Genome-Wide Identification and Characterization of TCP Gene Family Members in Melastoma candidum

Abstract

It has been confirmed that the plant-specific Teosinte-branched 1/Cycloidea/Proliferating (TCP) gene family plays a pivotal role during plant growth and development. M. candidum is a native ornamental species and has a wide range of pharmacodynamic effects. However, there is still a lack of research on TCP’s role in controlling M. candidum’s development, abiotic stress responses and hormone metabolism. A comprehensive description of the TCP gene family in M. candidum is urgently needed. In this study, we used the HMMER search method in conjunction with the BLASTp method to identify the members of the TCP gene family, and a total of 35 TCP genes were identified. A domain analysis further confirmed that all 35 TCPs contained a TCP superfamily, a characteristic involved in dimerization and DNA binding that can be found in most genes from this gene family, suggesting that our identification was effective. As a result of the domain conservation analysis, the 35 TCP genes could be classified into two classes, TCP-P and TCP-C, based on the conservative regions of 55 and 59 amino acids, respectively. Gene-duplication analysis revealed that most TCP genes were present in duplication events that eventually led to TCP gene expansion in M. candidum. All the detected gene pairs had a Ka/Ks value of less than one, suggesting that purification selection is the most important factor that influences the evolution of TCP genes. Phylogenetic analysis of three species displayed the evolutionary relationship of TCP genes across different species and further confirmed our results. The real-time quantitative PCR (qRT-PCR) results showed that McTCP2a, McTCP7a, McTCP10, McTCP11, McTCP12a, McTCP13, McTCP16, McTCP17, McTCP18, McTCP20 and McTCP21 may be involved in leaf development; McTCP4a, McTCP1, McTCP14, McTCP17, McTCP18, McTCP20, McTCP22 and McTCP24 may be involved in flower development; and McTCP2a, McTCP3, McTCP5a, McTCP6, McTCP7a, McTCP9, McTCP11, McTCP14 and McTCP16 may be involved in seed development. Our results dissect the TCP gene family across the genome of M. candidum and provide valuable information for exploring TCP genes to promote molecular breeding and property improvement of M. candidum in the future.

Keywords: Melastoma candidum; TCP gene family; collinearity analysis; gene pairs; phylogenetic analysis.

Figure 1

Gene location in different chromosomes. Length of the bars represents the size of the chromosome. Different color within each bar represents gene density on the chromosome. Red means high gene density, and blue means low gene density.

Figure 2

Phylogenetic evolution of TCP family members. Different colors of the outer ring denote the three main TCP genes. The blue arc represents TCP-C-type genes. The red dots on the tree branches represent bootstrap value. The size of the dots is in proportion to the bootstrap value.

Figure 3

Motif, domain and gene structure analyses of TCP family members. Rectangles with different colors represent different motifs, domains, UTRs and exons, respectively.

Figure 4

Promoter analysis of TCP family members. The red dot on branches of the phylogeny trees denotes bootstrap value. Different color models on the black lines mean elements of promoters.

Figure 5

Statistics of different Cis elements in the promoter of the identified 35 TCP genes.

Figure 6

Sequence alignment and seqlogo of TCP TFs. (a) Alignment of the TCP superfamily domain in all identified TCP TFs; (b) Alignment of the R domain in all identified TCP TFs. The same color in the column and the big size of the letters in the seqlogo graph denote a high level of conservation in the corresponding position.

Figure 7

TCP gene pairs within M. candidum. (a) circos graph of TCP family members in M. candidum. Red lines within the circos graph represent a gene pair relationship. (b) Divergence time estimation of TCP gene pairs. Ka means non-synonymous substitution rate; Ks means synonymous substitution rate; DT means divergence time.

Figure 8

Multi-collinearity analysis of three species. The orange lines between two species denote collinearity genes among different species.

Figure 9

Phylogenetic evolution of TCP family members in three species. Different color models represent different clades. The pink triangle represents the bootstrap value, and the size of the triangle is in proportion to the bootstrap value. Before the gene name, blue dots represent P. trichocarpa, brown dots represent M. candidum, sapphire blue dots represent A. thaliana.

Figure 10

Expression analysis of TCP-family genes in nine tissues by qRT-PCR. YL: young leaves; AL: adult leaves; YS: young stems; AS: adult stems; S: seeds; R: roots; EF: early-stage flowers; MF: middle-stage flowers; BF: blooming flowers. Hollow circles in these graphs represent the relative expression of three biological repeats. The relative expression levels are shown as the means ± SDs. Duncan’s test was used to evaluate significant difference levels. Lowercase letters mean p ≤ 0.05, capital letters mean p ≤ 0.01.