Genome-Wide Identification, Evolution, and Expression Analysis of the TCP Gene Family in Rose (Rosa chinensis Jacq.)

Abstract

Roses have not only high ornamental and economic values but also cultural importance worldwide. As a plant-specific transcription factor gene family, the TCP (TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTOR LAND 2) genes have been indicated to be involved in various aspects of plant biological processes, such as leaf morphogenesis and senescence, lateral branching, flower development, stress response and hormone signaling. Currently, TCP genes have been identified and analyzed in many plants, yet there is no systematic analysis in Rosa chinensis. Here, we identified 16 RcTCP genes from R. chinensis genome, which were unevenly distributed in five out of all seven chromosomes. Phylogenetic and structural analyses showed that RcTCP family could be classified into two classes, I (namely PCF) and II, and class II genes can be further divided into CIN and CyC/TB1 subclasses. The different classes of TCP genes were showed to have undergone different evolutionary processes, and genes in the same branch shared similar motifs, gene structures and conserved structural domains. Promoter analysis showed that RcTCPs had many cis-acting elements that are mainly associated with plant growth and development, plant hormones and abiotic/biotic stress responses. Furthermore, the expression levels of RcTCPs under vegetative and reproductive growth and drought stress treatments were analyzed based on public RNA-seq dataset, and it was shown that RcTCPs exhibited serious tissue-specific expression, with most of them dominantly expressed in flowers, leaves and stems, with high levels of expression at different stages of flower and bud differentiation, particularly during petal formation and gametophyte development. The high inducement of seven RcTCP genes from PCF class in drought stress indicated their important roles in biological processes against drought stress. Our results provide valuable information for the evolution and functional characterization of TCP genes in R. chinensis.