Newbler v3

For full genome sequences, 500 ng of input material were fragmented using Covaris M220 Focused-ultrasonicator™ (Covaris), and ligated to suitable Illumina adapters (NEXTflex-96™ DNA Barcodes, BiooScientific) using a SPRI-TE library system (Beckman Coulter) with SPRIworks Fragment Library Cartridges II (for Roche FLX DNA sequencer; Beckman Coulter). Size exclusion was performed manually with AMPure XP magnetic beads in two steps for a final size distribution of 500–600 bp long fragments. After quality control of the libraries on a Bioanalyzer 2100 (Agilent Technologies), the libraries were quantified using using Kapa Library Quantification Kit for Illumina platforms (Kapa Biosystems), pooled and sequenced on a MiSeq instrument (Illumina) with MiSeq reagent Kit v3 in 2 × 300 bp PE mode (Illumina). For data analysis, the reads were mapped against the nearest reference genome (Newbler v3.0, Roche). All mapped reads were extracted and de novo assembled (Newbler v3.0, Roche). Since this approach delivered three or more contigs, the software ContigGraph (unpublished) was used to determine the connections of single contigs for manual assembly of the full genome. Afterwards the whole data set was mapped against the full genome (Newbler v3.0, Roche).

DNA sequencing was performed using an Illumina MiSeq instrument in paired-end mode using a v3 chemistry kit. The obtained sequence reads were filtered for quality using cutAdapt v1.9.0 (trimming bases on 3’ ends with quality lower than 20 and removing reads shorter than 100 bp) and assembled using Newbler v3.0 software (Roche, Basel, Switzerland). Final gap closure and TEs sequencing were performed by capillary sequencing of PCR products using an ABI3730xl DNA Analyser (Applied Biosystems, Waltham, MA, USA) applying a primer walking technique. The summary of the sequencing of particular Pseudomonas plasmids was presented in Table S2.

The complete nucleotide sequences of ΦAH14a and ΦAH14b were determined at the Laboratory of DNA Sequencing and Oligonucleotide Synthesis, IBB PAS (Poland). The phage genomes were sequenced on the Illumina MiSeq instrument in paired-end mode using v3 chemistry kit. The genome of each virus was obtained as a single contig with 3390 reads and 17.2 coverage for ΦAH14a and 5160 reads and 83.8 coverage for ΦAH14b. The obtained sequence reads were filtered for quality and assembled using Newbler v3.0 software (Roche). The end closing was performed by PCR and subsequent sequencing of the PCR products.