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For plate assays, thanapeptin derivatives at a concentration of 50 ��M were added directly at the border of a 1/5th PDA, after which an agar plug (4 mm diameter) from a freshly grown plate with the target fungal or oomycete strain was positioned in the center of the plate. Hyphal growth was monitored from 2 days after incubation up to 2 weeks after incubation, dependent on the growth speed. Testing of compound activity against fungal and oomycete strains in liquid culture was performed by addition of the compound to 1 ml of liquid 1/5th PDB in a 12 wells culture plate (Greiner Bio-One), in which an agar plug (4 mm diameter) from a freshly grown plate with the target organism was submerged. Growth experiments were incubated at 25��C, except for P. infestans, which was cultured at 18��C. Results General genome features and phylogeny Sequencing and assembly showed that the genome size of Pseudomonas sp. SH-C52 is ~6.3 Mb with a GC content of 61.0%. The genome was assembled in 596 contigs and 25 scaffolds, with an estimated coverage of 99.2%. For annotation, 384 contigs of at least 100-bp and covering 6.3 MB were used. In total, 5579 ORFs were annotated with 5523 CDSs and 56 tRNAs (Table ?(Table1).1). Previous analysis of the 16S rRNA sequence placed SH-C52 within the P. fluorescens clade (Mendes et al., 2011). At that time, however, no conclusive species designation was obtained. Expanding the former genome-wide phylogenetic analysis on P. fluorescens species (Redondo-Nieto et al., 2012) with the SH-C52 genome and the recent draft genomes of P. Ulixertinib ic50 corrugata CFBP5454 and P. mediteranea CFBP5447, showed that strain SH-C52 clusters within subgroup I of the P. fluorescens group. Within subgroup I, SH-C52 and the strains of P. corrugata and P. mediterranea form a separate clade (Figure ?(Figure11). Table 1 General genome sequence information of Pseudomonas sp. SH-C52. Figure 1 Whole genome phylogenetic analysis of Pseudomonas sp. SH-C52. Phylogenetic tree constructed by use of CVtree, and based on the analysis performed previously by Redondo-Nieto et al. (2012), with the addition of strains SH-C52, P. corrugata CFBP5454 and ... In silico analysis of pseudomonas sp. SH-C52 primary metabolism The metabolic potential of Pseudomonas sp. SH-C52 was analyzed by comparing genes from primary metabolism with those known for the P. fluorescens clade (Loper et al., 2012). In this analysis, also its close relative P. corrugata strain CFBP5454 was included as well as P. mandelii strain JR-1 as a representative strain for subgroup III. The comparative analysis showed that for several of the metabolic activities in species of the P. fluorescens clade, the gene sequences are also found in strain SH-C52. These include genes involved in catabolism of L-arabinose, mannitol, myo-inositol, and ethanol, as well as genes coding for gelatinase and lipase.