​pseudomonas.​com[3]. Strain Pf-5 is a model biological control agent that inhabits the rhizosphere of plants and suppresses diseases caused by BIBF 1120 in vivo a wide variety of soilborne pathogens [3–15]. The original analysis of the Pf-5 VX-680 genome [3] focused primarily on the strain’s metabolic capaCity and on the pathways involved in the production of secondary metabolites. The latter encompass nearly six percent

of the genome and include antibiotics that are toxic to plant pathogenic fungi and Oomycetes and contribute to Pf-5′s broad-spectrum biocontrol activity. The aim of the present study was to more thoroughly analyze and annotate sections of the Pf-5 genome that contain MGEs.

Here, we describe one transposase, six regions containing prophages (termed Prophage 01 to 06) and two genomic islands that are present in the Pf-5 genome. Results and discussion The genome of P. fluorescens Pf-5 contains six prophage regions that vary in G+C content from 62.6% to 46.8% and two putative genomic islands (Table 1). Three of the prophages exceed 15 kb in length and contain genes for transcriptional regulators, DNA metabolism enzymes, structural bacteriophage proteins and lytic enzymes. Table 1 Phage-related elements and genomic islands of P. fluorescens Pf-5 genome Feature Gene range 5′ end 3′ end Size (bp) %GC Presence of integrase Type of feature Prophage 01 PFL_1210 Smad phosphorylation to PFL_1229 1386082 1402957 16875 62.6 No SfV-like prophage Prophage 02 PFL_1842 to PFL_1846 2042157 2050549 8392 46.8 Yes* Defective prophage in tRNASer Prophage 03 Aldehyde dehydrogenase PFL_1976 to PFL_2019 2207060 2240619 33559 61.2 Yes P2-like prophage Prophage 04 PFL_2119 to PFL_2127 2338296

2351794 13498 56.3 Yes Defective prophage in tRNAPro Prophage 05 PFL_3464 to PFL_3456 3979487 3982086 2599 55.3 Yes* Defective prophage in tRNACys Prophage 06 PFL_3739 to PFL_3780 4338335 4395005 56670 57.3 Yes Lambdoid prophage in tRNASer Genomic island 1 (PFGI-1) PFL_4658 to PFL_4753 5378468 5493586 115118 56.4 Yes Putative mobile island PFGI-1 in tRNALys Genomic island 2 (PFGI-2) PFL_4977 to PFL_4984 5728474 5745256 16782 51.5 Yes Genomic island in tRNALeu *, the predicted integrase gene contains frameshift mutation(s). Prophage 01 of Pf-5 and homologous prophages in closely related strains Prophage 01 spans 16,875 bp and consists of genes encoding a myovirus-like tail, holin and lysozyme lytic genes, a putative chitinase gene (PFL_1213), and genes for a repressor protein (PFL_1210) and a leptin binding protein-like bacteriocin, LlpA1 (PFL_1229) (Fig. 1, see Additional file 1).