Compared with the non-inoculated plants, there were 693 up-regulated unigenes and 2456 down-regulated unigenes in the inoculated plants (Figure 6). Moreover, up- and down-regulated unigenes were aligned to the GO and COG database for classifying and predicting gene functions. GO term annotations for these up-regulated unigenes were classified to three major categories including molecular function, cellular component and biological process. Of these, assignments to biological process constituted the majority, followed by cellular component and molecular function (Figure 7). The most overrepresented categories in the up-regulated DEGs were mainly related to some important pathways such as ‘response to salt stress,’ ‘response to water deprivation,’ ‘response to iron ion,’ and ‘hydrogen peroxide catabolic process’ in biological processes; ‘plasma membrane,’ ‘plant-type vacuole,’ ‘plastide,’ and ‘peroxisome’ in cellular component; ‘peroxidase activity,’ ‘glutathione transferase activity,’ ATPase activity,’ and ‘ferric-chelate reductase activity’ in molecular function. Among these up-regulated DEGs, some genes involved in Fe acquisition, Na+ transport and antioxidant systems were observably activated in the inoculated plants (Supplementary Table S4). Thus, the enhanced stress tolerance of plants by SA03 was closely associated with multiple signaling pathways involving Fe uptake and stress adaption. Moreover, qRT-PCR was used to confirm gene expression profiles that were found in the DEGs (eight unigenes: IRT1, FRD3, NHX1, AHA2, ZEP1, YSL1, SAUR21, and NAS1). The changing patterns of gene expression were in accordance with that detected by RNA-Seq (Supplementary Figure S1), indicating a high reliability of RNA-Seq data.