Genome-wide identification and transcript analysis of TCP transcription factors in grapevine

Abstract

BackgroundThe plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development.ResultsA total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, 11 VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses.ConclusionsOur study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.

Genome-Wide Identification of the TCP Gene Family in Broussonetia papyrifera and Functional Analysis of BpTCP8, 14 and 19 in Shoot Branching

“…The analysis of evolution relationship exhibited that 20 BpTCP proteins were classified into three major subclades, which was similar to the previous studies of A. thaliana , O. sativa , V. vinifera , Z. mays and P. vulgaris [ 42 , 43 , 44 , 48 ]. In addition, the composition of conserved motifs in each subclade member showed its particular features.…”

“…The analysis of duplication events of BpTCP genes showed that there were no tandem duplication events, but there were four segment gene pairs. It suggested that segmental duplications may be the primary driving force for the expansion of the BpTCP gene family, as described previously, in V. vinifera and Gossypium raimondii [ 42 , 53 ].…”

“…For instance, motif 2, motif 4 and motif 10 were unique to the PCF subclade. All CYC/TB1 subclade members (BpTCP8, BpTCP14 and BpTCP19) and two CIN subclade members (BpTCP10 and BpTCP15) contained motif 6 (that is, R domain), which is similar to that in VvTCPs , PmTCPs and FvTCPs [ 42 , 49 , 50 ]. R domain is hypothesized to form a hydrophilic α-helix or a coiled coil structure that may mediate protein–protein interactions [ 1 ].…”

“…Thus, the number of branches is great importance for B. papyrifera , because the architecture with plenty branches and leaves is needed to ramp up production. To date, the TCP gene family has been identified in multiple species, for instance, Arabidopsis , Oryza sativa (rice), Panicum virgatum (switchgrass), Vitis vinifera (grape), Z. mays (maize), Phaseolus vulgaris (common bean) and Citrullus lanatus (watermelon) [ 6 , 41 , 42 , 43 , 44 , 45 ]. It is proved that TCP genes have important functions in shoot branching and plant growth.…”

Versatile physiological functions of the Nudix Hydrolase family in berry development and stress response in grapevine

“…Grapevine plantlets grown in the standard conditions were used as a control. The RPKM (Reads Per Kilobase per Million mapped reads) values were used to represent the gene expression level as previous method [42]. The heatmap of VvNUDX genes was exhibited using R software (http://www.bioconductor.org/).…”