*2.6. Spatiotemporal Expression Patterns Analysis of UGlcAE Genes in Tomato*

To gain the expression patterns of *UGlcAE* genes in different tissues and organs of tomato, and in the developmental stages of the fruit, we performed expression patterns analysis of the *SlUGlcAE* genes (Figure 5) with the RNA-Seq database on the website of the functional genomics database of the tomato plant. The expression profiles of the nine tomato *UGlcAE* genes showed different patterns of temporal- and tissue-specific expression (Figure 5). The results of the tomato cultivar showed that three genes, including *SlUGlcAE1*, *SlUGlcAE1-like*, and *SlUGlcAE6*, were strongly expressed in the bud, flower, leaf, root, and most fruit ripening stages (Figure 5A). The same three genes (*SlUGlcAE1*, *SlUGlcAE1-like*, *SlUGlcAE6*) showed a similar expression characteristic in the cultivated tomato, with a lower expression at the breaker stage (Figure 5A). In addition, *SlUGlcAE1* and *SlUGlcAE6* had a high expression in leaf and most fruit development stages, and *SlUGlcAE1-like* and *SlUGlcAE3* exhibited a high expression in leaf of currant tomato (Figure 5B). Specifically, *SlUGlcAE6-like* exhibited a very low expression level in root, bud, leave, flower, and fruit of the cultivar tomato and wild relative *Solanum pimpinellifolium* plants (Figure 5A,B).


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**Figure 4.** Amino acid sequence alignment of SlUGlcAE in tomato and AtUGlcAE in *Arabidopsis thaliana*. The black backgrounds indicate the strictly conserved residues, and the gray backgrounds indicate the similar amino acid residues. The GxxGxxG and YxxxK motifs are marked above the sequence alignment in red. **Figure 4.** Amino acid sequence alignment of SlUGlcAE in tomato and AtUGlcAE in *Arabidopsis thaliana*. The black backgrounds indicate the strictly conserved residues, and the gray backgrounds indicate the similar amino acid residues. The GxxGxxG and YxxxK motifs are marked above the sequence alignment in red.

#### *2.6. Spatiotemporal Expression Patterns Analysis of UGlcAE Genes in Tomato 2.7. GO Analysis of the UGlcAE Genes in the Tomato*

To gain the expression patterns of *UGlcAE* genes in different tissues and organs of tomato, and in the developmental stages of the fruit, we performed expression patterns analysis of the *SlUGlcAE* genes (Figure 5) with the RNA-Seq database on the website of the functional genomics database of the tomato plant. The expression profiles of the nine tomato *UGlcAE* genes showed different patterns of temporal- and tissue-specific expression (Figure 5). The results of the tomato cultivar In order to compare the product functions of *UGlcAE* genes in tomato and *Arabidopsis*, we analyzed *SlUGlcAE* genes and its six orthologous genes in *Arabidopsis*. As it is shown in the gene ontology (GO) map (Figure 6), all of the *UGlcAE* genes of *A. thaliana* are involved in cellular components, molecular functions, and biological processes. However, the *SlUGlcAE* genes just have roles in molecular functions and biological processes.

showed that three genes, including *SlUGlcAE1*, *SlUGlcAE1-like*, and *SlUGlcAE6*, were strongly expressed in the bud, flower, leaf, root, and most fruit ripening stages (Figure 5A). The same three genes (*SlUGlcAE1*, *SlUGlcAE1-like*, *SlUGlcAE6*) showed a similar expression characteristic in the cultivated tomato, with a lower expression at the breaker stage (Figure 5A). In addition, *SlUGlcAE1* and *SlUGlcAE6* had a high expression in leaf and most fruit development stages, and *SlUGlcAE1-like*  and *SlUGlcAE3* exhibited a high expression in leaf of currant tomato (Figure 5B). Specifically,

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*SlUGlcAE6-like* exhibited a very low expression level in root, bud, leave, flower, and fruit of the

cultivar tomato and wild relative *Solanum pimpinellifolium* plants (Figure 5A,B).

cultivar tomato and wild relative *Solanum pimpinellifolium* plants (Figure 5A,B).

**Figure 5.** Heatmap analysis of UGlcAE family gene expression in various organs of tomato. (**A**) tomato cultivar *Solanum lycopersicum* (mature green stage (MG), breaker stage (B), ten days after breaker stage (B10)); (**B**) wild relative *Solanum pimpinellifolium* (immature green stage (IMG), breaker stage (B), five days after breaker stage (B5)). The expression data was gained from pubic RNA-seq data and shown as log2 as calculated by FPKM values (fragments per kilo base of exon model per million) mapped reads. The green boxes represent the lower expression level, whereas the red boxes represent the higher expression level. **Figure 5.** Heatmap analysis of UGlcAE family gene expression in various organs of tomato. (**A**) tomato cultivar *Solanum lycopersicum* (mature green stage (MG), breaker stage (B), ten days after breaker stage (B10)); (**B**) wild relative *Solanum pimpinellifolium* (immature green stage (IMG), breaker stage (B), five days after breaker stage (B5)). The expression data was gained from pubic RNA-seq data and shown as log<sup>2</sup> as calculated by FPKM values (fragments per kilo base of exon model per million) mapped reads. The green boxes represent the lower expression level, whereas the red boxes represent the higher expression level. *2.7. GO Analysis of the UGlcAE Genes in the Tomato* In order to compare the product functions of *UGlcAE* genes in tomato and *Arabidopsis*, we analyzed *SlUGlcAE* genes and its six orthologous genes in *Arabidopsis*. As it is shown in the gene ontology (GO) map (Figure 6), all of the *UGlcAE* genes of *A. thaliana* are involved in cellular components, molecular functions, and biological processes. However, the *SlUGlcAE* genes just have roles in molecular functions and biological processes.

**Figure 6.** Assignment of Gene Ontology categories to *UGlcAE* genes in tomato. The lengths of the rectangular columns indicate the number of genes that participated in the corresponding classification. The purple rectangular columns mean gene functions of *UGlcAE* in *Arabidopsis*, the red rectangular columns represent gene functions of *UGlcAE* in tomato. All of the gene functions were classified into three categories, which were further divided into eight minor terms. **Figure 6.** Assignment of Gene Ontology categories to *UGlcAE* genes in tomato. The lengths of the rectangular columns indicate the number of genes that participated in the corresponding classification. The purple rectangular columns mean gene functions of *UGlcAE* in *Arabidopsis*, the red rectangular columns represent gene functions of *UGlcAE* in tomato. All of the gene functions were classified into three categories, which were further divided into eight minor terms.
