Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa)
Abstract Background The jasmonate ZIM domain (JAZ) protein is a key repressor of the jasmonate signal transduction pathway, which plays an important role in plant growth and development and defense responses. In this study, based on the published whole-genome data, we identified members of the JAZ g...
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| Format: | Article |
| Language: | English |
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BMC
2023-09-01
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| Series: | BMC Genomic Data |
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| Online Access: | https://doi.org/10.1186/s12863-023-01150-5 |
| _version_ | 1797451371432116224 |
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| author | Gaixia Yang Shijie Wang Lianxiang Long Xiaoyue Yu Hongyu Cai Pengyun Chen Lijiao Gu Minsheng Yang |
| author_facet | Gaixia Yang Shijie Wang Lianxiang Long Xiaoyue Yu Hongyu Cai Pengyun Chen Lijiao Gu Minsheng Yang |
| author_sort | Gaixia Yang |
| collection | DOAJ |
| description | Abstract Background The jasmonate ZIM domain (JAZ) protein is a key repressor of the jasmonate signal transduction pathway, which plays an important role in plant growth and development and defense responses. In this study, based on the published whole-genome data, we identified members of the JAZ gene family in Populus trichocarpa. Through a series of bioinformatic approaches, their expression patterns under various stress conditions have been analyzed to explore and excavate the endogenous resistance genes of poplar and provide a theoretical basis for breeding new varieties of poplar resistance. Results A total of 13 PtJAZ genes have been identified in P. trichocarpa and designated as PtJAZ1–PtJAZ13. Those 13 PtJAZ genes were unevenly distributed on nine chromosomes, and they could be divided into four subfamilies. The gene structures and motif composition of the members derived from the same subfamily were similar. Collinearity analysis demonstrated that, compared with Arabidopsis thaliana and Oryza sativa, the most collinear pairs (13) were found in P. trichocarpa and Eucalyptus robusta. Cis-acting element analysis suggested that the promoter regions of PtJAZs contained a large number of hormones and stress response elements, of which abscisic acid (ABA) and methyl jasmonate (MeJA) hormone response elements were the most abundant. The PtJAZ genes not only had diverse expression patterns in different tissues, but they also responded to various abiotic and biotic stress conditions. The co-expression network and GO and KEGG analyses showed that JAZ genes were closely related to insect resistance. Conclusions In this study, applying bioinformatic methods, 13 PtJAZ gene family members from P. trichocarpa were identified and comprehensively analyzed. By further studying the function of the poplar JAZ gene family, the aim is to select genes with better insect resistance and stress resistance so as to lay a solid foundation for the subsequent breeding of new poplar varieties. |
| first_indexed | 2024-03-09T14:52:45Z |
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| id | doaj.art-ed2844405c8242c9bff86a5f7c960b3f |
| institution | Directory Open Access Journal |
| issn | 2730-6844 |
| language | English |
| last_indexed | 2024-03-09T14:52:45Z |
| publishDate | 2023-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomic Data |
| spelling | doaj.art-ed2844405c8242c9bff86a5f7c960b3f2023-11-26T14:22:26ZengBMCBMC Genomic Data2730-68442023-09-0124111310.1186/s12863-023-01150-5Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa)Gaixia Yang0Shijie Wang1Lianxiang Long2Xiaoyue Yu3Hongyu Cai4Pengyun Chen5Lijiao Gu6Minsheng Yang7Forest Department, Forestry College, Hebei Agricultural UniversityForest Department, Forestry College, Hebei Agricultural UniversityForest Department, Forestry College, Hebei Agricultural UniversityCollege of Landscape Architecture and Tourism, Hebei Agricultural UniversityForest Department, Forestry College, Hebei Agricultural UniversityState Key Laboratory of Cotton Biology, School of Life Sciences, College of Agriculture, Henan UniversityForest Department, Forestry College, Hebei Agricultural UniversityForest Department, Forestry College, Hebei Agricultural UniversityAbstract Background The jasmonate ZIM domain (JAZ) protein is a key repressor of the jasmonate signal transduction pathway, which plays an important role in plant growth and development and defense responses. In this study, based on the published whole-genome data, we identified members of the JAZ gene family in Populus trichocarpa. Through a series of bioinformatic approaches, their expression patterns under various stress conditions have been analyzed to explore and excavate the endogenous resistance genes of poplar and provide a theoretical basis for breeding new varieties of poplar resistance. Results A total of 13 PtJAZ genes have been identified in P. trichocarpa and designated as PtJAZ1–PtJAZ13. Those 13 PtJAZ genes were unevenly distributed on nine chromosomes, and they could be divided into four subfamilies. The gene structures and motif composition of the members derived from the same subfamily were similar. Collinearity analysis demonstrated that, compared with Arabidopsis thaliana and Oryza sativa, the most collinear pairs (13) were found in P. trichocarpa and Eucalyptus robusta. Cis-acting element analysis suggested that the promoter regions of PtJAZs contained a large number of hormones and stress response elements, of which abscisic acid (ABA) and methyl jasmonate (MeJA) hormone response elements were the most abundant. The PtJAZ genes not only had diverse expression patterns in different tissues, but they also responded to various abiotic and biotic stress conditions. The co-expression network and GO and KEGG analyses showed that JAZ genes were closely related to insect resistance. Conclusions In this study, applying bioinformatic methods, 13 PtJAZ gene family members from P. trichocarpa were identified and comprehensively analyzed. By further studying the function of the poplar JAZ gene family, the aim is to select genes with better insect resistance and stress resistance so as to lay a solid foundation for the subsequent breeding of new poplar varieties.https://doi.org/10.1186/s12863-023-01150-5Populus trichocarpaJAZ gene familyBioinformatics analysisExpression patternsFunctional prediction |
| spellingShingle | Gaixia Yang Shijie Wang Lianxiang Long Xiaoyue Yu Hongyu Cai Pengyun Chen Lijiao Gu Minsheng Yang Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa) BMC Genomic Data Populus trichocarpa JAZ gene family Bioinformatics analysis Expression patterns Functional prediction |
| title | Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa) |
| title_full | Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa) |
| title_fullStr | Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa) |
| title_full_unstemmed | Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa) |
| title_short | Genome-wide identification and expression analysis of PtJAZ gene family in poplar (Populus trichocarpa) |
| title_sort | genome wide identification and expression analysis of ptjaz gene family in poplar populus trichocarpa |
| topic | Populus trichocarpa JAZ gene family Bioinformatics analysis Expression patterns Functional prediction |
| url | https://doi.org/10.1186/s12863-023-01150-5 |
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