Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe

Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. In...

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Published in:	BMC genomics 2024-01, Vol.25 (1), p.83-83, Article 83
Main Authors:	Zhang, Pan, Liu, Deqi, Ma, Jiawei, Sun, Chong, Wang, Zhaofei, Zhu, Yongxing, Zhang, Xuemei, Liu, Yiqing
Format:	Article
Language:	eng
Subjects:	Abscisic acid Amino acid sequence Amino acids Binding sites Botanical research Cell cycle Chilling Chilling stress Chromosomes Collinearity Drought Environmental stress Enzymes Functional analysis Gene expression Gene Expression Profiling Gene Expression Regulation, Plant Genes Genetic aspects Genetic engineering Genome, Plant Genome-wide analysis Genomes Ginger Hormones Kinases Localization Maximum likelihood method Pattern analysis Phosphatase Phosphoprotein Phosphatases - genetics Phosphorylation Phylogenetics Phylogeny Physiological aspects Physiology Plant growth Plant Proteins - genetics Plant Proteins - metabolism Plant resistance PP2C gene family Proteins Regulatory sequences Seeds Stress, Physiological - genetics Stresses Zingiber officinale - genetics
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Summary:	Protein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published. In this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress. Taken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.
ISSN:	1471-2164 1471-2164