Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress
Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play crucial roles in plant signaling pathways and stress adaptive responses by activating protein phosphorylation pathways. However, there have been no comprehensive studies of the SnRK gene family in the widely plan...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-12-01
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| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-022-03961-7 |
| _version_ | 1811188222563188736 |
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| author | Di Ai Yujiao Wang Yongcheng Wei Jie Zhang Jingxiang Meng Yong Zhang |
| author_facet | Di Ai Yujiao Wang Yongcheng Wei Jie Zhang Jingxiang Meng Yong Zhang |
| author_sort | Di Ai |
| collection | DOAJ |
| description | Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play crucial roles in plant signaling pathways and stress adaptive responses by activating protein phosphorylation pathways. However, there have been no comprehensive studies of the SnRK gene family in the widely planted salt-tolerant tree species Casuarina equisetifolia. Here, we comprehensively analyze this gene family in C. equisetifolia using genome-wide identification, characterization, and profiling of expression changes in response to salt stress. Results A total of 26 CeqSnRK genes were identified, which were divided into three subfamilies (SnRK1, SnRK2, and SnRK3). The intron–exon structures and protein‑motif compositions were similar within each subgroup but differed among groups. Ka/Ks ratio analysis indicated that the CeqSnRK family has undergone purifying selection, and cis-regulatory element analysis suggested that these genes may be involved in plant development and responses to various environmental stresses. A heat map was generated using quantitative real‑time PCR (RT-qPCR) data from 26 CeqSnRK genes, suggesting that they were expressed in different tissues. We also examined the expression of all CeqSnRK genes under exposure to different salt concentrations using RT-qPCR, finding that most CeqSnRK genes were regulated by different salt treatments. Moreover, co-expression network analysis revealed synergistic effects among CeqSnRK genes. Conclusions Several CeqSnRK genes (CeqSnRK3.7, CeqSnRK3.16, CeqSnRK3.17) were up-regulated following salt treatment. Among them, CeqSnRK3.16 expression was significantly up-regulated under various salt treatments, identifying this as a candidate gene salt stress tolerance gene. In addition, CeqSnRK3.16 showed significant expression change correlations with multiple genes under salt stress, indicating that it might exhibit synergistic effects with other genes in response to salt stress. This comprehensive analysis will provide a theoretical reference for CeqSnRK gene functional verification and the role of these genes in salt tolerance. |
| first_indexed | 2024-04-11T14:16:41Z |
| format | Article |
| id | doaj.art-8c694122c5254dc095b4bc89287ca42e |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-11T14:16:41Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-8c694122c5254dc095b4bc89287ca42e2022-12-22T04:19:24ZengBMCBMC Plant Biology1471-22292022-12-0122111810.1186/s12870-022-03961-7Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stressDi Ai0Yujiao Wang1Yongcheng Wei2Jie Zhang3Jingxiang Meng4Yong Zhang5Research Institute of Tropical Forestry, Chinese Academy of ForestryResearch Institute of Tropical Forestry, Chinese Academy of ForestryResearch Institute of Tropical Forestry, Chinese Academy of ForestryCollege of Landscape Architecture, Northeast Forestry UniversityResearch Institute of Tropical Forestry, Chinese Academy of ForestryResearch Institute of Tropical Forestry, Chinese Academy of ForestryAbstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play crucial roles in plant signaling pathways and stress adaptive responses by activating protein phosphorylation pathways. However, there have been no comprehensive studies of the SnRK gene family in the widely planted salt-tolerant tree species Casuarina equisetifolia. Here, we comprehensively analyze this gene family in C. equisetifolia using genome-wide identification, characterization, and profiling of expression changes in response to salt stress. Results A total of 26 CeqSnRK genes were identified, which were divided into three subfamilies (SnRK1, SnRK2, and SnRK3). The intron–exon structures and protein‑motif compositions were similar within each subgroup but differed among groups. Ka/Ks ratio analysis indicated that the CeqSnRK family has undergone purifying selection, and cis-regulatory element analysis suggested that these genes may be involved in plant development and responses to various environmental stresses. A heat map was generated using quantitative real‑time PCR (RT-qPCR) data from 26 CeqSnRK genes, suggesting that they were expressed in different tissues. We also examined the expression of all CeqSnRK genes under exposure to different salt concentrations using RT-qPCR, finding that most CeqSnRK genes were regulated by different salt treatments. Moreover, co-expression network analysis revealed synergistic effects among CeqSnRK genes. Conclusions Several CeqSnRK genes (CeqSnRK3.7, CeqSnRK3.16, CeqSnRK3.17) were up-regulated following salt treatment. Among them, CeqSnRK3.16 expression was significantly up-regulated under various salt treatments, identifying this as a candidate gene salt stress tolerance gene. In addition, CeqSnRK3.16 showed significant expression change correlations with multiple genes under salt stress, indicating that it might exhibit synergistic effects with other genes in response to salt stress. This comprehensive analysis will provide a theoretical reference for CeqSnRK gene functional verification and the role of these genes in salt tolerance.https://doi.org/10.1186/s12870-022-03961-7Phylogenetic analysisCis-regulatory element analysisExpression patternSalt stress |
| spellingShingle | Di Ai Yujiao Wang Yongcheng Wei Jie Zhang Jingxiang Meng Yong Zhang Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress BMC Plant Biology Phylogenetic analysis Cis-regulatory element analysis Expression pattern Salt stress |
| title | Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress |
| title_full | Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress |
| title_fullStr | Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress |
| title_full_unstemmed | Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress |
| title_short | Comprehensive identification and expression analyses of the SnRK gene family in Casuarina equisetifolia in response to salt stress |
| title_sort | comprehensive identification and expression analyses of the snrk gene family in casuarina equisetifolia in response to salt stress |
| topic | Phylogenetic analysis Cis-regulatory element analysis Expression pattern Salt stress |
| url | https://doi.org/10.1186/s12870-022-03961-7 |
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