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Objective To explore the physiological and molecular mechanism of saline-alkali tolerance in Catalpa bungei, we studied the influence of different saline-alkali stress on the growth, photosynthetic and physiological indicators of C. bungei seedlings combing with transcriptome sequencing. Methods Pot experiment was used to study the different responses of biomass, photosynthetic and physiological indicators of C. bungei seedlings to different saline-alkali stress. Illumina high-throughput sequence technology was used to sequence the transcriptome, and the effect of saline-alkali stress on transcriptional level was analyzed by bioinformatics. Results Under different saline-alkali stress, the damage degree of leaves was Na2CO3>mixed saline-alkali>NaCl. Net growth of plant height and stem diameter, fresh weight and dry weight of overground part and root, biomass, root-shoot ratio were all significantly suppressed with increasing saline-alkali concentration. But the growth stress index decreased with increasing concentration. Contents of MDA and relative conductivity both rose to varying degrees with increasing concentration. SOD enzymatic activity, contents of soluble sugar and Pro, contents of total chlorophyll and photosynthetic rate increased firstly and decreased then with increasing concentration. Transcriptome sequencing generated a total of 60.4Gb of raw data. Finally, we obtained 55 793 Unigenes after assembling, of which 29 534 (52.93%) Unigeneswere annotated. Through differentially expressed genes (DEGs) analysis, 1 779, 2 835 and 4 059 DEGs were screened from three comparison groups (CK vs NaCl, CK vs Na2CO3 and CK vs mixed saline-alkali) respectively. GO functional enrichment analysis of these DEGs indicated that they were significantly enriched in integral component of membrane, intrinsic component of membrane, catalytic activity, isoprenoid metabolic and biosynthetic process, oxidoreductase activity. KEGG functional enrichment analysis of these DEGs indicated that they were significantly enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, plant hormone signal transduction, terpenoid backbone biosynthesis and arginine biosynthesis. Moreover, the most abundant differentially expressed transcription factors (TFs) were bHLH, ERF, MYB-related, NAC, C2H2, WRKY, MYB and bZIP families. Conclusion C. bungei mainly resists from saline-alkali stress by accumulating contents of soluble sugars and Pro, improving SOD enzymatic activity and photosynthesis, but all of them show the phenomenon of "low promotion and high suppression", indicating that it has a certain threshold value. C. bungei common responses to saline-alkali stress by regulating biological processes and metabolic pathways including component of membrane, catalytic activity, isoprenoid metabolic and biosynthetic process, phenylpropanoid biosynthesis, starch and sucrose metabolism, plant hormone signal transduction, and interacting with TFs. This study provides a scientific theoretical basis for deeply studying the physiological and molecular mechanisms of saline-alkali tolerance in C. bungei.