Genome-Wide Identification, Characterization and Expression Analysis of the TCP Gene Family in Prunus mume

Abstract

TCP proteins, belonging to a plant-specific transcription factors family, are known to have great functions in plant development, especially flower and leaf development. However, there is little information about this gene family in Prunus mume, which is widely cultivated in China as an ornamental and fruit tree. Here a genome-wide analysis of TCP genes was performed to explore their evolution in P. mume. Nineteen PmTCPs were identified and three of them contained putative miR319 target sites. Phylogenetic and comprehensive bioinformatics analyses of these genes revealed that different types of TCP genes had undergone different evolutionary processes and the genes in the same clade had similar chromosomal location, gene structure, and conserved domains. Expression analysis of these PmTCPs indicated that there were diverse expression patterns among different clades. Most TCP genes were predominantly expressed in flower, leaf, and stem, and showed high expression levels in the different stages of flower bud differentiation, especially in petal formation stage and gametophyte development. Genes in TCP-P subfamily had main roles in both flower development and gametophyte development. The CIN genes in double petal cultivars might have key roles in the formation of petal, while they were correlated with gametophyte development in the single petal cultivar. The CYC/TB1 type genes were highly detected in the formation of petal and pistil. The less-complex flower types of P. mume might result from the fact that there were only two CYC type genes present in P. mume and a lack of CYC2 genes to control the identity of flower types. These results lay the foundation for further study on the functions of TCP genes during flower development.

Genome-wide Analysis and Expression Profiling Suggest Diverse Roles of TCP Genes During Development and Stress Responses in Grapevine (Vitis vinifera L)

“…Hence, the detailed biological functions of TCP transcription factors in grapevine bud break would be an issue worthy of further investigation. the two groups was also consistent with that in other species (Xu et al, 2014;Zhou et al, 2016). Most members, such as VvTCP2, VvTCP5, VvTCP6, VvTCP7 and VvTCP14, had higher expression in young leaves (Fig.…”

“…Family members of TCP genes in Arabidopsis (Arabidopsis thaliana) (Yao et al, 2007), rice (Oryza sativa) (Yao et al, 2007), cotton (Gossypium arboretum and Gossypium raimondii) (Ma et al, 2014(Ma et al, , 2016, apple (Malus domestica) (Xu et al, 2014), tomato (Solanum lycopersicum) (Parapunova et al, 2014), watermelon (Citrullus lanatus) (Shi et al, 2016) and Prunus mume (Zhou et al, 2016) have been identified, and some of the genes have been well characterised, while no comprehensive analysis of grapevine has been reported until now. In our study, 15 TCP members in the grapevine genome were identified.…”

Genome-Wide Identification, Characterization, and Transcript Analysis of the TCP Transcription Factors in Vitis vinifera

“…The sequences of TCP family members in C. lanatus, O. sativa, Brassica rapa for constructing phylogenetic tree were obtained from PlantTFDB TF database (http://planttfdb.cbi.pku.edu.cn/, v3.0). The number of TCP family genes were obtained in Arabidopsis thaliana (Wei et al, 2016), O. sativa (Yao et al, 2007), L. esculentum (Parapunova et al, 2014), P. mume (Zhou et al, 2016), C. lanatus (Shi et al, 2016), turnip (Du et al, 2017), Chinese cabbage (Liu et al, 2018), and Gossypium raimondii (Ma et al, 2014).…”

“…Recently, TCP gene family has been reported in various plants, for instance, 24 TCP genes in Arabidopsis,30 in Lycopersicon esculentum,28 in Oryza sativa,33 in Populus euphratica,36 in Populus trichocarpa,27 in Citrullus lanatus,19 in Prunus mume (Martin-Trillo and Cubas, 2010;Parapunova et al, 2014;Ma et al, 2016;Shi et al, 2016;Zhou et al, 2016). The grape is an ideal model for understanding the berry development in perennial fruit species.…”

Evolution of RADIALIS and DIVARICATA gene lineages in flowering plants with an expanded sampling in non‐core eudicots

“…Both CYC and DICH genes belong to the TCP gene family (abbreviation for TEOSINTE BRANCHED 1 [ TB1 ] from Zea mays , CYCLOIDEA [ CYC ] from Antirrhinum majus and PROLIFERATION CELL FACTOR 1 and 2 [ PCF1 and PCF2 ] from Oryza sativa ) and have been comprehensively studied in model and non‐model species (Boyden et al., ; Broholm, ; Damerval and Manuel, ; De Paolo et al., ; Fambrini and Pugliesi, ; Galego and Almeida, ; Hileman et al., ; Howarth and Donoghue, , ; Lei et al., ; Li et al., ; Lin et al., ; Luo et al., ; Madrigal et al., ; Reardon et al., ; Su et al., ; Wei et al., ; Zhong and Kellogg, ; Zhou et al., ). On the other hand, RAD and DIV belong to the MYB ( Myeloblastosis ) gene superfamily and have been less studied in comparison to the TCP genes (Corley et al., ; Costa et al., ; Galego and Almeida, ; Luo et al., ; MacHemer et al., ; Reardon et al., ; Su et al., ; Valoroso et al., ).…”