Genome-Based Taxonomy of Species in the <i>Pseudomonas syringae</i> and <i>Pseudomonas lutea</i> Phylogenetic Groups and Proposal of <i>Pseudomonas maioricensis</i> sp. <i>nov.,</i> Isolated from Agricultural Soil
Species in the phylogenetic group <i>Pseudomonas syringae</i> are considered the most relevant plant pathogenic bacteria, but their taxonomy is still controversial. Twenty named species are validated in the current taxonomy of this group and in recent years many strains have been genome-...
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-02-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/12/3/460 |
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| author | Magdalena Mulet Margarita Gomila Antonio Busquets David Sánchez Jorge Lalucat Elena García-Valdés |
| author_facet | Magdalena Mulet Margarita Gomila Antonio Busquets David Sánchez Jorge Lalucat Elena García-Valdés |
| author_sort | Magdalena Mulet |
| collection | DOAJ |
| description | Species in the phylogenetic group <i>Pseudomonas syringae</i> are considered the most relevant plant pathogenic bacteria, but their taxonomy is still controversial. Twenty named species are validated in the current taxonomy of this group and in recent years many strains have been genome-sequenced, putative new species have been proposed and an update in the taxonomy is needed. A taxonomic study based on the core-genome phylogeny, genomic indices (ANI and GGDC) and gene content (phyletic pattern and Jaccard index) have been applied to clarify the taxonomy of the group. A phylogenomic analysis demonstrates that at least 50 phylogenomic species can be delineated within the group and that many strains whose genomes have been deposited in the databases are not correctly classified at the species level. Other species names, like “<i>Pseudomonas coronafaciens</i>”, have been proposed but are not validated yet. One of the putative new species is taxonomically described, and the name <i>Pseudomonas maioricensis</i> sp. nov. is proposed. The taxonomies of <i>Pseudomonas avellanae</i> and <i>Pseudomonas viridiflava</i> are discussed in detail as case studies. Correct strain identification is a prerequisite for many studies, and therefore, criteria are given to facilitate identification. |
| first_indexed | 2024-04-24T18:00:55Z |
| format | Article |
| id | doaj.art-d96adb445d9d4e74a266ab5987818bec |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-04-24T18:00:55Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-d96adb445d9d4e74a266ab5987818bec2024-03-27T13:55:32ZengMDPI AGMicroorganisms2076-26072024-02-0112346010.3390/microorganisms12030460Genome-Based Taxonomy of Species in the <i>Pseudomonas syringae</i> and <i>Pseudomonas lutea</i> Phylogenetic Groups and Proposal of <i>Pseudomonas maioricensis</i> sp. <i>nov.,</i> Isolated from Agricultural SoilMagdalena Mulet0Margarita Gomila1Antonio Busquets2David Sánchez3Jorge Lalucat4Elena García-Valdés5Microbiología (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, SpainMicrobiología (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, SpainMicrobiología (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, SpainMicrobiología (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, SpainMicrobiología (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, SpainMicrobiología (Biology Department), Universitat de les Illes Balears, 07122 Palma de Mallorca, SpainSpecies in the phylogenetic group <i>Pseudomonas syringae</i> are considered the most relevant plant pathogenic bacteria, but their taxonomy is still controversial. Twenty named species are validated in the current taxonomy of this group and in recent years many strains have been genome-sequenced, putative new species have been proposed and an update in the taxonomy is needed. A taxonomic study based on the core-genome phylogeny, genomic indices (ANI and GGDC) and gene content (phyletic pattern and Jaccard index) have been applied to clarify the taxonomy of the group. A phylogenomic analysis demonstrates that at least 50 phylogenomic species can be delineated within the group and that many strains whose genomes have been deposited in the databases are not correctly classified at the species level. Other species names, like “<i>Pseudomonas coronafaciens</i>”, have been proposed but are not validated yet. One of the putative new species is taxonomically described, and the name <i>Pseudomonas maioricensis</i> sp. nov. is proposed. The taxonomies of <i>Pseudomonas avellanae</i> and <i>Pseudomonas viridiflava</i> are discussed in detail as case studies. Correct strain identification is a prerequisite for many studies, and therefore, criteria are given to facilitate identification.https://www.mdpi.com/2076-2607/12/3/460taxonomyphylogenomics<i>Pseudomonas syringae</i><i>Pseudomonas maioricensis</i> |
| spellingShingle | Magdalena Mulet Margarita Gomila Antonio Busquets David Sánchez Jorge Lalucat Elena García-Valdés Genome-Based Taxonomy of Species in the <i>Pseudomonas syringae</i> and <i>Pseudomonas lutea</i> Phylogenetic Groups and Proposal of <i>Pseudomonas maioricensis</i> sp. <i>nov.,</i> Isolated from Agricultural Soil Microorganisms taxonomy phylogenomics <i>Pseudomonas syringae</i> <i>Pseudomonas maioricensis</i> |
| title | Genome-Based Taxonomy of Species in the <i>Pseudomonas syringae</i> and <i>Pseudomonas lutea</i> Phylogenetic Groups and Proposal of <i>Pseudomonas maioricensis</i> sp. <i>nov.,</i> Isolated from Agricultural Soil |
| title_full | Genome-Based Taxonomy of Species in the <i>Pseudomonas syringae</i> and <i>Pseudomonas lutea</i> Phylogenetic Groups and Proposal of <i>Pseudomonas maioricensis</i> sp. <i>nov.,</i> Isolated from Agricultural Soil |
| title_fullStr | Genome-Based Taxonomy of Species in the <i>Pseudomonas syringae</i> and <i>Pseudomonas lutea</i> Phylogenetic Groups and Proposal of <i>Pseudomonas maioricensis</i> sp. <i>nov.,</i> Isolated from Agricultural Soil |
| title_full_unstemmed | Genome-Based Taxonomy of Species in the <i>Pseudomonas syringae</i> and <i>Pseudomonas lutea</i> Phylogenetic Groups and Proposal of <i>Pseudomonas maioricensis</i> sp. <i>nov.,</i> Isolated from Agricultural Soil |
| title_short | Genome-Based Taxonomy of Species in the <i>Pseudomonas syringae</i> and <i>Pseudomonas lutea</i> Phylogenetic Groups and Proposal of <i>Pseudomonas maioricensis</i> sp. <i>nov.,</i> Isolated from Agricultural Soil |
| title_sort | genome based taxonomy of species in the i pseudomonas syringae i and i pseudomonas lutea i phylogenetic groups and proposal of i pseudomonas maioricensis i sp i nov i isolated from agricultural soil |
| topic | taxonomy phylogenomics <i>Pseudomonas syringae</i> <i>Pseudomonas maioricensis</i> |
| url | https://www.mdpi.com/2076-2607/12/3/460 |
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