Identification and expression responses of TCP gene family in Opisthopappus taihangensis under abiotic stress

Abstract

The TCP gene family plays pivotal roles in the development and abiotic stress responses of plants; however, no data has been provided for this gene family in Opisthopappus taihangensis. Based on O. taihangensis genome, 14 TCP genes were identified and divided into two classes (I and II). After tandem and segmental duplication/whole-genome duplication (WGD), more loss and less gain events of OtTCPs occurred, which might be related with the underwent purifying selection during the evolution. The conserved motifs and structures of OtTCP genes contained light response, growth and development, hormone response, and stress-related cis-acting elements. Different OtTCP genes, even duplicated gene pairs, could be expressed in different tissues, which implied that OtTCP genes had diverse function. Among OtTCPs, OtTCP4, 9 and 11 of CYC clade (Class II) presented a relative wide expression pattern with no or one intron. The three TCP genes could be regarded as important candidate factors for O. taihangensis in growth, development and stress response. These results provided some clues and references for the further in-depth exploration of O. taihangensis resistance mechanisms, as well as those of other unique eco-environment plants.

Keywords: Opisthopappus taihangensis; TCP gene family; abiotic stress; evolution; gene expression analysis.

Figure 1

The constructed phylogenetic tree based on the TCP proteins of O. taihangensis (Ot), Arabidopsis thaliana (At), and Oryza sativa (Os). The TCP gene family was mainly divided into two clades: Class I (PCF) and Class II with possessing two subclades (CYC/TB1 and CIN).

Figure 2

Multiple sequence alignment of OtTCP protein was divided into an alkaline region basic and Helix I–Loop–Helix II.

Figure 3

(A) Phylogenetic tree of the OtTCPs with two classes. (B) Conserved motifs of the OtTCP proteins. Different color represented different motif. (C) Exon-intron organization of OtTCP genes. Yellow boxes represented exons (CDS), green boxes represented UTR, and grey lines represented introns. The scale was the sizes of exon or intron.

Figure 4

Replication events of OtTCP genes. Gray lines represented the duplicated genes, while the red lines represented the segmental duplicate TCP gene pairs. Additionally, the red lines connecting genes outside the chromosome represented the tandem duplicated pairs. Box with red line graph showed the gene densities. Gray rectangles represented the chromosomes, the corresponding names displayed externally for each chromosome.

Figure 5

The collinearity analysis among A. thaliana, O. sativa and 11 Asteraceae species. The red line represents TCP collinear gene pairs in O. taihangensis and other genomes.

Figure 6

The gain and loss events of TCP genes in the Asteraceae. The numbers at the branch nodes represented the gained and lost genes. The blue nodes represented the possible common ancestor of the Asteraceae.

Figure 7

Cis-acting elements in the OtTCP promoter regions. Different colors represented various elements.

Figure 8

Expression patterns of OtTCPs. (A) Expression profiles of the OtTCPs in different tissues. (B) Leaves treated with 20% PEG6000 for 3.5 hours or untreated (0 hours); Roots treated with 20% PEG6000 for 9 hours or untreated (0 hours). (C) 100 Mm/L, 300 Mm/L, and 500 Mm/L mixed salt solution for 24h treatment. (D) 500 Mm/L mixed salt solution in leaves for 6h, 24h, and 48h treatment. The different colored boxes indicated the different log2 (FPKM) values, the red blocks indicated high relative expression levels and blue blocks indicated low relative expression levels.

Figure 9

Expression patterns of OtTCP genes under qRT-PCR. (A) represented the treatment of 0h, 6h, 24h, and 48h of 500 Mm/L salt stress. (B) represented CK, 100 Mm/L, 300 Mm/L, and 500 Mm/L salt stress for 24h treatment. Vertical bars represented the mean ± SD of three biological replicates. Statistical significance was determined using one-way ANOVA (**** p < 0.0001 *** p < 0.001 ** p < 0.01* p < 0.05).