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      Phylogenomics and systematics in Pseudomonas

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          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.

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          Most cited references32

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          TreeView: an application to display phylogenetic trees on personal computers.

          R D Page (1996)
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            PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order.

            PermutMatrix is a work space designed to graphically explore gene expression data. It relies on the graphical approach introduced by Eisen and also offers several methods for the optimal reorganization of rows and columns of a numerical dataset. For example, several methods are proposed for optimal reorganization of the leaves of a hierarchical clustering tree, along with several seriation or unidimensional scaling methods that do not require any preliminary hierarchical clustering. This program, developed for MS Windows, with MS-Visual C++, has a clear and efficient graphical interface. Large datasets can be thoroughly and quickly analyzed.
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              Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

              Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5. Supplementary information The online version of this article (doi:10.1038/nbt1110) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                18 March 2015
                2015
                : 6
                : 214
                Affiliations
                [1] 1Microbiology, Department of Biology, Universitat de les Illes Balears Palma de Mallorca, Spain
                [2] 2Institut Mediterrani d'Estudis Avançats (Consejo Superior de Investigaciones Científicas-Universidad de las Islas Baleares) Palma de Mallorca, Spain
                Author notes

                Edited by: Frank T. Robb, University of Maryland, USA

                Reviewed by: Edward R. B. Moore, University of Gothenburg, Sweden; Kostas Konstantinidis, Georgia Institute of Technology, USA

                *Correspondence: Elena García-Valdés, Department of Biology, Universitat de les Illes Balears, Crtra. Valldemossa km 7.5, 07122 Palma de Mallorca, Spain elena.garciavaldes@ 123456uib.es

                This article was submitted to Evolutionary and Genomic Microbiology, a section of the journal Frontiers in Microbiology

                †These authors have contributed equally to this work.

                Article
                10.3389/fmicb.2015.00214
                4447124
                26074881
                38160ade-0f37-4605-b9da-30ebbff811db
                Copyright © 2015 Gomila, Peña, Mulet, Lalucat and García-Valdés.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 03 December 2014
                : 02 March 2015
                Page count
                Figures: 4, Tables: 1, Equations: 0, References: 54, Pages: 13, Words: 8002
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                pseudomonas,genomics,multilocus sequence analysis,taxonomy,systematics
                Microbiology & Virology
                pseudomonas, genomics, multilocus sequence analysis, taxonomy, systematics

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