Genome-wide identification and expression analysis of the Dof gene family reveals their involvement in hormone response and abiotic stresses in sunflower (Helianthus annuus L.)

Song, Huifang; Ji, Xuchao; Wang, Mingyang; Li, Juan; Wang, Xi; Meng, Liying; Wei, Peipei; Xu, Haiyan; Niu, Tianzeng; Liu, Ake

doi:10.1016/j.gene.2024.148336

Cited by 13 publications

(4 citation statements)

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“…In studies of motif composition, it was found that all members of the PSDOFs possess motif 1, indicating its potential conservatism and its determination of the functional role of DOF genes. Similar studies have also been conducted in sweet potato (Zhang et al, 2023) and sunflower (Song et al, 2024), where individual motifs were found to be present in all family members. This finding parallels our research results, suggesting that the motif Gene expression profiles derived from RNA-seq and qRT-PCR.…”

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confidence: 75%

Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

Cai,

Xie,

Han

et al. 2024

Front. Plant Sci.

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BackgroundPopulus simonii, a notable native tree species in northern China, demonstrates impressive resistance to stress, broad adaptability, and exceptional hybridization potential. DOF family is a class of specific transcription factors that only exist in plants, widely participating in plant growth and development, and also playing an important role in abiotic stress response. To date, there have been no reported studies on the DOF gene family in P. simonii, and the expression levels of this gene family in different tissues of poplar, as well as its expression patterns under cold, heat, and other stress conditions, remain unclear.MethodsIn this study, DOF gene family were identified from the P. simonii genome, and various bioinformatics data on the DOF gene family, gene structure, gene distribution, promoters and regulatory networks were analyzed. Quantitative real time PCR technology was used to verify the expression patterns of the DOF gene family in different poplar tissues.ResultsThis research initially pinpointed 41 PSDOF genes in P. simonii genome. The chromosomal localization results revealed that the PSDOF genes is unevenly distributed among 19 chromosomes, with the highest number of genes located on chromosomes 4, 5, and 11. A phylogenetic tree was constructed based on the homology between Arabidopsis thaliana and P. simonii, dividing the 41 PSDOF genes into seven subgroups. The expression patterns of PSDOF genes indicated that specific genes are consistently upregulated in various tissues and under different stress conditions, suggesting their pivotal involvement in both plant development and response to stress. Notably, PSDOF35 and PSDOF28 serve as pivotal hubs in the interaction network, playing a unique role in coordinating with other genes within the family.ConclusionThe analysis enhances our comprehension of the functions of the DOF gene family in tissue development and stress responses within P. simonii. These findings provide a foundation for future exploration into the biological roles of DOF gene family.

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confidence: 75%

Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

Cai,

Xie,

Han

et al. 2024

Front. Plant Sci.

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“…TGA-element (AACGAC) and AuxRR-core element (GGTCCAT) in the promoter region of DhDof were the negative auxin-responsive elements (Figure 8C). Dof TFs are ubiquitously found across the full spectrum of the plant kingdom, encompassing both lower plants, such as unicellular green algae, and higher plants, like angiosperms and gymnosperms (Yu et al, 2020;Song et al, 2024). D. huoshanense did not have as many Dof genes as other angiosperms, which meant it probably had not experienced large-scale genome duplication (Melgar and Zelada, 2021).…”

Section: Expression Pattern Analysis Of Dof Genesmentioning

confidence: 99%

“…Numerous studies have demonstrated that Dof TFs have a role in plant resistance responses to abiotic stress ( Song et al, 2024 ). The expression of AtDof1.1 was stimulated by MeJA, resulting in a 2-3-fold increment in expression level ( Skirycz et al, 2006 ).…”

Section: Introductionmentioning

confidence: 99%

Identification of Dof transcription factors in Dendrobium huoshanense and expression pattern under abiotic stresses

Gu,

Zhang,

Wang

et al. 2024

Front. Genet.

