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. 2023 Sep 7;12(18):3201.
doi: 10.3390/plants12183201.

Genome-Wide Identification and Analysis of TCP Gene Family among Three Dendrobium Species

Yaoting Li  1   2 , Lingli Li  3 , Jiapeng Yang  3 , Zhitao Niu  3 , Wei Liu  3 , Yi Lin  1 , Qingyun Xue  3 , Xiaoyu Ding  3
Affiliations

Genome-Wide Identification and Analysis of TCP Gene Family among Three Dendrobium Species

Yaoting Li et al. Plants (Basel). .

Abstract

Dendrobium orchids, which are among the most well-known species of orchids, are appreciated for their aesthetic appeal across the globe. Furthermore, due to their strict living conditions, they have accumulated high levels of active ingredients, resulting not only in their medicinal value but also in their strong ability to respond to harsh environments. The TCP gene family plays an important role in plant growth and development, and signal transduction. However, these genes have not been systematically investigated in Dendrobium species. In this study, we detected a total of 24, 23, and 14 candidate TCP members in the genome sequences of D. officinale, D. nobile, and D. chrysotoxum, respectively. These genes were classified into three clades on the basis of a phylogenetic analysis. The TCP gene numbers among Dendrobium species were still highly variable due to the independent loss of genes in the CIN clade. However, only three gene duplication events were detected, with only one tandem duplication event (DcTCP9/DcTCP10) in D. chrysotoxum and two pairs of paralogous DoTCP gene duplication events (DoTCP1/DoTCP23 and DoTCP16/DoTCP24) in D. officinale. A total of 25 cis-acting elements of TCPs related to hormone/stress and light responses were detected. Among them, the proportions of hormone response, light response, and stress response elements in D. officinale (100/421, 127/421, and 171/421) were similar to those in D. nobile (83/352, 87/352, and 161/352). Using qRT-PCR to determine their expression patterns under MeJA treatment, four DoTCPs (DoTCP2, DoTCP4, DoTCP6, and DoTCP14) were significantly upregulated under MeJA treatment, which indicates that TCP genes may play important roles in responding to stress. Under ABA treatment, seven DoTCPs (DoTCP3, DoTCP7, DoTCP9, DoTCP11, DoTCP14, DoTCP15, and DoTCP21) were significantly upregulated, indicating that TCP genes may also play an important role in hormone response. Therefore, these results can provide useful information for studying the evolution and function of TCP genes in Dendrobium species.

Keywords: Dendrobium; TCP proteins; expression profiles; gene family; genome-wide analysis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Chromosomal distributions of the identified TCP genes in D. officinale (A), D. nobile (B), and D. chrysotoxum (C). Green, blue, and yellow-green colors represent D. officinale, D. nobile, and D. chrysotoxum, respectively. The red letters represent the names of TCP genes.
Figure 2
Figure 2
Phylogenetic relationships of TCPs in D. officinale, D. nobile, D. chrysotoxum, and A. thaliana. The maximum likelihood evolutionary tree was constructed with RAxML with 1000 bootstraps replicates. Light-blue, dark-blue, green, and red colors represent TCP protein sequences from D. officinale (Do), D. nobile (Dn), D. chrysotoxum (Dc), and A. thaliana (At), respectively. Different subfamilies are shaded with different colors.
Figure 3
Figure 3
Phylogenetic relationships, conserved motifs, and exon–intron structures of TCP genes in D. officinale (A), D. nobile (B), and D. chrysotoxum (C). Different colors represent the 15 different motifs. Different branches are shaded with different colors. The black lines indicate introns.
Figure 4
Figure 4
Schematic representations of the gene duplications of TCP genes from D. officinale (A) and D. chrysotoxum (B). Blue and green lines highlight the syntenic gene pairs in D. officinale (Do) and D. chrysotoxum (Dc), respectively.
Figure 5
Figure 5
Collinearity analysis of TCP genes between D. officinale and five other plants, including D. nobile (A), D. chrysotoxum (B), V. planifolia (C), O. sativa (D), and A. thaliana (E). Gray lines indicate the collinear blocks. Syntenic genes of the TCP gene family are exhibited with red lines. The numbers in the figure represent the number of the corresponding chromosome.
Figure 6
Figure 6
Information on cis-acting elements in TCP genes of D. officinale (A), D. nobile (B), and D. chrysotoxum (C). The different colors in the histogram indicate the number of cis-elements in each category.
Figure 7
Figure 7
Expression analysis of DoTCPs in different tissues under MeJA treatment. (A) Expression profiles of TCP genes of D. officinale in different tissues including root, stem, leaf, and flower. Z-score-transformed FPKM values. (B) Relative expression levels of DoTCPs under MeJA treatments. (C) Relative expression levels of DoTCPs under ABA treatments.
Figure 8
Figure 8
Protein–protein interaction (PPI) networks of TCP proteins in D. officinale. The gradient circle size and color indicates the degree of importance. The important of yellow to a greater extent than blue.
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