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Defining the Pseudomonas genus: where do we draw the line with Azotobacter?

Özen AI, Ussery DW - Microb. Ecol. (2011)

Bottom Line: Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster.Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms.Third, exhaustive BLAST comparisons demonstrate that the fraction of shared genes between A. vinelandii and Pseudomonas genomes is similar to that of Pseudomonas species with each other.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark.

ABSTRACT
The genus Pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. The relationship of the Pseudomonas genus to Azotobacter vinelandii is examined using three genomic sequence-based methods. First, using 16S rRNA trees, it is shown that A. vinelandii groups within the Pseudomonas close to Pseudomonas aeruginosa. Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster. Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms. Third, exhaustive BLAST comparisons demonstrate that the fraction of shared genes between A. vinelandii and Pseudomonas genomes is similar to that of Pseudomonas species with each other. The results of these different methods point to a high similarity between A. vinelandii and the Pseudomonas genus, suggesting that Azotobacter might actually be a Pseudomonas.

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Related in: MedlinePlus

Pan genome family tree. The tree shows the phylogenetic relationships based on the gene families found in the pan genome, excluding the families found in only one genome. Color coding is again based on Table 1
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Fig2: Pan genome family tree. The tree shows the phylogenetic relationships based on the gene families found in the pan genome, excluding the families found in only one genome. Color coding is again based on Table 1

Mentions: For the second method, the pan genome family tree (Fig. 2) of all the genomes was generated using BLASTP similarity between each proteome, as described in Snipen and Ussery's method [45]. The “50/50 rule” was used to define the homology, meaning that a protein is assumed to be in the same family if 50% of its length shows 50% sequence identity with the reference protein [51]. According to this criterion, genes that have a significant hit to each other are considered to be in one gene family. In order to see the relations between the different gene families, a matrix is constructed containing the gene families in columns and the genomes in rows, assigning 1 for the presence of that gene family in the corresponding genome and 0 otherwise. Manhattan distances are calculated from this matrix and hierarchical clustering is made. This tree shows the similarities based on the shared gene families, excluding the gene families that are represented only in one genome (ORFans) [45].Figure 2


Defining the Pseudomonas genus: where do we draw the line with Azotobacter?

Özen AI, Ussery DW - Microb. Ecol. (2011)

Pan genome family tree. The tree shows the phylogenetic relationships based on the gene families found in the pan genome, excluding the families found in only one genome. Color coding is again based on Table 1
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3275731&req=5

Fig2: Pan genome family tree. The tree shows the phylogenetic relationships based on the gene families found in the pan genome, excluding the families found in only one genome. Color coding is again based on Table 1
Mentions: For the second method, the pan genome family tree (Fig. 2) of all the genomes was generated using BLASTP similarity between each proteome, as described in Snipen and Ussery's method [45]. The “50/50 rule” was used to define the homology, meaning that a protein is assumed to be in the same family if 50% of its length shows 50% sequence identity with the reference protein [51]. According to this criterion, genes that have a significant hit to each other are considered to be in one gene family. In order to see the relations between the different gene families, a matrix is constructed containing the gene families in columns and the genomes in rows, assigning 1 for the presence of that gene family in the corresponding genome and 0 otherwise. Manhattan distances are calculated from this matrix and hierarchical clustering is made. This tree shows the similarities based on the shared gene families, excluding the gene families that are represented only in one genome (ORFans) [45].Figure 2

Bottom Line: Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster.Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms.Third, exhaustive BLAST comparisons demonstrate that the fraction of shared genes between A. vinelandii and Pseudomonas genomes is similar to that of Pseudomonas species with each other.

View Article: PubMed Central - PubMed

Affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark.

ABSTRACT
The genus Pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. The relationship of the Pseudomonas genus to Azotobacter vinelandii is examined using three genomic sequence-based methods. First, using 16S rRNA trees, it is shown that A. vinelandii groups within the Pseudomonas close to Pseudomonas aeruginosa. Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster. Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms. Third, exhaustive BLAST comparisons demonstrate that the fraction of shared genes between A. vinelandii and Pseudomonas genomes is similar to that of Pseudomonas species with each other. The results of these different methods point to a high similarity between A. vinelandii and the Pseudomonas genus, suggesting that Azotobacter might actually be a Pseudomonas.

Show MeSH
Related in: MedlinePlus