Limits...
Phylogenomics and systematics in Pseudomonas.

Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E - Front Microbiol (2015)

Bottom Line: MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC).The correct species classification is a prerequisite for most diversity and evolutionary studies.This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.

View Article: PubMed Central - PubMed

Affiliation: Microbiology, Department of Biology, Universitat de les Illes Balears Palma de Mallorca, Spain.

ABSTRACT
The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.

No MeSH data available.


Phylogenetic tree of the 112 complete or draft genomes of strains related to the genus Pseudomonas and the 141 well described Pseudomonas strains used in this study based on the phylogenetic analysis of four concatenated genes (16S rRNA, gyrB, rpoB, and rpoD). The strains analyzed in this study whose genomes have been sequenced are labeled in red. Distance matrices were calculated by the Jukes-Cantor method. Dendrograms were generated by neighbor-joining. Cellvibrio japonicum Ueda107 was used as outgroup. The bar indicates sequence divergence. Percentage bootstrap values only of groups and subgroups higher than 50% of 1000 replicates are indicated at branching nodes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4447124&req=5

Figure 1: Phylogenetic tree of the 112 complete or draft genomes of strains related to the genus Pseudomonas and the 141 well described Pseudomonas strains used in this study based on the phylogenetic analysis of four concatenated genes (16S rRNA, gyrB, rpoB, and rpoD). The strains analyzed in this study whose genomes have been sequenced are labeled in red. Distance matrices were calculated by the Jukes-Cantor method. Dendrograms were generated by neighbor-joining. Cellvibrio japonicum Ueda107 was used as outgroup. The bar indicates sequence divergence. Percentage bootstrap values only of groups and subgroups higher than 50% of 1000 replicates are indicated at branching nodes.

Mentions: A phylogenetic tree (Figure 1) was generated based on the concatenated sequences with a total length of 3711 nucleotides in the following order: 16S rRNA (1278 nt), gyrB (801 nt), rpoD (717 nt), and rpoB (915 nt). Phylogenetic assignation to a known species, group or subgroup of the 112 complete or draft genomes analyzed was congruent in all the trees (data not shown). Forty-eight of the 112 strains (42.8% of the genomes analyzed) were located in the same phylogenetic branch as the corresponding species type strain (or genomovar reference strains in the P. stutzeri species) with a similarity higher than 97%, which was the accepted species threshold (Mulet et al., 2010, 2012a), and their species assignations were considered correct. As observed in Table 1, 22 of the whole genome sequenced strains studied (20%) were only assigned to the genus and 34 strains (30%) were not correctly identified at the species level. For example, strain BBc6R8, which had been identified as P. fluorescens, was included in the P. gessardii phylogenetic subgroup, and P. fulva 12-X was closer to P. straminea than to the P. fulva type strain. The closest species type strain for the 112 complete or draft genomes analyzed based on the concatenated analysis of four genes is listed in Table 1 and in Supplementary Table 2. Thirty-seven of the genomes were less than 97% similar to the closest type strain and might be considered representatives of Pseudomonas species not yet described or have to be assigned to genomovars in the case of P. stutzeri.


Phylogenomics and systematics in Pseudomonas.

Gomila M, Peña A, Mulet M, Lalucat J, García-Valdés E - Front Microbiol (2015)

Phylogenetic tree of the 112 complete or draft genomes of strains related to the genus Pseudomonas and the 141 well described Pseudomonas strains used in this study based on the phylogenetic analysis of four concatenated genes (16S rRNA, gyrB, rpoB, and rpoD). The strains analyzed in this study whose genomes have been sequenced are labeled in red. Distance matrices were calculated by the Jukes-Cantor method. Dendrograms were generated by neighbor-joining. Cellvibrio japonicum Ueda107 was used as outgroup. The bar indicates sequence divergence. Percentage bootstrap values only of groups and subgroups higher than 50% of 1000 replicates are indicated at branching nodes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4447124&req=5

Figure 1: Phylogenetic tree of the 112 complete or draft genomes of strains related to the genus Pseudomonas and the 141 well described Pseudomonas strains used in this study based on the phylogenetic analysis of four concatenated genes (16S rRNA, gyrB, rpoB, and rpoD). The strains analyzed in this study whose genomes have been sequenced are labeled in red. Distance matrices were calculated by the Jukes-Cantor method. Dendrograms were generated by neighbor-joining. Cellvibrio japonicum Ueda107 was used as outgroup. The bar indicates sequence divergence. Percentage bootstrap values only of groups and subgroups higher than 50% of 1000 replicates are indicated at branching nodes.
Mentions: A phylogenetic tree (Figure 1) was generated based on the concatenated sequences with a total length of 3711 nucleotides in the following order: 16S rRNA (1278 nt), gyrB (801 nt), rpoD (717 nt), and rpoB (915 nt). Phylogenetic assignation to a known species, group or subgroup of the 112 complete or draft genomes analyzed was congruent in all the trees (data not shown). Forty-eight of the 112 strains (42.8% of the genomes analyzed) were located in the same phylogenetic branch as the corresponding species type strain (or genomovar reference strains in the P. stutzeri species) with a similarity higher than 97%, which was the accepted species threshold (Mulet et al., 2010, 2012a), and their species assignations were considered correct. As observed in Table 1, 22 of the whole genome sequenced strains studied (20%) were only assigned to the genus and 34 strains (30%) were not correctly identified at the species level. For example, strain BBc6R8, which had been identified as P. fluorescens, was included in the P. gessardii phylogenetic subgroup, and P. fulva 12-X was closer to P. straminea than to the P. fulva type strain. The closest species type strain for the 112 complete or draft genomes analyzed based on the concatenated analysis of four genes is listed in Table 1 and in Supplementary Table 2. Thirty-seven of the genomes were less than 97% similar to the closest type strain and might be considered representatives of Pseudomonas species not yet described or have to be assigned to genomovars in the case of P. stutzeri.

Bottom Line: MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC).The correct species classification is a prerequisite for most diversity and evolutionary studies.This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.

View Article: PubMed Central - PubMed

Affiliation: Microbiology, Department of Biology, Universitat de les Illes Balears Palma de Mallorca, Spain.

ABSTRACT
The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.

No MeSH data available.