Previous evidence indicated that different hormones play important roles in stress signal transduction and cell responses
[22,23,24][22][23][24]. Here, we investigated the expression profiles of
SlADKs in response to Eth, IAA, ABA, SA, and MeJA treatments (
Figure 7). With Eth treatment, in general, the expression of most
SlADKs showed little difference, but that of
SlADK1,
2, and
7 increased gradually to different levels during 0–2 h (
Figure 7A). With IAA treatment, the expression maxima of
SlADK1,
2, and
4 were at 2, 0.5, and 6 h, respectively. Interestingly,
SlADK11 showed decreased transcription at the early stage and almost no expression at later time points (
Figure 7B). At 0.5 h after ABA treatment, expression of
SlADK5,
7, and
10 showed no significant differences; however, expression of
SlADK3,
4,
6,
8,
9, and
11 decreased, and that of
SlADK1 and
2 increased at the first time point. Moreover, most
SlADKs did not change significantly after 1–12 h of treatment.
SlADK6 showed decreased transcription at the early stage and almost none at following time points (
Figure 7C). With SA treatment, transcription of most
SlADKs was repressed in the first 0.5 h. Expression of most
SlADKs showed mild change under SA treatment, except for
SlADK2,
6, and
7.
SlADK2 and
7 showed especially similar expression patterns throughout all time points, with maximum expression at 12 h (
Figure 7D). The plant regulator MeJA mediates diverse developmental processes and defense responses. It rapidly induced upregulation of
SlADK4 and
2 during 1–6 h and 3–12 h time points, respectively. Expression of
SlADK6 increased gradually during 1–6 h, with opposite results for expression of
SlADK9 during 0–3 h. As in IAA treatment,
SlADK11 showed decreased transcription at the early stage and almost no expression for later time points (
Figure 7E). Hence, transcription of
SlADKs was responsive to most of the applied stress treatments. Interestingly,
SlADK2 and
4 exhibited significant changes under multiple hormone treatments, suggesting that they may have unique roles in hormone regulation. Notably, the result of gene clustering showed that the homologous genes of
SlADK6 and
10 had similar expression patterns under treatment with Eth and IAA (
Figure 3A left and
Figure 7A,B), and
SlADK8 and
11 had similar expression patterns under treatment with Eth and ABA (
Figure 3A left and
Figure 7A,C).
Figure 7. Expression profiles of SlADKs under various hormone treatments by qRT-PCR. The treated tomato leaves were harvested at the indicated time points. To ensure that expression of the same gene in different treatments, as well as expression of different genes in the same treatment, can both be clearly displayed and compared, for treatment with Eth (A), SA (D), and MeJA (E), the color scale represents log2 mean value of relative expression levels from three independent biological replicas (n = 3); for treatment with IAA (B) and ABA (C), the color scale represents mean value of relative expression levels from three independent biological replicas (n = 3). Primers specific for SlADKs are listed in Supplementary Materials Table S5.
2.10. SlADK Expression Patterns under Stress Based on RNA-Seq Data
As introduced above, TomExpress provides a unified and standard method to judge tomato gene expression from released RNA-Seq data sets. Here,
SlADKs expression patterns under treatment with different plant hormone and multiple hormones were analyzed (
Figure 8 and
Figure S2). In general, the expression of most
SlADKs (
SlADK3,
5,
6,
7, and
10) were lower in leaves (C10 to C17) than in roots (C1–C2, C4–C5, C7–C8) whether these tissues were treated with cytokinin or not. Also, the expression of
SlADK1 was lower in many tissues, and even could not be detected in roots (C2, C4, C5, C7) and leaves (C10, C13, C16) under special stress conditions. With the treatment of auxin in tip of roots, the expression of
SlADK7 and
10 were downregulated significantly. In fruit, several
SlADK genes such as
SlADK3,
5,
8, and
10 displayed higher expression levels. Compared with treatment of ACC in fruit, multiple-hormone treatment of ACC + IAA could upregulate the expression of
SlADK3 and
5 (
Figure S2). Heatmap can be very convenient to show gene clustering. As shown in
Figure 8, under treatment with different plant hormone and multiple hormones,
SlADK3,
4,
5,
7, and
10 showed similar expression patterns in many tissues, as did the groups of
SlADK2,
6, and
11 and of
SlADK1,
8, and
9 (
Figure 8).
Figure 8. Expression patterns of SlADK genes under stress based on RNA-seq data. Heatmap of the expression pattern of tomato SlADK family genes in root, leaves and fruit with different and multiple hormones treatment. The distance used for the clustering is based on the classical Euclidean distance which allows clustering gene expression by expression levels. For a given row of the heatmap, green and red colors present high and low values of expression of the considered gene, respectively. Details of C1 to C22 are provided in Figure S2.