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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.

No MeSH data available.


Combined UPGMA dendrogram of Pseudomonas-specific gene region of FLPs on the basis of ARDRA with AluI, RsaI and BamHI
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Fig2: Combined UPGMA dendrogram of Pseudomonas-specific gene region of FLPs on the basis of ARDRA with AluI, RsaI and BamHI

Mentions: The phylogenetic trees obtained from 16SrRNA and Pseudomonas-specific genes were almost similar. Cluster I and II delineated in both the dendrogram (Figs. 1, 2), but their relationships within subclusters were modified. Isolate AS9 which was the sole representative of SCII of CI in 16S rDNA-based dendrogram was now placed in SCI of CI along with AS1 and AS2 in dendrogram obtained by Pseudomonas-specific gene region. Also isolates AS16, AS20, AS21 and AS22 presented in SCI shifted to SCIII in Pseudomonas-specific gene region-based dendrogram. Isolates AS5, AS6 and AS7 presented as SCIII in 16S rDNA-based dendrogram were now placed in a new position as SCII. Similarly, isolates AS8, AS17, AS19 and AS10, AS11, AS14, AS18 were representing two subclusters SC V (AS8, AS17, AS19) and SC VI (AS10, AS11, AS14, AS18) in Pseudomonas-specific gene region-based dendrogram while these were arranged within three subclusters in 16S rDNA-based dendrogram SC V (AS10 and AS14), SC VI (AS8, AS17 and AS19) and SC VII (AS11 and AS18).Fig. 1


Phylogenetic relationships of fluorescent pseudomonads deduced from the sequence analysis of 16S rRNA, Pseudomonas -specific and rpo D genes
Combined UPGMA dendrogram of Pseudomonas-specific gene region of FLPs on the basis of ARDRA with AluI, RsaI and BamHI
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Combined UPGMA dendrogram of Pseudomonas-specific gene region of FLPs on the basis of ARDRA with AluI, RsaI and BamHI
Mentions: The phylogenetic trees obtained from 16SrRNA and Pseudomonas-specific genes were almost similar. Cluster I and II delineated in both the dendrogram (Figs. 1, 2), but their relationships within subclusters were modified. Isolate AS9 which was the sole representative of SCII of CI in 16S rDNA-based dendrogram was now placed in SCI of CI along with AS1 and AS2 in dendrogram obtained by Pseudomonas-specific gene region. Also isolates AS16, AS20, AS21 and AS22 presented in SCI shifted to SCIII in Pseudomonas-specific gene region-based dendrogram. Isolates AS5, AS6 and AS7 presented as SCIII in 16S rDNA-based dendrogram were now placed in a new position as SCII. Similarly, isolates AS8, AS17, AS19 and AS10, AS11, AS14, AS18 were representing two subclusters SC V (AS8, AS17, AS19) and SC VI (AS10, AS11, AS14, AS18) in Pseudomonas-specific gene region-based dendrogram while these were arranged within three subclusters in 16S rDNA-based dendrogram SC V (AS10 and AS14), SC VI (AS8, AS17 and AS19) and SC VII (AS11 and AS18).Fig. 1

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.