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Additional file 2: Table S1.Overview of RNA sequencing data. Table S2. Sequencing production statistics. Table S3. Summary of sequence annotation. Table S4. DEGs related to MYBs and HSFs in roots of Z. xanthoxylum under heat treatments. Fold change equals to log2 (the RPKM value of a gene undertreatment / the RPKM value of a gene under control condition) and indicates thetranscript abundance change of each DEGs. Homologous gene and homologous species were obtained by NCBI blast according to the sequence corresponding to the gene ID. Table S5. DEGs relatedto AP2/ERFs in roots of Z. xanthoxylum identified only at 40°C for 0.5 h. Foldchange equals to log2 (40°C-0.5 h RPKM / 25°C-0.5 h RPKM) and indicates thetranscript abundance change of each DEGs. Homologous gene and homologous species were obtained by NCBI blast according to the sequence corresponding tothe gene ID. Table S6. DEGs relatedto WRKYs in roots of Z. xanthoxylum identified only at 40°C for 0.5 h. Foldchange equals to log2 (40°C-0.5 h RPKM / 25°C-0.5 h RPKM) and indicates thetranscript abundance change of each DEGs. Homologous gene and homologousspecies were obtained by NCBI blast according to the sequence corresponding tothe gene ID. Table S7. DEGs related to HSFs in roots of Z. xanthoxylum identified only at 40°C for 0.5 h. Foldchange equals to log2 (40°C-0.5 h RPKM / 25°C-0.5 h RPKM) and indicates thetranscript abundance change of each DEGs. Homologous gene and homologous species were obtained by NCBI blast according to the sequence corresponding tothe gene ID. Table S8. DEGs relatedto HSPs in roots of Z. xanthoxylum identified under heat treatments. Foldchange equals to log2 (the RPKM value of a gene under treatment / the RPKM value of a gene under control condition) and indicates the transcript abundancechange of each DEGs. Homologous gene and homologous species were obtained by NCBI blast according to the sequence corresponding to the gene ID. Table S9. DEGs related to HSPs in roots of Z. xanthoxylum identified only at 40°C for 6 h. Fold change equals to log2 (40°C-6 h RPKM / 25°C-6 h RPKM) and indicates the transcript abundance change of each DEGs. Homologous gene and homologous species were obtained by NCBI blast according to the sequence corresponding to the gene ID. Table S10. DEGs related to PSI inleaves of Z. xanthoxylum identified only at 40°C for 0.5 h. Fold change equalsto log2 (40°C-0.5 h RPKM / 25°C-0.5 h RPKM) and indicates the transcript abundance change of each DEGs. Homologous gene and homologous species were obtained by NCBI blast according to the sequence corresponding to the gene ID. Table S11. The sequences used for RT-qPCR validation.

Additional file 1: Figure S1.The water content (a), osmotic potential (b) and relative membrane permeability(c) of leaves in Z. xanthoxylum under control and heat treatments for 10 days(6 h/d). Values in (a-c) are mean ± SE (n = 5). Asterisks indicate significantdifferences in comparison with control (25°C) (* P < 0.05, ** P < 0.01,*** P < 0.001, Student’s t-test). Figure S2. Functional annotation of the assembled transcriptome. (a) Lengthdistribution of all assembled unigenes; (b) Map of GO functional categories; (c) Map of KOG function classifications. Figure S3. Number of DEGs in leaves (a) and roots (b) of Z. xanthoxylum under heat treatments. Figure S4. Enriched GO terms for DEGs in leaves of Z. xanthoxylum at 40°C (a, c) and 45°C (b, d) for 0.5 h (a, b) and 6 h (c, d). Figure S5. Enriched GO terms for DEGs in roots of Z. xanthoxylum at 40°C (a, c) and 45°C(b, d) for 0.5 h (a, b) and 6 h (c, d). Figure S6. Enriched KEGG terms for DEGs in leaves of Z. xanthoxylum at 40°C (a, c) and 45°C (b, d) for 0.5 h (a, b) and 6 h (c, d). Figure S7. Enriched KEGG terms for DEGs in roots of Z. xanthoxylumat 40°C (a, c) and 45°C (c, d) for 0.5 h (a, b) and 6 h (b, d). Figure S8. Correlation analysis for 20 selected DEGs betweenRNA-seq and RT-qPCR results in leaves (a-d) and roots (e-h) of Z. xanthoxylum under heat treatments.