Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of <i>DREB</i> Genes That Respond to Biotic and Abiotic Stresses in Cucumber
The production of cucumber (<i>Cucumis sativus</i> L.) is often harmed by biotic and abiotic stresses. Although the dehydration-responsive element-binding (DREB) transcription factors, playing vital roles in stress responses, have been characterized in several plant species, little is kn...
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MDPI AG
2022-11-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/12/11/1879 |
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| author | Can Wang Jing Han Ting Wang Chunhua Chen Junyi Liu Zhixuan Xu Qingxia Zhang Lina Wang Zhonghai Ren |
| author_facet | Can Wang Jing Han Ting Wang Chunhua Chen Junyi Liu Zhixuan Xu Qingxia Zhang Lina Wang Zhonghai Ren |
| author_sort | Can Wang |
| collection | DOAJ |
| description | The production of cucumber (<i>Cucumis sativus</i> L.) is often harmed by biotic and abiotic stresses. Although the dehydration-responsive element-binding (DREB) transcription factors, playing vital roles in stress responses, have been characterized in several plant species, little is known about the pan-genome characteristics of <i>DREB</i> genes and their expression patterns under different stresses in cucumber. In this study, we identified 55 CsDREBs from the cucumber pan-genomes of 13 accessions, but only four accessions had all the genes. Most of the CsDREB proteins had sequence length and/or amino acid variations, and only four of them had no variation among different accessions. Using the 55 <i>CsDREBs</i> from ‘9930’, we analyzed their gene structures, conserved domains, phylogenetic relationships, gene promoter’s cis-elements and syntenic relationships, and classified them into six groups. Expression pattern analysis revealed that eight <i>CsDREBs</i> showed constitutive expression (FPKM > 1 in all samples), and different <i>CsDREBs</i> showed specifically high expression in root, stem, leaf, tendril, male-flower, female flower, and ovary, respectively, suggesting that these genes might be important for morphogenesis and development in cucumber. Additionally, a total of 31, 22, 30 and nine <i>CsDREBs</i> were differentially expressed in responding to the treatments of heat, NaCl and/or silicon, power mildew and downy mildew, respectively. Interestingly, <i>CsDREB33</i> could respond to all the tested stresses. Our results provide a reference and basis for further investigation of the function and mechanism of the <i>DREB</i> genes for resistance breeding in cucumber. |
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| spelling | doaj.art-36c15f32cc0a427ba0705c1fb4889ced2023-11-24T03:18:37ZengMDPI AGAgriculture2077-04722022-11-011211187910.3390/agriculture12111879Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of <i>DREB</i> Genes That Respond to Biotic and Abiotic Stresses in CucumberCan Wang0Jing Han1Ting Wang2Chunhua Chen3Junyi Liu4Zhixuan Xu5Qingxia Zhang6Lina Wang7Zhonghai Ren8State Key Laboratory of Crop Biology, Shandong 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, ChinaState Key Laboratory of Crop Biology, Shandong 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, ChinaState Key Laboratory of Crop Biology, Shandong 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, ChinaState Key Laboratory of Crop Biology, Shandong 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, ChinaState Key Laboratory of Crop Biology, Shandong 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, ChinaState Key Laboratory of Crop Biology, Shandong 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, ChinaState Key Laboratory of Crop Biology, Shandong 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, ChinaState Key Laboratory of Crop Biology, Shandong 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, ChinaState Key Laboratory of Crop Biology, Shandong 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, ChinaThe production of cucumber (<i>Cucumis sativus</i> L.) is often harmed by biotic and abiotic stresses. Although the dehydration-responsive element-binding (DREB) transcription factors, playing vital roles in stress responses, have been characterized in several plant species, little is known about the pan-genome characteristics of <i>DREB</i> genes and their expression patterns under different stresses in cucumber. In this study, we identified 55 CsDREBs from the cucumber pan-genomes of 13 accessions, but only four accessions had all the genes. Most of the CsDREB proteins had sequence length and/or amino acid variations, and only four of them had no variation among different accessions. Using the 55 <i>CsDREBs</i> from ‘9930’, we analyzed their gene structures, conserved domains, phylogenetic relationships, gene promoter’s cis-elements and syntenic relationships, and classified them into six groups. Expression pattern analysis revealed that eight <i>CsDREBs</i> showed constitutive expression (FPKM > 1 in all samples), and different <i>CsDREBs</i> showed specifically high expression in root, stem, leaf, tendril, male-flower, female flower, and ovary, respectively, suggesting that these genes might be important for morphogenesis and development in cucumber. Additionally, a total of 31, 22, 30 and nine <i>CsDREBs</i> were differentially expressed in responding to the treatments of heat, NaCl and/or silicon, power mildew and downy mildew, respectively. Interestingly, <i>CsDREB33</i> could respond to all the tested stresses. Our results provide a reference and basis for further investigation of the function and mechanism of the <i>DREB</i> genes for resistance breeding in cucumber.https://www.mdpi.com/2077-0472/12/11/1879pan-genomecucumberDREBtranscription factorabiotic stress responsebiotic stress response |
| spellingShingle | Can Wang Jing Han Ting Wang Chunhua Chen Junyi Liu Zhixuan Xu Qingxia Zhang Lina Wang Zhonghai Ren Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of <i>DREB</i> Genes That Respond to Biotic and Abiotic Stresses in Cucumber Agriculture pan-genome cucumber DREB transcription factor abiotic stress response biotic stress response |
| title | Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of <i>DREB</i> Genes That Respond to Biotic and Abiotic Stresses in Cucumber |
| title_full | Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of <i>DREB</i> Genes That Respond to Biotic and Abiotic Stresses in Cucumber |
| title_fullStr | Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of <i>DREB</i> Genes That Respond to Biotic and Abiotic Stresses in Cucumber |
| title_full_unstemmed | Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of <i>DREB</i> Genes That Respond to Biotic and Abiotic Stresses in Cucumber |
| title_short | Pan-Genome-Wide Identification and Transcriptome-Wide Analysis of <i>DREB</i> Genes That Respond to Biotic and Abiotic Stresses in Cucumber |
| title_sort | pan genome wide identification and transcriptome wide analysis of i dreb i genes that respond to biotic and abiotic stresses in cucumber |
| topic | pan-genome cucumber DREB transcription factor abiotic stress response biotic stress response |
| url | https://www.mdpi.com/2077-0472/12/11/1879 |
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