Pan-Genome Analysis of <i>TRM</i> Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber
Cucumber (<i>Cucumis sativus</i> L.) is a vital economic vegetable crop, and the TONNEAU1 Recruiting Motif (TRM) gene plays a key role in cucumber organ growth. However, the pan-genomic characteristics of the <i>TRM</i> gene family and their expression patterns under differen...
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MDPI AG
2024-08-01
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| Series: | Horticulturae |
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| author | Lili Zhao Ke Wang Zimo Wang Shunpeng Chu Chunhua Chen Lina Wang Zhonghai Ren |
| author_facet | Lili Zhao Ke Wang Zimo Wang Shunpeng Chu Chunhua Chen Lina Wang Zhonghai Ren |
| author_sort | Lili Zhao |
| collection | DOAJ |
| description | Cucumber (<i>Cucumis sativus</i> L.) is a vital economic vegetable crop, and the TONNEAU1 Recruiting Motif (TRM) gene plays a key role in cucumber organ growth. However, the pan-genomic characteristics of the <i>TRM</i> gene family and their expression patterns under different stresses have not been reported in cucumber. In this study, we identified 29 <i>CsTRMs</i> from the pan-genomes of 13 cucumber accessions, with <i>CsTRM29</i> existing only in PI183967. Most CsTRM proteins exhibited differences in sequence length, except five CsTRMs having consistent protein sequence lengths among the 13 accessions. All CsTRM proteins showed amino acid variations. An analysis of <i>CsTRM</i> gene expression patterns revealed that six <i>CsTRM</i> genes strongly changed in short-fruited lines compared with long-fruited lines. And four <i>CsTRM</i> genes strongly responded to salt and heat stress, while <i>CsTRM14</i> showed responses to salt stress, powdery mildew, gray mold, and downy mildew. Some <i>CsTRM</i> genes were induced or suppressed at different treatment timepoints, suggesting that cucumber <i>TRM</i> genes may play different roles in responses to different stresses, with expression patterns varying with stress changes. Remarkably, the expression of <i>CsTRM21</i> showed considerable change between long and short fruits and in responses to abiotic stresses (salt stress and heat stress), as well as biotic stresses (powdery mildew and gray mold), suggesting a dual role of <i>CsTRM21</i> in both fruit shape determination and stress resistance. Collectively, this study provided a base for the further functional identification of <i>CsTRM</i> genes in cucumber plant growth and stress resistance. |
| format | Article |
| id | doaj-art-61472267c6124d24a35ec60dc67e8d97 |
| institution | OA Journals |
| issn | 2311-7524 |
| language | English |
| publishDate | 2024-08-01 |
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| series | Horticulturae |
| spelling | doaj-art-61472267c6124d24a35ec60dc67e8d972025-08-20T01:55:32ZengMDPI AGHorticulturae2311-75242024-08-0110990810.3390/horticulturae10090908Pan-Genome Analysis of <i>TRM</i> Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in CucumberLili Zhao0Ke Wang1Zimo Wang2Shunpeng Chu3Chunhua Chen4Lina Wang5Zhonghai Ren6Shandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, ChinaShandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, ChinaShandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, ChinaShandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, ChinaShandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, ChinaShandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, ChinaShandong Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in Huang-Huai Region, Ministry of Agriculture, College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an 271018, ChinaCucumber (<i>Cucumis sativus</i> L.) is a vital economic vegetable crop, and the TONNEAU1 Recruiting Motif (TRM) gene plays a key role in cucumber organ growth. However, the pan-genomic characteristics of the <i>TRM</i> gene family and their expression patterns under different stresses have not been reported in cucumber. In this study, we identified 29 <i>CsTRMs</i> from the pan-genomes of 13 cucumber accessions, with <i>CsTRM29</i> existing only in PI183967. Most CsTRM proteins exhibited differences in sequence length, except five CsTRMs having consistent protein sequence lengths among the 13 accessions. All CsTRM proteins showed amino acid variations. An analysis of <i>CsTRM</i> gene expression patterns revealed that six <i>CsTRM</i> genes strongly changed in short-fruited lines compared with long-fruited lines. And four <i>CsTRM</i> genes strongly responded to salt and heat stress, while <i>CsTRM14</i> showed responses to salt stress, powdery mildew, gray mold, and downy mildew. Some <i>CsTRM</i> genes were induced or suppressed at different treatment timepoints, suggesting that cucumber <i>TRM</i> genes may play different roles in responses to different stresses, with expression patterns varying with stress changes. Remarkably, the expression of <i>CsTRM21</i> showed considerable change between long and short fruits and in responses to abiotic stresses (salt stress and heat stress), as well as biotic stresses (powdery mildew and gray mold), suggesting a dual role of <i>CsTRM21</i> in both fruit shape determination and stress resistance. Collectively, this study provided a base for the further functional identification of <i>CsTRM</i> genes in cucumber plant growth and stress resistance.https://www.mdpi.com/2311-7524/10/9/908cucumberpan-genome<i>TRM</i> genefruit shapeabiotic stress responsebiotic stress response |
| spellingShingle | Lili Zhao Ke Wang Zimo Wang Shunpeng Chu Chunhua Chen Lina Wang Zhonghai Ren Pan-Genome Analysis of <i>TRM</i> Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber Horticulturae cucumber pan-genome <i>TRM</i> gene fruit shape abiotic stress response biotic stress response |
| title | Pan-Genome Analysis of <i>TRM</i> Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber |
| title_full | Pan-Genome Analysis of <i>TRM</i> Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber |
| title_fullStr | Pan-Genome Analysis of <i>TRM</i> Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber |
| title_full_unstemmed | Pan-Genome Analysis of <i>TRM</i> Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber |
| title_short | Pan-Genome Analysis of <i>TRM</i> Gene Family and Their Expression Pattern under Abiotic and Biotic Stresses in Cucumber |
| title_sort | pan genome analysis of i trm i gene family and their expression pattern under abiotic and biotic stresses in cucumber |
| topic | cucumber pan-genome <i>TRM</i> gene fruit shape abiotic stress response biotic stress response |
| url | https://www.mdpi.com/2311-7524/10/9/908 |
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