Phylogeny and expression pattern analysis of TCP transcription factors in cassava seedlings exposed to cold and/or drought stress

Ning Lei,Ming Peng,Xiang Yu,Shuxia Li,Liangping Zou,Changying Zeng,Wenbin Liao

doi:10.1038/s41598-017-09398-5

Abstract

The TCP transcription factors usually act as integrators of multiple growth regulatory and environmental stimuli. However, little is known about this gene family in the important tropical crop cassava (Manihot esculenta). In this study, 36 TCP genes were identified and renamed based on cassava whole-genome sequence and their sequence similarity with Arabidopsis TCPs. Typical TCP domains were detected in these proteins by multiple sequence alignment analysis. Evolutionary analysis indicated that MeTCPs could be divided into 8 subgroups, which was further supported by gene structure and conserved motif analyses. qRT-PCR analysis revealed tissue-specific and hormone-responsive expression patterns of MeTCP genes. Moreover, with global expression and promoter analysis, we found that MeTCPs showed similar or distinct expression patterns under cold and/or drought stress, suggesting that they might participate in distinct signaling pathways. Our study provides the first comprehensive analysis of TCP gene family in the cassava genome. The data will be useful for uncovering the potential functions of MeTCP genes, and their possible roles in mediating hormone and abiotic stress responses in cassava.

Highlights

As sessile organism, plant growth and yield are strongly influenced by environmental stimuli such as cold and drought[1]
36 candidate TCP genes were identified in cassava, and further conserved domain detection confirmed that all the identified TCPs harbor the conserved TCP domain that is the basic characteristics of this family
Due to the lack of standard annotation designated to the 36 cassava TCP genes, we named them MeTCP2 to MeTCP23 according to the Arabidopsis TCP proteins with highest sequence similarity

Summary

Introduction

Plant growth and yield are strongly influenced by environmental stimuli such as cold and drought[1]. GGNCCCAC while class II prefer to bind the DNA motif G(T/C)GGNCCC10 Both class I and class II include TCPs that can function as transcriptional activators and repressors[12]. Increasing evidences have indicated that proteins of TCP family take part in the regulation of many biological processes during plant growth and development, including plant architecture[12, 13], leaf morphogenesis[14,15,16], hormone pathways[13, 17,18,19] and response to environmental stimuli among various species[20,21,22]. We performed strand specific RNA sequencing for cassava TMS60444 shoot apices and young leaves under cold and PEG-induced drought stress, providing an excellent resource for analysis of stress responsive genes globally

Methods

Results

Conclusion