Truseq nano dna lt library prep

Genomic DNA was extracted using QIAamp® DNA Mini Kit (Qiagen) and quantified with an Agilent Bioanalyzer 2100 instrument (Agilent, California, USA). Paired-end libraries were previously prepared with the TruSeq Nano DNA LT Library Prep (Illumina) and sequenced on an Illumina HiSeq 2500 sequencing system at the Life Sciences Core Facility (LaCTAD; UNICAMP, Campinas, Brazil). Sequencing reads (2 x 100 bp) were assembled de novo with SPAdes v.10.3.1 [19] and scaffolded with Gfinisher v.1.4 [20] , using as references the complete genome of S. maltophilia JV3 (GCF_000223885.1) and an alternative assembly generated with Velvet 1.2.10 [21] . The assembly statistics were assessed with QUAST v.3.0 [22] . Genome completeness was assessed with BUSCO v.4.0 [23] , using the Gammaproteobacteria dataset as reference. PlasmidSpades [24] was used to predict plasmids. The assembled genome was annotated with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) [25] . The UENF-4GII genome was deposited into DDBJ/EMBL/GenBank under the accession number JABUNQ000000000.
Genes involved in antimicrobial metabolite biosynthesis were predicted using antiSMASH [26] . Insertion sequences (ISs) and GIs were predicted with ISEscan v.1.5.4 [27] and Islandviewer4 [28] , respectively. Bacteriophage signatures were analyzed with PHASTER [29] .