Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato
The bHLH (basic helix–loop–helix) transcription factors function as crucial regulators in numerous biological processes including abiotic stress responses and plant development. According to our RNA-seq analysis of tomato seedlings under salt stress, we found that, although the bHLH gene family in t...
Saved in:
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-01-01
|
| Series: | Plants |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2223-7747/14/2/200 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832587624576974848 |
|---|---|
| author | Jianling Zhang Xiaoying Liu Zuozhen Yin Tiantian Zhao Dan Du Jing Li Mingku Zhu Yueying Sun Yu Pan |
| author_facet | Jianling Zhang Xiaoying Liu Zuozhen Yin Tiantian Zhao Dan Du Jing Li Mingku Zhu Yueying Sun Yu Pan |
| author_sort | Jianling Zhang |
| collection | DOAJ |
| description | The bHLH (basic helix–loop–helix) transcription factors function as crucial regulators in numerous biological processes including abiotic stress responses and plant development. According to our RNA-seq analysis of tomato seedlings under salt stress, we found that, although the bHLH gene family in tomato has been studied, there are still so many tomato bHLH genes that have not been identified and named, which will hinder the later study of <i>SlbHLHs</i>. In total, 195 <i>SlbHLHs</i> that were unevenly distributed onto 12 chromosomes were identified from the tomato genome and were classified into 27 subfamilies based on their molecular features. The collinearity between SlbHLHs and interrelated orthologs from 10 plants further revealed evolutionary insights into <i>SlbHLHs</i>. Cis-element investigations of <i>SlbHLHs</i> promotors further suggested the potential roles of <i>SlbHLHs</i> in tomato development and stress responses. A total of 30 <i>SlbHLHs</i> were defined as the differentially expressed genes in response to salt stress by RNA-seq. The expression profiles of selected <i>SlbHLHs</i> were varyingly and markedly induced by multiple abiotic stresses and hormone treatments. These results provide valuable information to further understand the significance and intricacy of the bHLH transcription factor family, and lay a foundation for further exploring functions and possible regulatory mechanisms of SlbHLH members in abiotic stress tolerance, which will be significant for the study of tomato stress resistance and agricultural productivity. |
| format | Article |
| id | doaj-art-12d3b3c1ce0f41f7bd395c6d1b7c10de |
| institution | Kabale University |
| issn | 2223-7747 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj-art-12d3b3c1ce0f41f7bd395c6d1b7c10de2025-01-24T13:46:43ZengMDPI AGPlants2223-77472025-01-0114220010.3390/plants14020200Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in TomatoJianling Zhang0Xiaoying Liu1Zuozhen Yin2Tiantian Zhao3Dan Du4Jing Li5Mingku Zhu6Yueying Sun7Yu Pan8Laboratory of Plant Germplasm Resources Innovation and Utilization, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaLaboratory of Plant Germplasm Resources Innovation and Utilization, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaLaboratory of Plant Germplasm Resources Innovation and Utilization, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaLaboratory of Plant Germplasm Resources Innovation and Utilization, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaCollege of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, ChinaChongqing Academy of Agricultural Sciences, Chongqing 850030, ChinaSchool of Life Sciences, Jiangsu Normal University, 101 Shanghai 16 Road, Xuzhou 221008, ChinaLaboratory of Plant Germplasm Resources Innovation and Utilization, College of Agriculture and Biology, Liaocheng University, Liaocheng 252000, ChinaCollege of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, ChinaThe bHLH (basic helix–loop–helix) transcription factors function as crucial regulators in numerous biological processes including abiotic stress responses and plant development. According to our RNA-seq analysis of tomato seedlings under salt stress, we found that, although the bHLH gene family in tomato has been studied, there are still so many tomato bHLH genes that have not been identified and named, which will hinder the later study of <i>SlbHLHs</i>. In total, 195 <i>SlbHLHs</i> that were unevenly distributed onto 12 chromosomes were identified from the tomato genome and were classified into 27 subfamilies based on their molecular features. The collinearity between SlbHLHs and interrelated orthologs from 10 plants further revealed evolutionary insights into <i>SlbHLHs</i>. Cis-element investigations of <i>SlbHLHs</i> promotors further suggested the potential roles of <i>SlbHLHs</i> in tomato development and stress responses. A total of 30 <i>SlbHLHs</i> were defined as the differentially expressed genes in response to salt stress by RNA-seq. The expression profiles of selected <i>SlbHLHs</i> were varyingly and markedly induced by multiple abiotic stresses and hormone treatments. These results provide valuable information to further understand the significance and intricacy of the bHLH transcription factor family, and lay a foundation for further exploring functions and possible regulatory mechanisms of SlbHLH members in abiotic stress tolerance, which will be significant for the study of tomato stress resistance and agricultural productivity.https://www.mdpi.com/2223-7747/14/2/200genome-wide analysistranscriptome characterizationstress-responsive gene expressionplant tolerancesalt stressbHLH transcription factors |
| spellingShingle | Jianling Zhang Xiaoying Liu Zuozhen Yin Tiantian Zhao Dan Du Jing Li Mingku Zhu Yueying Sun Yu Pan Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato Plants genome-wide analysis transcriptome characterization stress-responsive gene expression plant tolerance salt stress bHLH transcription factors |
| title | Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato |
| title_full | Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato |
| title_fullStr | Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato |
| title_full_unstemmed | Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato |
| title_short | Genome- and Transcriptome-Wide Characterization and Expression Analyses of bHLH Transcription Factor Family Reveal Their Relevance to Salt Stress Response in Tomato |
| title_sort | genome and transcriptome wide characterization and expression analyses of bhlh transcription factor family reveal their relevance to salt stress response in tomato |
| topic | genome-wide analysis transcriptome characterization stress-responsive gene expression plant tolerance salt stress bHLH transcription factors |
| url | https://www.mdpi.com/2223-7747/14/2/200 |
| work_keys_str_mv | AT jianlingzhang genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato AT xiaoyingliu genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato AT zuozhenyin genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato AT tiantianzhao genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato AT dandu genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato AT jingli genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato AT mingkuzhu genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato AT yueyingsun genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato AT yupan genomeandtranscriptomewidecharacterizationandexpressionanalysesofbhlhtranscriptionfactorfamilyrevealtheirrelevancetosaltstressresponseintomato |