GHMP gene family: identification, evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomato
Abstract Background The GHMP kinase gene family is a class of structurally similar protein kinases that have been named by combining the first letter of its four members, galactokinase (GALK), homoserine kinase (HSK), mevalonate kinase (MK) and phosphomevalonate kinase (PMK). It plays a pivotal role...
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| Language: | English |
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BMC
2025-07-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-025-06857-4 |
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| author | Haitao Yang Xin Bai Tayeb Muhammad Tao Yang Chunping Jia Baike Wang Qinghui Yu Juan Wang |
| author_facet | Haitao Yang Xin Bai Tayeb Muhammad Tao Yang Chunping Jia Baike Wang Qinghui Yu Juan Wang |
| author_sort | Haitao Yang |
| collection | DOAJ |
| description | Abstract Background The GHMP kinase gene family is a class of structurally similar protein kinases that have been named by combining the first letter of its four members, galactokinase (GALK), homoserine kinase (HSK), mevalonate kinase (MK) and phosphomevalonate kinase (PMK). It plays a pivotal role in regulating plant growth and development, as well as mediating various responses. However, the identification and functional analysis of GHMP family members in tomato have not been carried out yet. Results This study presents a comprehensive analysis of the GHMP gene family in cultivated tomato and three wild tomato species. The analysis encompasses phylogenetic classification, gene structure, collinearity, physical and chemical features, cis-acting elements, tissue-specific expression, and hormonal and abiotic stress responses. A total of 56 GHMP genes were identified in the four tomato species. The phylogenetic analysis classified the GHMP members into 10 subfamilies, which is in agreement with the results of motif distribution and gene structure analysis. Members of the same subfamily tend to exhibit similar or identical motif types and order of distribution. The synteny analysis suggests that dispersed and single-copy replication may have played a role in the expansion of the GHMP gene family in tomatoes with pure selection. A diverse set of cis-acting elements was identified in the promoters of the GHMPs, includingelements related to growth and development, hormone and stress responses and transcription factor interaction binding sites, indicating a multifaceted role of the GHMPs in tomato. RNA-seq data analysis revealed that GHMP members exhibited differential expression in distinct tissues, signifying their involvement in tomato growth and development. In response to exogenous hormonal and abiotic treatments, FKGP, PMK1, ARA1, PMK2, GALAK2 and ISPE were upregulated by hormonal treatments, while ISPE, PMK1, ARA1, ARA2, and MK responded to abiotic stresses. Conclusions Overall, the findings of this study contribute to a deeper understanding of the GHMP gene family, which could serve as a foundation for future investigations of their biological function, particularly in response to hormonal and abiotic stress. |
| format | Article |
| id | doaj-art-d938dea5fc3243e3aa210ba074c2d49e |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-d938dea5fc3243e3aa210ba074c2d49e2025-08-20T04:01:23ZengBMCBMC Plant Biology1471-22292025-07-0125111910.1186/s12870-025-06857-4GHMP gene family: identification, evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomatoHaitao Yang0Xin Bai1Tayeb Muhammad2Tao Yang3Chunping Jia4Baike Wang5Qinghui Yu6Juan Wang7Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural SciencesKey Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural SciencesKey Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural SciencesKey Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural SciencesKey Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural SciencesKey Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural SciencesKey Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural SciencesKey Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural SciencesAbstract Background The GHMP kinase gene family is a class of structurally similar protein kinases that have been named by combining the first letter of its four members, galactokinase (GALK), homoserine kinase (HSK), mevalonate kinase (MK) and phosphomevalonate kinase (PMK). It plays a pivotal role in regulating plant growth and development, as well as mediating various responses. However, the identification and functional analysis of GHMP family members in tomato have not been carried out yet. Results This study presents a comprehensive analysis of the GHMP gene family in cultivated tomato and three wild tomato species. The analysis encompasses phylogenetic classification, gene structure, collinearity, physical and chemical features, cis-acting elements, tissue-specific expression, and hormonal and abiotic stress responses. A total of 56 GHMP genes were identified in the four tomato species. The phylogenetic analysis classified the GHMP members into 10 subfamilies, which is in agreement with the results of motif distribution and gene structure analysis. Members of the same subfamily tend to exhibit similar or identical motif types and order of distribution. The synteny analysis suggests that dispersed and single-copy replication may have played a role in the expansion of the GHMP gene family in tomatoes with pure selection. A diverse set of cis-acting elements was identified in the promoters of the GHMPs, includingelements related to growth and development, hormone and stress responses and transcription factor interaction binding sites, indicating a multifaceted role of the GHMPs in tomato. RNA-seq data analysis revealed that GHMP members exhibited differential expression in distinct tissues, signifying their involvement in tomato growth and development. In response to exogenous hormonal and abiotic treatments, FKGP, PMK1, ARA1, PMK2, GALAK2 and ISPE were upregulated by hormonal treatments, while ISPE, PMK1, ARA1, ARA2, and MK responded to abiotic stresses. Conclusions Overall, the findings of this study contribute to a deeper understanding of the GHMP gene family, which could serve as a foundation for future investigations of their biological function, particularly in response to hormonal and abiotic stress.https://doi.org/10.1186/s12870-025-06857-4TomatoBioinformaticsGHMPHormonal treatmentsAbiotic stresses |
| spellingShingle | Haitao Yang Xin Bai Tayeb Muhammad Tao Yang Chunping Jia Baike Wang Qinghui Yu Juan Wang GHMP gene family: identification, evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomato BMC Plant Biology Tomato Bioinformatics GHMP Hormonal treatments Abiotic stresses |
| title | GHMP gene family: identification, evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomato |
| title_full | GHMP gene family: identification, evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomato |
| title_fullStr | GHMP gene family: identification, evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomato |
| title_full_unstemmed | GHMP gene family: identification, evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomato |
| title_short | GHMP gene family: identification, evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomato |
| title_sort | ghmp gene family identification evolutionary and expression analysis under various exogenous hormones and abiotic stress in tomato |
| topic | Tomato Bioinformatics GHMP Hormonal treatments Abiotic stresses |
| url | https://doi.org/10.1186/s12870-025-06857-4 |
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