Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe
Abstract Background 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...
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-09966-w |
| _version_ | 1797350164390739968 |
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| author | Pan Zhang Deqi Liu Jiawei Ma Chong Sun Zhaofei Wang Yongxing Zhu Xuemei Zhang Yiqing Liu |
| author_facet | Pan Zhang Deqi Liu Jiawei Ma Chong Sun Zhaofei Wang Yongxing Zhu Xuemei Zhang Yiqing Liu |
| author_sort | Pan Zhang |
| collection | DOAJ |
| description | Abstract Background 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. Results 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. Conclusions 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. |
| first_indexed | 2024-03-08T12:40:50Z |
| format | Article |
| id | doaj.art-e0069044f9c947fcb57f06d1f22ec20e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-08T12:40:50Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e0069044f9c947fcb57f06d1f22ec20e2024-01-21T12:11:53ZengBMCBMC Genomics1471-21642024-01-0125112010.1186/s12864-024-09966-wGenome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale RoscoePan Zhang0Deqi Liu1Jiawei Ma2Chong Sun3Zhaofei Wang4Yongxing Zhu5Xuemei Zhang6Yiqing Liu7College of Horticulture and Gardening, Spice Crops Research Institute, Yangtze UniversityCollege of Horticulture and Gardening, Spice Crops Research Institute, Yangtze UniversityCollege of Horticulture and Gardening, Spice Crops Research Institute, Yangtze UniversitySpecial Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesSpecial Plants Institute, College of Landscape Architecture and Life Science, Chongqing University of Arts and SciencesCollege of Horticulture and Gardening, Spice Crops Research Institute, Yangtze UniversityCollege of Horticulture and Gardening, Spice Crops Research Institute, Yangtze UniversityCollege of Horticulture and Gardening, Spice Crops Research Institute, Yangtze UniversityAbstract Background 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. Results 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. Conclusions 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.https://doi.org/10.1186/s12864-024-09966-wPP2C gene familyGingerGenome-wide analysisChilling stressFunctional analysis |
| spellingShingle | Pan Zhang Deqi Liu Jiawei Ma Chong Sun Zhaofei Wang Yongxing Zhu Xuemei Zhang Yiqing Liu Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe BMC Genomics PP2C gene family Ginger Genome-wide analysis Chilling stress Functional analysis |
| title | Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe |
| title_full | Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe |
| title_fullStr | Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe |
| title_full_unstemmed | Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe |
| title_short | Genome-wide analysis and expression pattern of the ZoPP2C gene family in Zingiber officinale Roscoe |
| title_sort | genome wide analysis and expression pattern of the zopp2c gene family in zingiber officinale roscoe |
| topic | PP2C gene family Ginger Genome-wide analysis Chilling stress Functional analysis |
| url | https://doi.org/10.1186/s12864-024-09966-w |
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