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.

Genome-Wide Identification and Abiotic Stress Response Analysis of PP2C Gene Family in Woodland and Pineapple Strawberries

“…Both FvPP2C and FaPP2C were expressed mostly in the nucleus, cytoplasm, and chloroplast ( Supplementary Tables S1 and S2 ). Similar results were found in the cucumber study [ 52 ]. Therefore, we speculated that the PP2C protein was involved in respiration, photosynthesis, growth, and development of strawberry.…”

“…Gene replication involves fragment replication, tandem replication, and genome replication, as above-mentioned, and fragment replication is more conducive for maintaining gene function than tandem replication [ 55 ]. It was found that there was fragment replication of the PP2C gene in both woodland and pineapple strawberries ( Figure 3 A,B), and similar results were found in A. thaliana [ 29 ], cucumber [ 52 ], and paper mulberry [ 53 ].…”

“…Moreover, the amino acid sequence of motif 4 was consistent between the two species ( Supplementary Figure S3 ), suggesting that motif 4 played a stable and important role in the evolution of strawberry. This conserved motif was also found in cucumber studies [ 52 ], and it was presumed that the motif contained the conserved domain of PP2C.…”

Genome-wide identification, structural characterization and expression profiling of AP2/ERF gene family in bayberry (Myrica rubra)

“…To elucidate further the phylogenetic evolutionary relationships and structural characteristics of bayberry AP2/ERF genes, we conducted an analysis of their exon-intron gene structure and conserved motifs [44]. The structural domains show that each gene has at least one AP2 structural domain.…”

De novo transcriptome analysis of high-salinity stress-induced antioxidant activity and plant phytohormone alterations in Sesuvium portulacastrum

“…S. portulacastrum, as a halophyte, has different PP2C gene expression levels compared to the control plants. CsPP2C genes in different groups have different responses to different stressors (Zhang G. et al, 2022), and these results provide a reference for the study of PP2C under salt stress. Salt stress has been alleviated using GA 3 as a growth regulator, which has been utilized to accelerate the growth of wheat and rice (Forghani et al, 2018).…”