Dynamic change analysis of differentially co-expressed unigenes. (A) Dynamic expression pattern profiles after NaCl stress treatment. STEM clustering analysis was performed to identify clusters; each cluster contained various numbers of genes with similar expression patterns under NaCl stress. The top left hand corner indicates the ID of the cluster. The lower left hand corner contains the P-value of the number of assigned genes compared with the expected value. The black lines show model expression profiles. The red lines represent all individual gene expression profiles. The x-axis represents the stress treatment time in hours. The time series was log-normalized to start at 0. The y-axis of all genes in a cluster box are at the same scale; (B) Gene Ontology categories assigned to differentially expressed unigenes (DEUs) in response to 200 mM NaCl stress for 4 and 24 h. The x-axis represents the percentage of unigene numbers, and the y-axis shows the GO subcategories (at a level of 3 or below in the GO hierarchy); * P < 0.05; ** P < 0.01; (C) Comparison of salt-responsive transcription factor unigene co-expressed in NaCl-stressed Nan Dan Ba Di Da Hua and Earlistaple 7 leaves from the two clusters using hierarchical cluster analysis. The log2 Ratio values of salt responsive DEUs were used for hierarchical cluster analysis with the R pheatmap package. Unigene expression values are scaled ranging from +5 (magenta) to -5 (green). Red represents up-regulated unigenes, green represents down-regulated unigenes, and black indicates no significant difference in unigene expression. Details of annotated unigenes shown on the right are provided in Additional file 2I.