Genome-wide survey and expression analysis of calcium-dependent protein kinase in Gossypium raimondii

Abstract

Calcium-dependent protein kinases (CDPKs) are one of the largest protein kinases in plants and participate in different physiological processes through regulating downstream components of calcium signaling pathways. In this study, 41 CDPK genes, from GrCPK1 to GrCPK41, were identified in the genome of the diploid cotton, Gossypium raimondii. The phylogenetic analysis indicated that all these genes were divided into four subgroups and members within the same subgroup shared conserved exon-intron structures. The expansion of GrCPKs family in G. raimondii was due to the segmental duplication events, and the analysis of Ka/Ks ratios implied that the duplicated GrCPKs had mainly undergone strong purifying selection pressure with limited functional divergence. The cold-responsive elements in promoter regions were detected in the majority of GrCPKs. The expression analysis of 11 selected genes showed that GrCPKs exhibited tissue-specific expression patterns and the expression of GrCPKs were induced or repressed by cold treatment. These observations would lay an important foundation for functional and evolutionary analysis of CDPK gene family in Gossypium species.

Figure 1. Unrooted phylogenetic tree of CDPK genes from G. raimondii, Arabidopsis and rice.

Four subfamilies are labeled as I, II, III, and IV. And the branches of each subfamily are indicated in a specific color.

Figure 2. Phylogenetic relationship and gene structure of CDPK genes from G. raimondii.

Four subfamilies labeled as I, II, III, and IV are marked with different color backgrounds. Exons are represented by green boxes and introns by black lines. The untranslated regions (UTRs) are indicated by thick blue lines.

Figure 3. Distributions of CDPK genes from G. raimondii in 13 chromosomes.

Chromosome numbers are indicated above each vertical bar. The scale represents megabases (Mb). The duplicated gene pairs are connected with black lines.

Figure 4. Expression patterns of 11 GrCPKs in four representative tissues of G. raimondii seedlings.

The color bar represents the relative signal intensity values.

Figure 5. Expression profiling of 11 GrCPKs in leaves under 10°C treatment.

The color bar represents the relative signal intensity values.