To clarify the mechanisms underlying SA03-induced saline–alkaline tolerance in plants, gene transcriptional profiles were analyzed by RNA-Seq. A total of 28,837,670 and 29,075,976 raw reads were generated in both the non-inoculated and inoculated plants by 454 sequencing, respectively (Supplementary Table S2), and the raw reads data were submitted into the NCBI SRA database (accession No. SRR5388903). After filtering out low quality reads, 23,021,019 (79.82%) and 22,541,540 (77.52%) clean reads were remained in both the NI and I library, respectively. Moreover, 22,003,842 clean reads (76.3%) in the NI library and 21,924,113 clean reads (75.4%) in the I library were uniquely mapped. We further compared analyses of gene expression between the non-inoculated and inoculated plants for screening DEGs with an FDR-adjusted p-value < 0.05 as the threshold (Supplementary Table S3).