Computational protocol: Draft Genome Sequence of Pseudomonas sp. EpS/L25, Isolated from the Medicinal Plant Echinacea purpurea and Able To Synthesize Antimicrobial Compounds

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[…] The genus Pseudomonas consists of a group of bacteria particularly relevant from both medical and biotechnological viewpoints (). Thanks to their metabolic versatility, they successfully colonized several different niches, including water, soil, plants, and animals. Here, we present the draft genome sequence of Pseudomonas sp. EpS/L25, a strain close to Pseudomonas oleovorans, isolated from the stem/leaves of Echinacea purpurea, a medicinal plant whose essential oil possesses antimicrobial activity (). The E. purpurea plants were collected in October 2012 () at the “Giardino delle Erbe,” Casola Valsenio. Medicinal plants are known for their beneficial effects for humans (including their antibacterial activity), but, in spite of their high relevance, endophytic bacterial communities inhabiting their rhizosphere or internal tissues are almost totally unknown. Thus, it is still unknown if they contribute to the antimicrobial activity exerted by E. purpurea extracts.Previous characterization of Pseudomonas sp. EpS/L25 revealed the ability of this strain to inhibit the growth of other E. purpurea-associated bacteria () and, more interestingly, some opportunistic bacterial pathogens belonging to the Burkholderia cepacia complex. Furthermore, it showed resistance to several antibiotic compounds (). Due to these properties, it represents a good candidate for further molecular investigations on the genetic basis of such features, prompting for sequencing of its genome.The genome sequence of Pseudomonas sp. EpS/L25 was determined by a 2 × 300-bp paired-end approach using the MiSeq sequencing system (Illumina Inc., San Diego, CA, USA). A total of 3,020,786 paired-end reads were obtained, representing approximately 158× coverage of the whole genome. De novo assembly was performed using SPAdes version 3.5 (), which generated 300 contigs. Contigs with length less than 2,000 bp were discarded and the remaining ones used for a multi-draft-based analysis using 16 Pseudomonas genomes retrieved from the NCBI database (Pseudomonas ND6, Pseudomonas TKP, Pseudomonas VLB120, P. aeruginosa B136 33, P. aeruginosa UCBPP PA14, P. brassicacearum NFM421, P. denitrificans ATCC 13867, P. entomophila L48, P. fluorescens R124, P. mendocina NK 01, P. poae RE 1 1 14, P. putida BIRD 1, P. putida KT2440, P. stutzeri CCUG 29243, P. syringae B728a) through MeDuSa scaffolder (). The final version of the genome embeds 18 scaffolds, the longest of which is 1,664,566 bp long. The draft genome assembly of Pseudomonas sp. EpS/L25 has a total length of 5,435,234 bp. The G+C content is 65.5%, similar to that of other Pseudomonas genomes. Automated annotation of the Pseudomonas sp. EpS/L25 draft genome sequence using NCBI Prokaryotic Genome Annotation Pipeline detected 4,690 protein coding genes, 76 RNA coding genes (5 complete rRNAs, 57 tRNAs, 14 ncRNAs), and 105 pseudogenes. Three CRISPR arrays were also identified.Comparative genomics analysis confirmed the presence of antibiotic efflux pumps, some conferring specific resistance to beta-lactams (pdc), florfenicol (cfrA), and polymyxins (arnA and pmrF). Moreover, genes involved in the production of secondary metabolites with antimicrobial activity have also been detected (terpene, aryl-polyene, and two nonribosomal peptides). […]

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