Draft Genome Sequence of Pseudomonas sp. Strain Ep R1 Isolated from Echinacea purpurea Roots and Effective in the Growth Inhibition of Human Opportunistic Pathogens Belonging to the Burkholderia cepacia Complex

ABSTRACT

In this announcement, we detail the draft genome sequence of the Pseudomonas sp. strain Ep R1, isolated from the roots of the medicinal plant Echinacea purpurea. The elucidation of this genome sequence may allow the identification of genes associated with the production of antimicrobial compounds.

GENOME ANNOUNCEMENT

Endophytic bacterial communities inhabiting the rhizosphere or internal tissues of the medicinal plants (MPs) may contribute to the therapeutic properties of these plants (1). Here we report on the draft genome sequence of Pseudomonas sp. strain Ep R1, a strain isolated from the roots of Echinacea purpurea, an MP with immunomodulant, antiviral, and antimicrobial activity (2). The E. purpurea bacterial endophytes were isolated and molecular and phenotypic characterizations were conducted (3). In particular, Pseudomonas sp. Ep R1 showed the ability to inhibit the growth of other E. purpurea endophytes (4) and of cystic fibrosis bacterial pathogens belonging to the Burkholderia cepacia complex (5). Moreover, it has been demonstrated to be highly (50 μg/ml) resistant to chloramphenicol and streptomycin (6).

The genome sequence of Pseudomonas sp. Ep R1 was determined by a 2- × 300-bp paired-end approach using the MiSeq sequencing system (Illumina Inc., San Diego, CA). A total of 1,148,852 paired-end reads were obtained, representing approximately 100× coverage of the whole genome. De novo assembly was performed using SPAdes 2.3 (7), which generated 363 contigs. Contigs with length less than 2,000 bp were discarded. The remaining contigs were used for a multidraft-based analysis using genome sequences of 13 Pseudomonas strains retrieved from the NCBI database (P. aeruginosa PAO1, P. alkylphenolia KL28, P. denitrificans ATCC 13867, P. entomophila L48, P. fluorescens F113, P. fulva 12-X, P. knackmussii B13, P. mendocina ymp, P. protegens CHA0, P. putida KT2440, P. resinovorans NBRC, P. stutzeri CGMCC, and P. syringae pv. tomato DC3000) through MeDuSa scaffolder (8). The final version of the draft genome assembly of Pseudomonas sp. Ep R1 is 6,797,087 bp long and embeds 158 contigs (the longest of which is 1,954,067 bp long). The G+C content is 65.5%, similar to that of other Pseudomonas genomes sequenced so far. Automated annotation of the Pseudomonas sp. Ep R1 draft genome sequence using the NCBI Prokaryotic Genome Annotation Pipeline detected 6,001 protein-coding genes, 67 RNA-coding genes (7 complete rRNAs, 56 tRNAs, 4 noncoding RNAs [ncRNAs]), and 173 pseudogenes.

Genes involved in the biosynthesis of secondary metabolites with antimicrobial activity were searched. The analysis was performed within an antiSMASH shell (9), which revealed that the Pseudomonas Ep R1 genome harbors 6 clusters involved in the biosynthesis of streptomycin, stenothricin, pimaricin, type 3 polyketide synthase (T3PKS), siderophore (desferrioxamine B), and nonribosomal peptide synthetase (NRPS) (amychelin). Moreover, the genome sequence was analyzed through CARD (10), which led to the identification of several genes (mexABEJKMNW, omrMN, katG, triC, mfd, and mdtC) putatively involved in antibiotic resistance, some conferring specific resistance to fluoroquinolone, mupirocin, beta-lactam, aminocoumarin molecules, and others involved in regulatory or inactivating systems and efflux pumps.

Accession number(s).

This whole-genome shotgun project has been deposited in GenBank under the accession no. MWTQ00000000. The version described in this paper is the version MWTQ00000000.1.