The file includes Table A, Table B, Table C, Table D, Table E, Table F, Table G, Table H, Table I, Table J, Table K, Table L, Table M and Table N.

Table A in S1 File. Primers used in the RT-qPCR assay. Table B in S1 File. Statistics of unigenes in different expression-level interval. Table C in S1 File. Differentially expressed genes between P-6h and the untreated primary roots P-0h (early water-stress inducible and repressed genes). The significance of gene expression difference between samples was identified by using q-value1 as the threshold. Table D in S1 File. Differentially expressed genes between P-24h and the untreated primary roots P-0h (late water-stress inducible and repressed genes). The significance of gene expression difference between samples was identified by using q-value1 as the threshold. Table E in S1 File. Differentially expressed genes between Rh-6h and P-24h (rehydration inducible and repressed genes). The significance of gene expression difference between samples was identified by using q-value1 as the threshold. Table F in S1 File. Common genes between the early and late water-stress inducible genes. Table G in S1 File. Common genes between the early and late water-stress repressed genes. Table H in S1 File. Genes exclusively expressed as the early inducible genes. Table I in S1 File. Genes exclusively expressed as the late water-stress inducible genes. Table J in S1 File. Genes exclusively expressed as the early water-stress repressed genes. Table K in S1 File. Genes exclusively expressed as the late water-stress repressed genes. Table L in S1 File. Genes showed ‘up-up-down’ expression pattern in the course of 24h of PEG-treatment following 6h of rehydration. Table M in S1 File. Genes showed ‘down-down-up’ expression pattern in the course of 24h of PEG-treatment following 6h of rehydration. Table N in S1 File. The significant KEGG pathways enriched from the early and late water-stress inducible genes (P-6h vs. P-0h) the early and late water-stress repressed genes (P-24h vs. P-0h), the rehydration inducible and repressed genes (Rh-6h vs. P-24h). The corrected p-value cut-off of 0.05 was set as the threshold, and only the enriched pathways with p-value less than 0.05 were shown. (ZIP)