pseudomonas aeruginosa strain AS15 KM593262 and Pseudomonas fluorescens strain AS15 KM593261 and the type strains of closely related species of the genus Pseudomonas. Bootstrap values (expressed as percentages of 1000 replications) are shown at branch points. Bar 2 nt substitutions per 100 nt
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Fig6: Neighbour-joining phylogenetic tree based on rpoD gene sequences (736 nt) Pseudomonas aeruginosa strain AS5 KM593260, Pseudomonas aeruginosa strain AS15 KM593262 and Pseudomonas fluorescens strain AS15 KM593261 and the type strains of closely related species of the genus Pseudomonas. Bootstrap values (expressed as percentages of 1000 replications) are shown at branch points. Bar 2 nt substitutions per 100 nt

Mentions: The topology of the tree reconstructed from the rpoD gene sequences was different from those obtained from 16S rRNA and Pseudomonas-specific gene (Tayeb et al. 2005; Mulet et al. 2009, 2010, 2012; Ramos et al. 2013; Toro et al. 2013). When the whole rpoD sequences from the three tested strains were used for the analysis, these were arranged into two major clusters. The rpoD gene phylogenetic tree showed that strains AS5 and AS7 (P.aeruginosa) were clustered in a separate branch from other strains of genus Pseudomonas. Strain AS15 (P.fluorescens) earlier grouped in a same branch with P.aeruginosa (in 16S rRNA and Pseudomonas-specific gene phylogenies), was now placed in a separate branch. Now the closest relatives of AS15 were P.brenneri and P.gessardii. In this phylogenetic tree P.fluorescens and P.aeruginosa isolates were placed separately into two different branches (Fig. 6).Fig. 6


Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas -specific and rpo D genes
Neighbour-joining phylogenetic tree based on rpoD gene sequences (736 nt) Pseudomonas aeruginosa strain AS5 KM593260, Pseudomonas aeruginosa strain AS15 KM593262 and Pseudomonas fluorescens strain AS15 KM593261 and the type strains of closely related species of the genus Pseudomonas. Bootstrap values (expressed as percentages of 1000 replications) are shown at branch points. Bar 2 nt substitutions per 100 nt
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4764612&req=5

Fig6: Neighbour-joining phylogenetic tree based on rpoD gene sequences (736 nt) Pseudomonas aeruginosa strain AS5 KM593260, Pseudomonas aeruginosa strain AS15 KM593262 and Pseudomonas fluorescens strain AS15 KM593261 and the type strains of closely related species of the genus Pseudomonas. Bootstrap values (expressed as percentages of 1000 replications) are shown at branch points. Bar 2 nt substitutions per 100 nt
Mentions: The topology of the tree reconstructed from the rpoD gene sequences was different from those obtained from 16S rRNA and Pseudomonas-specific gene (Tayeb et al. 2005; Mulet et al. 2009, 2010, 2012; Ramos et al. 2013; Toro et al. 2013). When the whole rpoD sequences from the three tested strains were used for the analysis, these were arranged into two major clusters. The rpoD gene phylogenetic tree showed that strains AS5 and AS7 (P.aeruginosa) were clustered in a separate branch from other strains of genus Pseudomonas. Strain AS15 (P.fluorescens) earlier grouped in a same branch with P.aeruginosa (in 16S rRNA and Pseudomonas-specific gene phylogenies), was now placed in a separate branch. Now the closest relatives of AS15 were P.brenneri and P.gessardii. In this phylogenetic tree P.fluorescens and P.aeruginosa isolates were placed separately into two different branches (Fig. 6).Fig. 6

View Article: PubMed Central - PubMed

ABSTRACT

Phylogenetic relationship of 22 FLPs was revealed on the basis of polymorphism in three genes namely 16S rDNA, Pseudomonas-specific and rpoD gene regions. The primers for 16S rDNA, Pseudomonas-specific region and rpoD gene region were amplifying a region of 1492, 990 and 760 bp, respectively, from all the isolates investigated. The RFLP analysis of the PCR products resulted in a classification of these fluorescent pseudomonads which was best answered by rpoD-based RFLP analysis. The 22 FLPs were placed in two major clusters and seven subclusters suggesting that these were genotypically heterogenous and might belong to several species within Pseudomonas sensu stricto. Sequence analysis of these three genes for three selected isolates AS5, AS7 and AS15 showed 16S rDNA and Pseudomonas-specific gene region phylogenies were generally similar, but rpoD gene phylogeny was somewhat different from these two genes. These results were also congruent with the results of RFLP of these three genes. rpoD provided comparable phylogenetic resolution to that of the 16S rRNA and Pseudomonas-specific genes at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoD could complement and better justify the information provided by the 16S rRNA gene. Hence rpoD can be used further as an evolutionary chronometer for species-level identification.

No MeSH data available.


Related in: MedlinePlus