Genome-wide identification and expression analysis of the cucumber PP2C gene family

Abstract

Background: Type 2C protein phosphatase (PP2C) is a negative regulator of ABA signaling pathway, which plays important roles in stress signal transduction in plants. However, little research on the PP2C genes family of cucumber (Cucumis sativus L.), as an important economic vegetable, has been conducted.

Results: This study conducted a genome-wide investigation of the CsPP2C gene family. Through bioinformatics analysis, 56 CsPP2C genes were identified in cucumber. Based on phylogenetic analysis, the PP2C genes of cucumber and Arabidopsis were divided into 13 groups. Gene structure and conserved motif analysis showed that CsPP2C genes in the same group had similar gene structure and conserved domains. Collinearity analysis showed that segmental duplication events played a key role in the expansion of the cucumber PP2C genes family. In addition, the expression of CsPP2Cs under different abiotic treatments was analyzed by qRT-PCR. The results reveal that CsPP2C family genes showed different expression patterns under ABA, drought, salt, and cold treatment, and that CsPP2C3, 11-17, 23, 45, 54 and 55 responded significantly to the four stresses. By predicting the cis-elements in the promoter, we found that all CsPP2C members contained ABA response elements and drought response elements. Additionally, the expression patterns of CsPP2C genes were specific in different tissues.

Conclusions: The results of this study provide a reference for the genome-wide identification of the PP2C gene family in other species and provide a basis for future studies on the function of PP2C genes in cucumber.

Keywords: Cucumber; Protein phosphatase 2C; Stress response.

Fig. 1

Chromosomal distribution and localization of CsPP2Cs. The chromosome names are shown at the left of each chromosome. The chromosome scale is in millions of bases (Mb) on the left

Fig. 2

Collinearity analysis of the PP2C gene family in cucumber. a Chromosomes 1–7 are represented by gray rectangles. The gray lines indicate synteny blocks in the cucumber genome, while the lines of different colors between chromosomes delineate segmental duplicated gene pairs. b Synteny analysis of PP2Cs between cucumber and Arabidopsis. Gray lines denote the collinear blocks between cucumber and Arabidopsis genomes and the lines of different colors denote the syntenic gene pairs of PP2Cs. Gray rectangles represent respectively the cucumber chromosomes (1–7) and Arabidopsis chromosomes (1–5)

Fig. 3

Phylogenetic analysis of PP2C proteins among cucumber and Arabidopsis, red asterisks represent CsPP2C, black circles represent Arabidopsis. The phylogenetic tree was constructed by MEGA 7 using the Maximum Likelihood Method (1000 bootstrap)

Fig. 4

Phylogenetic tree, gene structure and motif analysis of CsPP2Cs. a The phylogenetic tree of CsPP2C is divided into ten groups. b Exon–intron structures of CsPP2C genes. c Distribution of all motifs identified by MEME

Fig. 5

Putative cis-elements existed in the 2 kb upstream region of cucumber PP2C genes. The elements which respond to hormones are displayed in differently coloured boxes. The homeopathic elements represented by different color boxes and their names and functions

Fig. 6

Expression patterns of CsPP2C genes in various wheat tissues. Heatmap of CsPP2C RNA-seq data in five tissues at three different developmental stages was created by TBTools. The expression values mapped to a color gradient from low (blue) to high expression (orange) are shown at the right of the figure

Fig. 7

Quantitative real-time PCR analysis of CsPP2C genes in response to ABA (a), NaCl (b), PEG (c), cold treatments (d). he gene relative expression was calculated using the 2^-∆∆Ct method with CsActin as an internal control, and value represents mean ± SE of three biological replicates. Statistical analyses were carried out by student’s t-test to determine the differences in gene abundances between 0 h and other treatment times. Asterisks indicated values that are significantly different from CK (0 h) (* p < 0.05, ** p < 0.01, one-way ANOVA)