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Comparative Study
. 2019 Dec 20;21(1):54.
doi: 10.3390/ijms21010054.

Comparative Analysis and Expression Patterns of the PLP_deC Genes in Dendrobium officinale

Lei Zhang  1   2 , Chunyan Jiao  1   2 , Yunpeng Cao  3   4 , Xi Cheng  1   2 , Jian Wang  1   2 , Qing Jin  1   2 , Yongping Cai  1   2
Affiliations
Comparative Study

Comparative Analysis and Expression Patterns of the PLP_deC Genes in Dendrobium officinale

Lei Zhang et al. Int J Mol Sci. .

Abstract

Studies have shown that the type II pyridoxal phosphate-dependent decarboxylase (PLP_deC) genes produce secondary metabolites and flavor volatiles in plants, and TDC (tryptophan decarboxylase), a member of the PLP_deC family, plays an important role in the biosynthesis of terpenoid indole alkaloids (TIAs). In this study, we identified eight PLP_deC genes in Dendrobium officinale (D. officinale) and six in Phalaenopsis equestris (P. equestris), and their structures, physicochemical properties, response elements, evolutionary relationships, and expression patterns were preliminarily predicted and analyzed. The results showed that PLP_deC genes play important roles in D. officinale and respond to different exogenous hormone treatments; additionally, the results support the selection of appropriate candidates for further functional characterization of PLP_deC genes in D. officinale.

Keywords: Dendrobium officinale; PLP_deC; bioinformatics; evolution; expression pattern analysis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic analysis of PLP_deC genes from Dendrobium officinale, Phalaenopsis equestris, Oryza sativa, and Arabidopsis thaliana. The maximum likelihood (ML) tree was created using IQ-TREE with 8 D. officinale (Do), 6 P. equestris (Pe), 15 O. sativa (Os) and 12 A. thaliana (At) PLP_deC protein sequences. The red, green, and blue colors indicate GADs, HDCs, and AADs, respectively. Bootstrap supports are indicated at each branch.
Figure 2
Figure 2
Distribution of 10 putative conserved motifs in PLP_deC proteins.
Figure 3
Figure 3
Sliding window analysis of Ka/Ks for each gene pair. The window size is 150 bp, and the step size is 9 bp. The grey region represents the conserved domain.
Figure 4
Figure 4
Expression profiles of PLP_deC genes in different tissues. (a) Heatmap of the in silico expression analysis in different tissues and organs. Blue and red indicate lower and higher transcript abundance, respectively. (b) PLP_deC genes expressed in different tissues and organs. Green, yellow, and red indicate low (0.01–0.71 FPKM), medium (1–1.71 FPKM), and high (3.42–28.4 FPKM) expression, respectively.
Figure 5
Figure 5
Numbers of cis-acting elements in all the PLP_deC genes of D. officinale and P. equestris. (a) The different colors and numbers in the grid indicate the numbers of different promoter elements in each PLP_deC gene. (b) The different colored histogram represents the numbers of cis-acting elements in the different categories. The red, blue, and green indicate plant growth and devolepment, phytohormone response, and biotic and abiotic stress, respectively. (c) The pie charts indicate the percentages of different promoter elements in the different categories.
Figure 6
Figure 6
The expression levels of PLP_deC genes in D. officinale under abscisic acid (ABA) treatment. The x-axis represents the treatment time, and the y-axis represents the gene expression level. Error bars indicate the mean and standard deviation (SD). The asterisks indicate significant difference relative to the time 0. ** significant difference (p < 0.01), * significant difference (p < 0.05).
Figure 7
Figure 7
The expression level of PLP_deC genes in D. officinale under methyl jasmonate (MeJA) treatment stress. The x-axis represents the treatment time, and the y-axis represents the gene expression level. Error bars indicate the mean and standard deviation (SD). The asterisks indicate significant difference relative to the time 0. ** significant difference (p < 0.01), * significant difference (p < 0.05).
Figure 8
Figure 8
The expression levels of PLP_deC genes in D. officinale under salicylic acid (SA) treatment. The x-axis represents the treatment time, and the y-axis represents the gene expression level. Error bars indicate the mean and standard deviation (SD). The asterisks indicate significant difference relative to the time 0. ** significant difference (p < 0.01), * significant difference (p < 0.05).
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