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Introduction: DNA-binding with one finger (Dof) transcription factors (TFs) are a unique family of TFs found in higher plants that regulate plant responses to light, hormones, and abiotic stresses. The specific involvement of Dof genes in the response to environmental stresses remains unknown in D. huoshanense.Methods: A total of 22 Dof family genes were identified from the D. huoshanense genome.Results: Chromosome location analysis showed that DhDof genes were distributed on 12 chromosomes, with the largest number of Dof genes located on chromosome 8. The phylogenetic tree revealed that DhDofs could be categorized into 11 distinct subgroups. In addition to the common groups, DhDof4, DhDof5, DhDof17, and the AtDof1.4 ortholog were clustered into the B3 subgroup. Group E was a newly identified branch, among which DhDof6, DhDof7, DhDof8, and DhDof9 were in an independent branch. The conserved motifs and gene structure revealed the differences in motif number and composition of DhDofs. The dof domain near the N-terminus was highly conserved and contained a C2-C2-type zinc finger structure linked with four cysteines. Microsynteny and interspecies collinearity revealed gene duplication events and phylogenetic tree among DhDofs. Large-scale gene duplication had not occurred among the DhDofs genes and only in one pair of genes on chromosome 13. Synteny blocks were found more often between D. huoshanense and its relatives and less often between Oryza sativa and Arabidopsis thaliana. Selection pressure analysis indicated that DhDof genes were subject to purifying selection. Expression profiles and correlation analyses revealed that the Dof gene under hormone treatments showed several different expression patterns. DhDof20 and DhDof21 had the highest expression levels and were co-expressed under MeJA induction. The cis-acting element analysis revealed that each DhDof had several regulatory elements involved in plant growth as well as abiotic stresses. qRT-PCR analysis demonstrated that DhDof2 was the main ABA-responsive gene and DhDof7 was the main cold stress-related gene. IAA suppressed the expression of some Dof candidates, and SA inhibited most of the candidate genes.Discussion: Our results may provide new insights for the further investigation of the Dof genes and the screening of the core stress-resistance genes.

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“…However, water availability remains a crucial factor affecting sunflower yield. When subjected to drought and salt stress, sunflower plants exhibit visual symptoms such as pale leaf color, slow growth, wilting, and even death ( Shen et al, 2023 ; Song et al, 2024 ). Drought and salt stress can also cause physiological changes to occur, including increased proline content, enhanced membrane permeability, and changes in protective enzyme activity.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress

Zhang,

et al. 2024

PeerJ

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Stress-associated proteins (SAPs) are known to play an important role in plant responses to abiotic stresses. This study systematically identified members of the sunflower SAP gene family using sunflower genome data. The genes of the sunflower SAP gene family were analyzed using bioinformatic methods, and gene expression was assessed through fluorescence quantification (qRT-PCR) under salt and drought stress. A comprehensive analysis was also performed on the number, structure, collinearity, and phylogeny of seven Compositae species and eight other plant SAP gene families. The sunflower genome was found to have 27 SAP genes, distributed across 14 chromosomes. The evolutionary analysis revealed that the SAP family genes could be divided into three subgroups. Notably, the annuus variety exhibited amplification of the SAP gene for Group 3. Among the Compositae species, C. morifolium demonstrated the highest number of collinearity gene pairs and the closest distance on the phylogenetic tree, suggesting relative conservation in the evolutionary process. An analysis of gene structure revealed that Group 1 exhibited the most complex gene structure, while the majority of HaSAP genes in Group 2 and Group 3 lacked introns. The promoter analysis revealed the presence of cis-acting elements related to ABA, indicating their involvement in stress responses. The expression analysis indicated the potential involvement of 10 genes (HaSAP1, HaSAP3, HaSAP8, HaSAP10, HaSAP15, HaSAP16, HaSAP21, HaSAP22, HaSAP23, and HaSAP26) in sunflower salt tolerance. The expression of these 10 genes were then examined under salt and drought stress using qRT-PCR, and the tissue-specific expression patterns of these 10 genes were also analyzed. HaSAP1, HaSAP21, and HaSAP23 exhibited consistent expression patterns under both salt and drought stress, indicating these genes play a role in both salt tolerance and drought resistance in sunflower. The findings of this study highlight the significant contribution of the SAP gene family to salt tolerance and drought resistance in sunflower.

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Genome-wide identification and expression analysis of the Dof gene family reveals their involvement in hormone response and abiotic stresses in sunflower (Helianthus annuus L.)

Cited by 13 publications

References 74 publications

Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

Identification of Dof transcription factors in Dendrobium huoshanense and expression pattern under abiotic stresses

Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress

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