Genome-wide identification and expression analysis of the ClTCP transcription factors in Citrullus lanatus.

Pibiao Shi,Mingfang Zhang,Weifang Wu,Kateta Malangisha Guy,Zhongyuan Hu,Jinghua Yang,Bingsheng Fang

doi:10.1186/s12870-016-0765-9

Abstract

BackgroundThe plant-specific TCP transcription factor family, which is involved in the regulation of cell growth and proliferation, performs diverse functions in multiple aspects of plant growth and development. However, no comprehensive analysis of the TCP family in watermelon (Citrullus lanatus) has been undertaken previously.ResultsA total of 27 watermelon TCP encoding genes distributed on nine chromosomes were identified. Phylogenetic analysis clustered the genes into 11 distinct subgroups. Furthermore, phylogenetic and structural analyses distinguished two homology classes within the ClTCP family, designated Class I and Class II. The Class II genes were differentiated into two subclasses, the CIN subclass and the CYC/TB1 subclass. The expression patterns of all members were determined by semi-quantitative PCR. The functions of two ClTCP genes, ClTCP14a and ClTCP15, in regulating plant height were confirmed by ectopic expression in Arabidopsis wild-type and ortholog mutants.ConclusionsThis study represents the first genome-wide analysis of the watermelon TCP gene family, which provides valuable information for understanding the classification and functions of the TCP genes in watermelon.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0765-9) contains supplementary material, which is available to authorized users.

Highlights

The plant-specific TCP transcription factor family, which is involved in the regulation of cell growth and proliferation, performs diverse functions in multiple aspects of plant growth and development
Due to the lack of standard annotations designated to the 27 TCP genes in watermelon, we named the genes ClTCP1a to ClTCP21 consistent with the Arabidopsis TCP proteins that showed the highest sequence similarity and following the gene nomenclature system applied to Arabidopsis
The ClTCP transcription factors (TF) can be classified into the two TCP classes based on the differences within their TCP domains: 12 of the TFs belong to Class I because of the presence of a four-amino-acid deletion in the basic domain relative to the other TFs; the 15 Class II ClTCP TFs can be further clustered into the CIN subclass and the CYC/ TEOSINTE BRANCHED 1 (TB1) subclass (Additional file 1: Figure S1)

Summary

Introduction

The plant-specific TCP transcription factor family, which is involved in the regulation of cell growth and proliferation, performs diverse functions in multiple aspects of plant growth and development. The family plays important roles in regulating diverse physiological and biological processes, including phytohormone biosynthesis and signal transduction, leaf morphogenesis and senescence, branching, flower development, pollen development and the circadian clock [2,3,4,5,6,7,8,9,10,11,12,13,14,15]. TCP proteins are characterized by a 59-amino-acid non-canonical basic-Helix-Loop-Helix (bHLH) motif that is responsible for DNA binding, nuclear targeting and pair-wise protein–protein interaction [1, 16]. This domain was first identified from four proteins with critical roles in the evolution and. AtTCP9 and AtTCP19 play a positive role in a redundant manner with AtTCP20 in the control of leaf senescence, as tcp tcp and tcp tcp double mutants exhibit earlier onset of senescence in comparison with the wild type, whereas none of the single mutants exhibit accelerated senescence [13, 15]

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Conclusion