*3.6. MicroRNA-Targeting TaPAL Genes*

We discovered 27 putative miRNAs targeting 37 *TaPAL* genes to create an interaction network using Cytoscape software to better understand the underlying regulatory mechanism of miRNAs involved in the regulation of *PALs* (Figure 5 and Supplementary Sheet S4). In the connection distribution and regulation network, we found that *TaPAL26* is one of the most-targeted *PAL* genes of wheat. The tae-miR1119 targets the wheat genes *TaPAL7*, *TaPAL32*, *TaPAL24*, *TaPAL3*, *TaPAL19*, *TaPAL30*, *TaPAL26*, *TaPAL27*, *TaPAL18*, *TaPAL9*, *TaPAL22*, *TaPAL23*, *TaPAL21*, *TaPAL6*, *TaPAL16*, *TaPAL15*, *TaPAL33*, *TaPAL31*, and *TaPAL4.* Our results also indicated that miRNA tae-miR9781 target *TaPAL22* and *TaPAL34*. Both these genes have low expression in shoots. Furthermore, the miRNAs tae-miR1119, tae-miR398, tae-miR444a, tae-miR444b, and tae-miR9664-3p targeting *TaPAL29* have high expression in root tissues.

used for the construction of phylogenetic tree, and 1000 replicates were also used for bootstrap test. (**B**) Ten conserve motifs with different lengths are shown. Motifs codes are presented at the right of the figure, with different colors. (**C**) Sequence logos of these motifs are presented. (**D**) Protein domain analysis showing the Pfam lyase aromatic domain.

**Figure 3.** Gene structure analysis. Exon and intron arrangement-based gene structure of *TaPAL* genes.
