Genome-wide identification and expression analysis of DREB family genes in cotton
Abstract Background Dehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-03-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12870-023-04180-4 |
| _version_ | 1797853944422072320 |
|---|---|
| author | Jiuchang Su Shanglin Song Yiting Wang Yunpeng Zeng Tianyu Dong Xiaoyang Ge Hongying Duan |
| author_facet | Jiuchang Su Shanglin Song Yiting Wang Yunpeng Zeng Tianyu Dong Xiaoyang Ge Hongying Duan |
| author_sort | Jiuchang Su |
| collection | DOAJ |
| description | Abstract Background Dehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have been studied in cotton, one of the most important fibre crops. Herein, the genome‑wide identification, phylogeny, and expression analysis of DREB family genes are performed in diploid and tetraploid cotton species. Results In total, 193, 183, 80, and 79 putative genes containing the AP2 domain were identified using bioinformatics approaches in G. barbadense, G. hirsutum, G. arboretum, and G. raimondii, respectively. Phylogenetic analysis showed that based on the categorization of Arabidopsis DREB genes, 535 DREB genes were divided into six subgroups (A1–A6) by using MEGA 7.0. The identified DREB genes were distributed unevenly across 13/26 chromosomes of A and/or D genomes. Synteny and collinearity analysis confirmed that during the evolution, the whole genome duplications, segmental duplications, and/or tandem duplications occurred in cotton DREB genes, and then DREB gene family was further expanded. Further, the evolutionary trees with conserved motifs, cis-acting elements, and gene structure of cotton DREB gene family were predicted, and these results suggested that DREB genes might be involved in the hormone and abiotic stresses responses. The subcellular localization showed that in four cotton species, DREB proteins were predominantly located in the nucleus. Further, the analysis of DREB gene expression was carried out by real-time quantitative PCR, confirming that the identified DREB genes of cotton were involved in response to early salinity and osmotic stress. Conclusions Collectively, our results presented a comprehensive and systematic understanding in the evolution of cotton DREB genes, and demonstrated the potential roles of DREB family genes in stress and hormone response. |
| first_indexed | 2024-04-09T19:57:54Z |
| format | Article |
| id | doaj.art-c5a36b3fabe044fcb90cbd9a7a493b3e |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-09T19:57:54Z |
| publishDate | 2023-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-c5a36b3fabe044fcb90cbd9a7a493b3e2023-04-03T05:22:06ZengBMCBMC Plant Biology1471-22292023-03-0123111610.1186/s12870-023-04180-4Genome-wide identification and expression analysis of DREB family genes in cottonJiuchang Su0Shanglin Song1Yiting Wang2Yunpeng Zeng3Tianyu Dong4Xiaoyang Ge5Hongying Duan6College of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityCollege of Life Sciences, Henan Normal UniversityState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural SciencesCollege of Life Sciences, Henan Normal UniversityAbstract Background Dehydration responsive element-binding (DREB) transcription factors are widely present in plants, and involve in signalling transduction, plant growth and development, and stress response. DREB genes have been characterized in multiple species. However, only a few DREB genes have been studied in cotton, one of the most important fibre crops. Herein, the genome‑wide identification, phylogeny, and expression analysis of DREB family genes are performed in diploid and tetraploid cotton species. Results In total, 193, 183, 80, and 79 putative genes containing the AP2 domain were identified using bioinformatics approaches in G. barbadense, G. hirsutum, G. arboretum, and G. raimondii, respectively. Phylogenetic analysis showed that based on the categorization of Arabidopsis DREB genes, 535 DREB genes were divided into six subgroups (A1–A6) by using MEGA 7.0. The identified DREB genes were distributed unevenly across 13/26 chromosomes of A and/or D genomes. Synteny and collinearity analysis confirmed that during the evolution, the whole genome duplications, segmental duplications, and/or tandem duplications occurred in cotton DREB genes, and then DREB gene family was further expanded. Further, the evolutionary trees with conserved motifs, cis-acting elements, and gene structure of cotton DREB gene family were predicted, and these results suggested that DREB genes might be involved in the hormone and abiotic stresses responses. The subcellular localization showed that in four cotton species, DREB proteins were predominantly located in the nucleus. Further, the analysis of DREB gene expression was carried out by real-time quantitative PCR, confirming that the identified DREB genes of cotton were involved in response to early salinity and osmotic stress. Conclusions Collectively, our results presented a comprehensive and systematic understanding in the evolution of cotton DREB genes, and demonstrated the potential roles of DREB family genes in stress and hormone response.https://doi.org/10.1186/s12870-023-04180-4DREBTranscription factorsPhylogenetic analysisGene expressionCotton |
| spellingShingle | Jiuchang Su Shanglin Song Yiting Wang Yunpeng Zeng Tianyu Dong Xiaoyang Ge Hongying Duan Genome-wide identification and expression analysis of DREB family genes in cotton BMC Plant Biology DREB Transcription factors Phylogenetic analysis Gene expression Cotton |
| title | Genome-wide identification and expression analysis of DREB family genes in cotton |
| title_full | Genome-wide identification and expression analysis of DREB family genes in cotton |
| title_fullStr | Genome-wide identification and expression analysis of DREB family genes in cotton |
| title_full_unstemmed | Genome-wide identification and expression analysis of DREB family genes in cotton |
| title_short | Genome-wide identification and expression analysis of DREB family genes in cotton |
| title_sort | genome wide identification and expression analysis of dreb family genes in cotton |
| topic | DREB Transcription factors Phylogenetic analysis Gene expression Cotton |
| url | https://doi.org/10.1186/s12870-023-04180-4 |
| work_keys_str_mv | AT jiuchangsu genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton AT shanglinsong genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton AT yitingwang genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton AT yunpengzeng genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton AT tianyudong genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton AT xiaoyangge genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton AT hongyingduan genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton |