Phylogenetic identification and genome comparison.

<p>Approximate maximum likelihood phylogenetic tree of SVBP6 and closely reated <i>Pseudomonas</i> assemblies <b>(A)</b> and Venn diagram for the comparison of genomes from the three known <i>P</i>. <i>donghuensis</i> isolates, HYS (China), P482 (Poland) and SVBP6 (Argentina) <b>(B)</b>. <b>A)</b> Phylogenetic tree of the <i>P</i>. <i>putida</i> complex based on 676 putative orthologous genes. The tree was inferred using FastTree version 2.1. The SH-like test was used to evaluate branch supports. Genomes from the same species based on two-way ANI score (> 95%) were indicated with brackets. The position of SVBP6 strain is indicated by a red arrow, and this sub-cluster was zoomed to distinguish the <i>Pseudomonas</i> species around SVBP6 (in red font). Indeed, <i>P</i>. <i>donghuensis</i> strains are grouped in a sub cluster with other environmental isolates, like <i>P</i>. <i>alkylphenolica</i> KL28 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194088#pone.0194088.ref089" target="_blank">89</a>], a biocontrol <i>P</i>. <i>putida</i> strain isolated from potato rhizosphere in France (PA14H7 strain, [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194088#pone.0194088.ref090" target="_blank">90</a>]), <i>P</i>. <i>vranovensis</i> DSM 16006 isolated from soil in the Czech Republic [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194088#pone.0194088.ref091" target="_blank">91</a>], and unidentified <i>Pseudomonas</i> sp. isolated from soil in the USA (2(2015) and 5 strains); <b>B)</b> The calculated core genome of <i>P</i>. <i>donghuensis</i> species is 4474 PEGs, between 87.7% and 89.0% of each representative. Particular PEGs of strains HYS, P482 and SVBP6 are 8.7%, 5.7% and 5.6%, respectively, and SVBP6 shares more PEGs with P482 (5.4% of total SVBP6 PEGs) than with HYS type strain (1.1% of total SVBP6 PEGs), suggesting that strains P482 and SVBP6 are more closely related than with HYS strain.