Genome-wide gene phylogeny of CIPK family in cassava and expression analysis of partial drought-induced genes.

Wei Hu,Yunxie Wei,Wenquan Wang,Zhiqiang Xia,Meiling Zou,Zehong Ding,Xiaowan Hou,Lianzhe Wang,Cheng Lu,Yan Yan,Ming Peng,Weiwei Tie

doi:10.3389/fpls.2015.00914

Abstract

Cassava is an important food and potential biofuel crop that is tolerant to multiple abiotic stressors. The mechanisms underlying these tolerances are currently less known. CBL-interacting protein kinases (CIPKs) have been shown to play crucial roles in plant developmental processes, hormone signaling transduction, and in the response to abiotic stress. However, no data is currently available about the CPK family in cassava. In this study, a total of 25 CIPK genes were identified from cassava genome based on our previous genome sequencing data. Phylogenetic analysis suggested that 25 MeCIPKs could be classified into four subfamilies, which was supported by exon-intron organizations and the architectures of conserved protein motifs. Transcriptomic analysis of a wild subspecies and two cultivated varieties showed that most MeCIPKs had different expression patterns between wild subspecies and cultivatars in different tissues or in response to drought stress. Some orthologous genes involved in CIPK interaction networks were identified between Arabidopsis and cassava. The interaction networks and co-expression patterns of these orthologous genes revealed that the crucial pathways controlled by CIPK networks may be involved in the differential response to drought stress in different accessions of cassava. Nine MeCIPK genes were selected to investigate their transcriptional response to various stimuli and the results showed the comprehensive response of the tested MeCIPK genes to osmotic, salt, cold, oxidative stressors, and ABA signaling. The identification and expression analysis of CIPK family suggested that CIPK genes are important components of development and multiple signal transduction pathways in cassava. The findings of this study will help lay a foundation for the functional characterization of the CIPK gene family and provide an improved understanding of abiotic stress responses and signaling transduction in cassava.

Highlights

Calcium signaling is involved in multiple physiological and developmental processes
Transcriptomic analysis of a wild subspecies and two cultivators suggested that most of cassava calcineurin B-like proteins (CBLs)-interacting protein kinases (CIPKs) genes had differential expression of different accessions for a special tissue, which might contribute to the function diversity of different accessions
Further transcriptomic analysis of different cassava accessions in response to drought revealed that the high ratio of CIPK members induced by drought in W14 subspecies might contribute to its strong tolerance to drought

Summary

Introduction

Calcium signaling is involved in multiple physiological and developmental processes. Calcium, an important second messenger, regulates various signal transduction pathways (Kolukisaoglu et al, 2004; Kanwar et al, 2014). Intracellular calcium levels are modulated when plants respond to light, pathogens, abiotic stresses, and hormones and undergo physiological processes, such as root hair elongation, guard cell regulation, and pollen tube growth (Evans et al, 2001; Harper, 2001; Knight and Knight, 2001; Kolukisaoglu et al, 2004). CBL-interacting protein kinases (CIPKs) can target CBLs to transduce the perceived calcium signal, belonging to the Ca2+-mediated CBL-CIPK network, in response to various stimuli (Deng et al, 2013; Zhang et al, 2014). In the C-terminal regulatory domain, the conserved NAF or FISL motif is responsible for interacting with Ca2+-bound CBLs, leading to the activation of the targeting CIPKs (Albrecht et al, 2001; Guo et al, 2001). The protein-phosphatase interaction (PPI) domain within the C-terminus of CIPKs can target specific members of the protein phosphatase 2C (PP2C; Ohta et al, 2003)

Methods

Results

Conclusion