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

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.

Keywords: CBL-interacting protein kinases; abiotic stress; cassava; gene expression; genome-wide; identification.

Figure 1

Phylogenetic analysis of CIPK proteins in cassava, rice, Arabidopsis, and Populus. A total of 25 CIPK proteins from cassava (triangle), 26 from Arabidopsis (square) and 34 from rice (round) and 27 Populus (diamond) were used to construct the maximum likelihood tree using ClustalX 2.0 and MEGA5 with 1000 bootstrap. Branches with less than 50% bootstrap support were collapsed. Five groups were labeled as A, B, C, D, and E.

Figure 2

The phylogenetic relationship and exon-intron structure analyses of CIPK family in cassava. Exon-intron structure analysis was performed by online tool GSDS. Lengths of exons and introns of each MeCIPK gene were exhibited proportionally. A, C, D, and E indicated the classification of cassava CIPKs according to the phylogenetic relationship.

Figure 3

Conserved motifs of cassava CIPK proteins according to the phylogenetic relationship. All motifs were identified by MEME with the complete amino acid sequences of 25 CIPKs from cassava. Lengths of motifs of each MeCIPK protein were displayed proportionally. A, C, D, and E indicated the classification of cassava CIPKs according to the phylogenetic relationship.

Figure 4

Expression patterns of cassava CIPK genes in different tissues of three cassava accessions. Log2 based FPKM value was used to create the heat map. The scale represents the relative signal intensity of FPKM values. A, C, D, and E indicated the classification of cassava CIPKs according to the phylogenetic relationship.

Figure 5

Expression patterns of CIPK genes in leaves and roots of three cassava accessions after drought treatment. Log2 based FPKM value was used to create the heat map. The scale represents the relative signal intensity of FPKM values. A, C, D, and E indicated the classification of cassava CIPKs according to the phylogenetic relationship.

Figure 6

Interaction network and co-expression analyses of CIPK genes in leaves of Arg7 (A) and W14 (B) and related genes in Arabidopsis. The homologous genes of cassava are in parentheses. The genes marked with red font show upregulation based on 1.5 fold change. The genes marked with green font show downregulation based on 1.5 fold change. The genes involved in CBL4/SOS3-CIPK24/SOS2-SOS1/NHX7 and the CBL1/CBL9-CIPK23-AKT1 pathways are boxed with purple and yellow, respectively.

Figure 7

Expression profiles of CIPK genes in leaves of cassava in response to osmotic, salt, cold, oxidative stresses, and ABA. Log2 based value was used to create the heat map. The scale represents the relative signal intensity values.