Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica

To investigate the broader effects of exogenous IAA on gene expression in S. plymuthica A153, we used transcriptome sequencing (RNA-seq) to analyze changes in the global transcriptome of A153 in response to IAA treatment. RNA sequencing was done at the GENYO Research Center (Granada, Spain). Prior to preparation of the RNA library, ribosomal RNAs were removed from the samples using the RiboZeroTM kit (Epicentre, Gram-Negative-Bacteria#MRZGN126) following the manufacturers’ instructions. Subsequently, samples were processed with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) following the provided sample preparation guide. The final library (adapter and index included) was validated using the DNA-specific chip Agilent DNA 1000.