Table 1.
The data quality of mRNA-seq and assembly.
Figure 1.
Data quality and annotation of transcripts assembled with mRNA-seq.
A: Length distribution of transcripts. B: Gap distribution of transcripts. C: Function annotation of the transcripts based on KEGG classification. The numbers of transcripts mapped to each pathway group are shown in the bar chart. The color indicates different KEGG categories: blue for metabolism, orange for genetic information processing, purple for environmental information processing, green for cellular processes, and red for organismal systems. D: Gene ontology (GO) classification of the transcripts. Each bar represents the number of transcripts mapped to each GO category. The color indicates different GO categories: blue for biological process (BP), green for cellular component (CC), and red for molecular function (MF). E: Principle components analysis (PCA) for the samples based on the raw reads of the transcripts. The red balls represent leaf samples, the gray balls represent stem samples, and the blue balls represent root samples. The color indicates the number range in PC #1 (Principal Component 1) shown in the color bar.
Figure 2.
Real-time RT-PCR validation for selected transcripts.
Twelve transcripts were selected for real-time RT-PCR to validate the expression patterns in different samples and treatments. The blue bars represent the relative intensity of real-time RT-PCR from independent biological replicates (using the left y-axis), the red bars represent the expression level (RPKM) of the transcript (using the right y-axis). The correlation coefficient (r) and its P-value between the RT-PCR values and RPKMs for each transcript are listed in each individual chart. The transcripts are: Unigene15416_All hits AT1G52340.1 (ABA2); Unigene28033_All hits AT5G49480.1 (ATCP1); Unigene1626_All hits AT2G38470.1 (WRKY33); Unigene13127_All hits AT4G11280.1 (ACS6); Unigene34386_All hits AT1G72520.1 (lipoxygenase); Unigene34627_All hits AT3G45640.1 (ATMPK3); Unigene51275_All hits AT2G43710.1 (SSI2); Unigene1238_All hits AT1G32450.1 (POT family protein); Unigene12278_All hits AT4G08500.1 (MEKK1); Unigene38344_All hits AT1G05010.1 (EFE); Unigene2122_All hits AT1G70700.3 (JAZ9); and Unigene25367_All hits AT3G06490.1 (MYB108). The real-time RT-PCR primers for each transcript are listed in Table S1.
Figure 3.
Summary of the differential expression transcripts across cotton tissue samples and treatments.
A: Venn diagrams illustrate the differential expression transcripts under PEG and NaCl treatment in root, stem, and leaf samples. The red and blue colors represent the up-regulated and down-regulated transcripts under PEG treatment, respectively. The purple and green colors represent the up-regulated and down-regulated transcripts under NaCl treatment, respectively. B: Cluster and gene ontology (GO) analysis of the transcripts’ response to PEG or NaCl treatments in different cotton tissues. The overview hierarchical cluster result of the centroids of SOM cluster (listed in Fig. S4), the red (high) and blue (low) colors represent the relative expression level across the samples. The marked centroid groups represent the transcripts in these clusters preferentially expressed in the leaf (marked in light green background), stem (light yellow background), or root (light purple background) tissue. In the comparison of the enriched GO terms in the transcripts preferentially expressed in the leaf, stem, or root tissue, the red bars represent the percentage of transcripts belonging to enriched terms in the query list (Input), whereas the gray bars represent the percentage in all transcripts (Reference).
Table 2.
Transcription factor (TF) members that responded to PEG and NaCl treatments in cotton tissues.
Figure 4.
Summary of transcripts related to plant hormone signal transduction pathways and their response to PEG and NaCl treatments across cotton tissue samples.
The colored bars represent the percentage of the transcripts in each bin (re-annotated to MapMan classification) whether up-regulated (red) or down-regulated (blue) under PEG or NaCl treatment in different cotton tissues. A: represents the differential expression transcripts related to auxin (IAA) signalling transduction pathway. B: represents the differential expression transcripts related to cytokinin (CK) signalling transduction pathway. C: represents the differential expression transcripts related to gibberellin (GA) signalling transduction pathway. D: represents the differential expression transcripts related to abscisic acid (ABA) signalling transduction pathway. E: represents the differential expression transcripts related to ethylene signalling transduction pathway. F: represents the differential expression transcripts related to brassinosteroid (BR) signalling transduction pathway. G: represents the differential expression transcripts related to jasmonate (JA) signalling transduction pathway. H: represents the differential expression transcripts related to salycylic acid (SA) signalling transduction pathway.