Nanovue plus uv vis spectrophotometer

Genomic DNA from parental strains NB1854, NB1855 and six revertant derivatives of each parental strain was extracted using the GenCatch Genomic DNA Extraction Kit (Epoch Life Sciences). After measuring DNA concentration and quality (NanoVue Plus UV/Vis Spectrophotometer, GE), 150–300 ng/μl samples were submitted to The Center for Applied Genomics (TCAG; Toronto) for Nextera XT library preparation and whole genome sequencing (paired end, Illumina HiSeq2500). Quality checking of raw reads was performed using FastQC (Babraham Bioinformatics) analysis software followed by trimming using fastp (Chen et al., 2018 (link)). The trimmed reads were mapped to the S. meliloti Rm1021 reference genome (NCBI Accession number: ASM696v1) with Bowtie2 (Langmead and Salzberg, 2012 (link)) and the output (.sam file) was converted into .bam format using SAMtools.
As a comparator, an assembly for all sequence reads was performed via the SPAdes assembler tool using an in-house python script and the output files were aligned to the S. meliloti reference genome. MindTheGap and Ingap were used to detect single nucleotide polymorphisms (SNPs) or gene deletions. A visualization analysis was carried out using Geneious Prime 8.0.

The existence of the RNA content of the LSV2 and delta-N48 LSV1 VLPs was examined by measuring the absorbance at UV wavelengths of 260 nm (A₂₆₀) and 280 nm (A₂₈₀) with NanoVue Plus UV–Vis Spectrophotometer (GE Healthcare). A matching formulation buffer blank was used for zero adjustments of the instrument before the measurements of each sample. The UV A₂₆₀/A₂₈₀ ratios were calculated with the corrected A₂₆₀ divided by the corrected A₂₈₀.