Whole-Genome Sequencing of Sm-Resistant Strains

Whole-genome sequencing was performed for the six Sm-resistant strains listed above, as well as the wild-type parent strain. Genomic DNA samples were produced with a final concentration greater than 20 ng/µL, using Proteinase K-mediated lysis followed by column purification using the DNeasy PowerLyzer Microbial Kit (Qiagen). These seven samples were sent to Microbial Genome Sequencing Center (MiGS) for Illumina sequencing to return 200 Mbp of data per strain. Resulting FASTQ files were inputted with the GenBank file for the C58 strain of A. fabrum into the command-line tool, breseq, using Windows Subsystem for Linux and R (46 (link)). The breseq output allowed for the discernment of sequence variants compared to the reference. Whole-genome raw sequence reads for all seven strains are available on NCBI under the BioProject accession number PRJNA993692 (https://www.ncbi.nlm.nih.gov/sra/PRJNA993692).