Five strains of KPC-2-producing CRKP and five strains of CSKP were used for RNA-seq (Gene Denovo Biotechnology). Illumina NovaSeq 6000 sequencing and FASTP (https://github.com/opengene/fastp ) software were used to obtain valid data.
The resulting data were compared with the reference genome assembly GCF_022869665.1 (https://www.ncbi.nlm.nih.gov/assembly/12472981 ) to obtain known genes by using Bowtie2 (version 2.2.8).
According to previous studies [31 (link),32 (link)], we annotated the unmatched genes with the NR database using Rockhopper. Unannotated genes with 50–500 nt of length and stable secondary structures were listed as candidate sRNAs [46 (link)]. In addition, we used the sRNAMap database (version 2009) and the Rfam database (version 13) to match known sRNAs.
The resulting data were compared with the reference genome assembly GCF_022869665.1 (
According to previous studies [31 (link),32 (link)], we annotated the unmatched genes with the NR database using Rockhopper. Unannotated genes with 50–500 nt of length and stable secondary structures were listed as candidate sRNAs [46 (link)]. In addition, we used the sRNAMap database (version 2009) and the Rfam database (version 13) to match known sRNAs.
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