Cargando…

Genome-wide identification and expression analysis of DREB family genes in cotton

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 st...

Descripción completa

Detalles Bibliográficos
Autores principales: Su, Jiuchang, Song, Shanglin, Wang, Yiting, Zeng, Yunpeng, Dong, Tianyu, Ge, Xiaoyang, Duan, Hongying
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10061749/
https://www.ncbi.nlm.nih.gov/pubmed/36997878
http://dx.doi.org/10.1186/s12870-023-04180-4
_version_ 1785017355501305856
author Su, Jiuchang
Song, Shanglin
Wang, Yiting
Zeng, Yunpeng
Dong, Tianyu
Ge, Xiaoyang
Duan, Hongying
author_facet Su, Jiuchang
Song, Shanglin
Wang, Yiting
Zeng, Yunpeng
Dong, Tianyu
Ge, Xiaoyang
Duan, Hongying
author_sort Su, Jiuchang
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04180-4.
format Online
Article
Text
id pubmed-10061749
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-100617492023-03-31 Genome-wide identification and expression analysis of DREB family genes in cotton Su, Jiuchang Song, Shanglin Wang, Yiting Zeng, Yunpeng Dong, Tianyu Ge, Xiaoyang Duan, Hongying BMC Plant Biol Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04180-4. BioMed Central 2023-03-30 /pmc/articles/PMC10061749/ /pubmed/36997878 http://dx.doi.org/10.1186/s12870-023-04180-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Su, Jiuchang
Song, Shanglin
Wang, Yiting
Zeng, Yunpeng
Dong, Tianyu
Ge, Xiaoyang
Duan, Hongying
Genome-wide identification and expression analysis of DREB family genes in 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 Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10061749/
https://www.ncbi.nlm.nih.gov/pubmed/36997878
http://dx.doi.org/10.1186/s12870-023-04180-4
work_keys_str_mv AT sujiuchang genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton
AT songshanglin genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton
AT wangyiting genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton
AT zengyunpeng genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton
AT dongtianyu genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton
AT gexiaoyang genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton
AT duanhongying genomewideidentificationandexpressionanalysisofdrebfamilygenesincotton