Genome Sequencing of Bacterial Strains

The genome sequencing was performed for strains: IN53, IN129, and IN118. The DNA was isolated using Sherlock AX kit (A&A Biotechnology, Poland) following the manufacturer’s protocol; then, DNA was quantified using Quant-it™ PicoGreen dsDNA Kit (Thermo Fisher Scientific, USA). DNA libraries were obtained with NEBNext DNA Library Prep Master Mix Set for Illumina (Illumina, USA). Short insert paired-end libraries (insert size 350 bp) and mate-pair libraries were sequenced on the MiSeq Illumina platform (Illumina, USA) in the paired-end reads technology (2 × 250 bp) using MiSeq Reagent Kit v2 (500 cycles, Illumina, USA). Adapter trimming and quality filtering of raw reads were conducted with Cutadapt version 3.0 (Martin 2011 ). The de novo assembly was done using Spades version 3.15.5 (Bankevich et al. 2012 (link)); the resulted assemblies were polished with Pilon (Walker et al. 2014 ). The genome sequences were annotated by the NCBI Prokaryotic Genomes Annotation Pipeline (PGAP; Tatusova et al. 2016 (link)). The genome sequences were deposited in the NCBI GenBank; the accession numbers are provided in Supplementary material, Table S1.