Transcriptome of P. salmonis fur knockdown

Piscirickettsia salmonis is the causative agent of Salmonid Rickettsial Septicemia (SRS). In this work, we implemented a Mobile-CRISPRi system to generate gene silencing using a catalytically inactive dCas9 protein and an IPTG-inducible single-guide RNA (sgRNA). fur knockdown strains were created using the Mobile-CRISPRi by using triparental mating with P. salmonis CGR02 as a recipient and as donor strains E. coli SM10 pJMP2782:sgRNA-fur1 (containing gentamycin resistance, inducible dcas9 and the sgRNA directed to fur) together with E. coli SM10 pTNS3 (encoding TN7 transposase). The fur knockdown strain (P. salmonis sgRNA-fur1) was grown for 38 hours (mid-exponential phase) at 18C in NPB supplemented (fur knockdown) or not (control) with IPTG 100 uM. RNA was purified with TRIzol and sequenced on a NovaSeq X Plus instrument (Illumina) with read lengths of 150 bp.