Genome-wide characterization and expression analysis of Erf gene family in cotton

Zafar, Muhammad Mubashar; Rehman, Abdul; Razzaq, Abdul; Parvaiz, Aqsa; Mustafa, Ghulam; Sharif, Faiza; Mo, Huijuan; Yuán, Yǒulù; Shakeel, Amir; Ren, Maozhi

doi:10.1186/s12870-022-03521-z

Cited by 49 publications

(40 citation statements)

References 81 publications

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“…The similarity in gene structure and distribution of conserved motifs in the same subclade suggested that they had similar roles in plant growth ( Zafar et al., 2022 ). The distribution of motifs varied among different subclades.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the HVA22 gene family in cotton and functional analysis of GhHVA22E1D in drought and salt tolerance

Zhang

Yuan²,

Xing³

et al. 2023

Front. Plant Sci.

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The HVA22 family of genes, induced by abscisic acid and stress, encodes a class of stress response proteins with a conserved TB2/DP1/HVA22 domain that are unique among eukaryotes. Previous studies have shown that HVA22s play an important role in plant responses to abiotic stresses. In the present study, 34, 32, 16, and 17 HVA22s were identified in G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively. These HVA22 genes were classified into nine subgroups, randomly distributed on the chromosomes. Synteny analysis showed that the amplification of the HVA22s were mainly due to segmental duplication or whole genome replication (WGD). Most HVA22s promoter sequences contain a large number of drought response elements (MYB), defense and stress response elements (TC-rich repeats), and hormone response elements (ABRE, ERE, SARE, etc.), suggesting that HVA22s may respond to adversity stresses. Expression profiling demonstrated that most GhHVA22s showed a constitutive expression pattern in G. hirsutum and could respond to abiotic stresses such as salt, drought, and low temperature. Overexpression of GhHVA22E1D (GH_D07G0564) in Arabidopsis thaliana enhances salt and drought tolerance in Arabidopsis. Virus-induced gene silencing of GhHVA22E1D reduced salt and drought tolerance in cotton. This indicates that GhHVA22E1D plays an active role in the plant response to salt stress and drought stress. GhHVA22E1D may act in plant response to adversity by altering the antioxidant capacity of plants. This study provides valuable information for the functional genomic study of the HVA22 gene family in cotton. It also provides a reference for further elucidation of the functional studies of HVA22 in plant resistance to abiotic stress response.

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Section: Discussionmentioning

confidence: 99%

Genome-wide identification and expression analysis of the HVA22 gene family in cotton and functional analysis of GhHVA22E1D in drought and salt tolerance

Zhang

Yuan²,

Xing³

et al. 2023

Front. Plant Sci.

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“…The phylogenetic trees of DREB subfamily genes from four cottons were constructed by MEGA (V7.0) software. The multiple sequence alignment of protein sequences for DREB genes coding region in Arabidopsis and four cottons ( G. barbadense , G. hirsutum , G. arboreum , and G. raimondii ) were carried out by ClustalW tool with default parameters [ 55 ]. The best model of phylogenetic tree was calculated and constructed with MEGA, and then a phylogenetic tree of all DREB proteins was constructed using the maximum likelihood method with the following parameters: poisson correction, pairwise deletion, and 1000 bootstrap replicate.…”

Section: Methodsmentioning

confidence: 99%

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

Song

Wang

et al. 2023

BMC Plant Biol

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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.

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“…Synteny analysis can identify chromosome structural changes and homologous gene evolutionary and functional connections in multiple genomes [ 50 , 51 ]. In this study, synteny analysis showed that the collinear gene pairs of E. fulvus and sorghum were densely distributed on chromosomes and had one-to-one correspondence, indicating that the genes E. fulvus and sorghum were homologous, and both of these species may have emerged in the same period of evolution ( Figure 7 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

Qian

Rao

Zhang

et al. 2023

IJMS

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The AP2/ERF transcription factor family is one of the most important gene families in plants and plays a vital role in plant abiotic stress responses. Although Erianthus fulvus is very important in the genetic improvement of sugarcane, there are few studies concerning AP2/ERF genes in E. fulvus. Here, we identified 145 AP2/ERF genes in the E. fulvus genome. Phylogenetic analysis classified them into five subfamilies. Evolutionary analysis showed that tandem and segmental duplication contributed to the expansion of the EfAP2/ERF family. Protein interaction analysis showed that twenty-eight EfAP2/ERF proteins and five other proteins had potential interaction relationships. Multiple cis-acting elements present in the EfAP2/ERF promoter were related to abiotic stress response, suggesting that EfAP2/ERF may contribute to adaptation to environmental changes. Transcriptomic and RT-qPCR analyses revealed that EfDREB10, EfDREB11, EfDREB39, EfDREB42, EfDREB44, EfERF43, and EfAP2-13 responded to cold stress, EfDREB5 and EfDREB42 responded to drought stress, and EfDREB5, EfDREB11, EfDREB39, EfERF43, and EfAP2-13 responded to ABA treatment. These results will be helpful for better understanding the molecular features and biological role of the E. fulvus AP2/ERF genes and lay a foundation for further research on the function of EfAP2/ERF genes and the regulatory mechanism of the abiotic stress response.

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Genome-wide characterization and expression analysis of Erf gene family in cotton

Cited by 49 publications

References 81 publications

Genome-wide identification and expression analysis of the HVA22 gene family in cotton and functional analysis of GhHVA22E1D in drought and salt tolerance

Genome-wide identification and expression analysis of the HVA22 gene family in cotton and functional analysis of GhHVA22E1D in drought and salt tolerance

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

Genome-Wide Identification, Evolution, and Expression Analyses of AP2/ERF Family Transcription Factors in Erianthus fulvus

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