Genome-Wide Identification and Characterization of the TCP Gene Family in Cucumber (Cucumis sativus L.) and Their Transcriptional Responses to Different Treatments.

Haifan Wen,Junsong Pan,Run Cai,Hui Du,Keyan Zhang,Leyu Zhang,Gang Wang,Huanle He,Yue Chen

doi:10.3390/genes11111379

Abstract

TCP proteins are plant-specific transcription factors widely implicated in leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, the relationship between the transcription pattern of TCPs and organ development in cucumber has not been systematically studied. In this study, we performed a genome-wide identification of putative TCP genes and analyzed their chromosomal location, gene structure, conserved motif, and transcript expression. A total of 27 putative TCP genes were identified and characterized in cucumber. All 27 putative CsTCP genes were classified into class I and class II. Class I comprised 12 CsTCPs and Class II contained 15 CsTCPs. The 27 putative CsTCP genes were randomly distributed in five of seven chromosomes in cucumber. Four putative CsTCP genes were found to contain putative miR319 target sites. Quantitative RT-PCR revealed that 27 putative CsTCP genes exhibited different expression patterns in cucumber tissues and floral organ development. Transcript expression and phenotype analysis showed that the putative CsTCP genes responded to temperature and photoperiod and were induced by gibberellin (GA)and ethylene treatment, which suggested that CsTCP genes may regulate the lateral branching by involving in multiple signal pathways. These results lay the foundation for studying the function of cucumber TCP genes in the future.

Highlights

Transcription factors play significant roles in plant growth development
27 candidate CsTCPs were screened out, all of which were verified the existence of the TCP domains with the SMART and Pfam databases
The SMART analysis revealed that all putative cucumber TCP proteins contained the TCP domain, implying that there are at least 27 putative TCP genes in cucumber

Summary

Introduction

The TCP gene family is a plant-specific transcription factor family [1]. The TCP transcription factors contain a conserved TCP domain, which constitutes a basic helix-loop-helix (bHLH) structure at the N-terminus. This domain is important for DNA binding and involved in protein–protein interactions [5]. According to the amino acid sequence similarity of the TCP domain, TCP factors were divided into two major classes: class I (PCF or TCP-P class) and class II (TCP-C class) [5,6]. The most significant difference between these two classes is a four-amino acid deletion in the basic domain of class I relative to class II proteins. The class II group can be further divided into subclasses, CIN and

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Conclusion