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. 2023 Jun 22;12(13):2418.
doi: 10.3390/plants12132418.

Genome-Wide Identification of the PP2C Gene Family and Analyses with Their Expression Profiling in Response to Cold Stress in Wild Sugarcane

Xing Huang  1 , Yongsheng Liang  2 , Ronghua Zhang  1 , Baoqing Zhang  1 , Xiupeng Song  1 , Junxian Liu  1 , Manman Lu  1 , Zhenqiang Qin  1 , Dewei Li  1 , Song Li  1 , Yangrui Li  1
Affiliations

Genome-Wide Identification of the PP2C Gene Family and Analyses with Their Expression Profiling in Response to Cold Stress in Wild Sugarcane

Xing Huang et al. Plants (Basel). .

Abstract

Type 2C protein phosphatases (PP2Cs) represent a major group of protein phosphatases in plants, some of which have already been confirmed to play important roles in diverse plant processes. In this study, analyses of the phylogenetics, gene structure, protein domain, chromosome localization, and collinearity, as well as an identification of the expression profile, protein-protein interaction, and subcellular location, were carried out on the PP2C family in wild sugarcane (Saccharum spontaneum). The results showed that 145 PP2C proteins were classified into 13 clades. Phylogenetic analysis suggested that SsPP2Cs are evolutionarily closer to those of sorghum, and the number of SsPP2Cs is the highest. There were 124 pairs of SsPP2C genes expanding via segmental duplications. Half of the SsPP2C proteins were predicted to be localized in the chloroplast (73), with the next most common predicted localizations being in the cytoplasm (37) and nucleus (17). Analysis of the promoter revealed that SsPP2Cs might be photosensitive, responsive to abiotic stresses, and hormone-stimulated. A total of 27 SsPP2Cs showed cold-stress-induced expressions, and SsPP2C27 (Sspon.01G0007840-2D) and SsPP2C64 (Sspon.03G0002800-3D) were the potential hubs involved in ABA signal transduction. Our study presents a comprehensive analysis of the SsPP2C gene family, which can play a vital role in the further study of phosphatases in wild sugarcane. The results suggest that the PP2C family is evolutionarily conserved, and that it functions in various developmental processes in wild sugarcane.

Keywords: cold stress; gene expression profiling; phylogenetic analysis; type 2C protein phosphatase (PP2C); wild sugarcane.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic analysis of PP2C proteins among wild sugarcane and Arabidopsis.
Figure 2
Figure 2
Analysis of gene structure and protein conserved motif of Sspp2Cs: (A) phylogenetic tree of SsPP2Cs; (B) gene structure; (C) conserved motifs.
Figure 3
Figure 3
Conserved motif sequence of SsPP2C proteins.
Figure 4
Figure 4
Chromosomal locations of SsPP2C genes.
Figure 5
Figure 5
Duplication analysis of SsPP2C genes.
Figure 6
Figure 6
Synteny analysis among PP2C genes in wild surgacane and other plant species.
Figure 7
Figure 7
The heatmap of SsPP2C genes responding to low temperatures at transcription.
Figure 8
Figure 8
Protein–protein interaction analysis of all SsPP2Cs.
Figure 9
Figure 9
The protein–protein interaction analysis of SsPP2Cs responding to low temperature.
Figure 10
Figure 10
Subcellular localization of SsPP2C27, SsPP2C31, SsPP2C64, and SsPP2C110 in rice leaf protoplasts expressing green fluorescent protein (GFP). Scale bars represent 5 μm.
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