Figure 1.
Dendrogram of 548 tissue-specifically expressed genes in five tissues of Sorghum propinquum.
1. Rhizome tips, 2. Shoot tips, 3. Rhizome internodes, 4. Stem internodes, 5. Young leaves. The suffixes a, b, and c indicate the three biological replicates. In the color panels, each horizontal line represents a single gene and the color of the line indicates the expression level (in a log scale) of the gene relative to the median in a specific sample: high expression in red, low expression in green. The raw data represented here are detailed in Table S3.
Table 1.
The list of genes enriched specifically in rhizome tips relative to other tissues.
Table 2.
Identification of distinct cis-regulatory elements in the tissue-enriched genes.
Figure 2.
Real time PCR profiles of 12 selected tissue-enriched genes.
RT, ST, RI, SI, and YL represent the rhizome tip, shoot tip, rhizome internodes, shoot internodes, and young leaves, respectively. Expression levels were calculated based on the expression level of YL genes set to 1. Expression profiles obtained by real time PCR for one gene, Sb01g036550, were not consistent with data obtained from microarray analysis. Correlation coefficients (r) for the remaining 11 genes were 0.74, 0.74, 0.74, 0.74, 0.77, 0.74, 0.82, 0.76, 0.76, 0.94, and 0.76, from left to right, respectively. Bars donate standard deviation.
Figure 3.
Validation of microarray data by in situ hybridization.
In situ localization of transcripts corresponding to the genes (a) Sb01g047010 and (c) Sb06g028820 in S. propinquum rhizome tips are illustrated; (b) and (d) represent the sense probe for control. Corresponding microarray-based expression profiles of these two genes are also shown as bar graphs for comparison.
Figure 4.
GO slim categories in up- and down-regulated RT genes combined from this experiment and three other reported studies.
Bars show number of genes with significantly higher relative transcript abundance. All GO slim categories significantly over- or underrepresented are calculated based on a hypergeometric distribution. Significant over- or under-represented categories are indicated by * for p ≤ 0.05, ** for p ≤ 0.01, and *** for p ≤ 0.001.
Figure 5.
Heat map showing the relationship between rhizome related differentially expressed genes (DEGs) and hormone target genes.
The heat map was produced by analyzing genes comprising rhizome related DEGs for methyl jasmonate (MJ), ethylene (C2H4), abscisic acid (ABA), auxin (AUX), gibberellic acid (GA), zeatin, brassinosteroids (BR), and salicylic acid (SA). Subfigures a–g represent the seven gene sets analyzed: DEGs of RT vs. ST in O. longistaminata from (a) transcriptome sequencing and (c) microarray analysis, and (e) results of the present study in S. propinquum; DEGs of underground tissues (RT and RI) vs. above-ground tissues (ST, SI, and YL) in O. longistaminata from (b) transcriptome sequencing and (d) microarray analysis, and (f) results of the present study in S. propinquum; and (g) candidate rhizome-enriched genes in S. halepense (pSH) and S. propinquum. In the HORMONOMETER analysis, orange (1) = complete correlation, white (0) = no correlation, and blue (-1) = anti-correlation.
Table 3.
The list of up regulated genes in the comparison of the rhizome related DEGs.
Table 4.
Identification of distinct cis-regulatory elements in the DEGs shown the same expression pattern in at least two different platforms.