Genome-Wide Analysis of Dof Genes and Their Response to Abiotic Stress in Rose (Rosa chinensis)

Nan, Hong; Ludlow, Richard A.; Lü, Min; An, Hongyu

doi:10.3389/fgene.2021.538733

Cited by 19 publications

(11 citation statements)

References 56 publications

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“…Phylogenetic analysis showed that 43 IbDofs were classified into nine subgroups based on sequence homologies from known Dof family members from Arabidopsis and rice ( Lijavetzky et al., 2003 ), consistent with the results of the Dof TFs in multiple plants such as rose ( Nan et al., 2021 ), watermelon ( Zhou et al., 2020 ), Tartary buckwheat ( Li et al., 2022 ), Gossypium hirsutum (114) ( Li et al., 2018 ), and Brassica napus (117) ( Lohani et al., 2021 ). The gene structures can be applied as supporting evidence to confirm the evolutionary relationships among genes or organisms ( Koralewski and Krutovsky, 2011 ).…”

Section: Discussionsupporting

confidence: 64%

“…To examine the evolutionary connections of IbDofs in sweetpotato, a phylogenetic tree was created using the full amino acid sequences of 43 IbDofs, 36 Arabidopsis AtDofs and 30 rice OsDofs by Maximum Likelihood method using MEGA-X software. Previously, 36 AtDofs and 30 OsDofs were divided into nine subgroups (A, B1, B2, C1, C2.1, C2.2, C3, D1 and D2) ( Lohani et al., 2021 ; Nan et al., 2021 ). Accordingly, 43 IbDofs were also divided into nine subgroups, and the sizes of each subgroup varied substantially as shown by the phylogenetic analysis ( Figure 2 ).…”

Section: Resultsmentioning

confidence: 99%

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Genome-wide survey and expression analysis of Dof transcription factor family in sweetpotato shed light on their promising functions in stress tolerance

Zhang

Dong

et al. 2023

Front. Plant Sci.

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DNA-binding with one finger (Dof) transcription factors play a crucial role in plant abiotic stress regulatory networks, although massive Dofs have been systematically characterized in plants, they have not been identified in the hexaploid crop sweetpotato. Herein, 43 IbDof genes were detected to be disproportionally dispersed across 14 of the 15 chromosomes of sweetpotato, and segmental duplications were discovered to be the major driving force for the expansion of IbDofs. The collinearity analysis of IbDofs with their related orthologs from eight plants revealed the potential evolutionary history of Dof gene family. Phylogenetic analysis displayed that IbDof proteins were assigned into nine subfamilies, and the regularity of gene structures and conserved motifs was consistent with the subgroup classification. Additionally, five chosen IbDof genes were shown to be substantially and variably induced under various abiotic conditions (salt, drought, heat, and cold), as well as hormone treatments (ABA and SA), according to their transcriptome data and qRT-PCR experiments. Consistently, the promoters of IbDofs contained a number of cis-acting elements associated with hormone and stress responses. Besides, it was noted that IbDof2 had transactivation activity in yeasts, while IbDof-11/-16/-36 did not, and protein interaction network analysis and yeast two-hybrid experiments revealed a complicated interaction connection amongst IbDofs. Collectively, these data lay a foundation for further functional explorations of IbDof genes, especially with regards to the possible application of multiple IbDof members in breeding the tolerant plants.

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Section: Discussionsupporting

confidence: 64%

Section: Resultsmentioning

confidence: 99%

Genome-wide survey and expression analysis of Dof transcription factor family in sweetpotato shed light on their promising functions in stress tolerance

Zhang

Dong

et al. 2023

Front. Plant Sci.

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“…Most Dof genes in apple show changes in expression in response to external treatments, such as osmotic stress, salt, cold, and ABA [ 53 ]. A recent study reported that the Dof gene is regulated in response to drought and salt treatment in rose plants [ 43 ].…”

Section: Discussionmentioning

confidence: 99%

“…The involvement of DOFs in biotic/abiotic stress responses has been described in several plant species, including rice [27,[40][41][42][43][44]. Zhou et al investigated ABA, salt, and PEG treatments in rice seedlings and found that 27 OsDofs were either induced or suppressed by at least two of the treatments [42].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

Liu

Meng

Xiang³

et al. 2021

BMC Genomics

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Background Rice (Oryza sativa L.) is a food crop for humans worldwide. However, temperature has an effect during the vegetative and reproductive stages. In high-latitude regions where rice is cultivated, cold stress is a major cause of yield loss and plant death. Research has identified a group of plant-specific transcription factors, DNA binding with one zinc fingers (DOFs), with a diverse range of functions, including stress signaling and stress response during plant growth. The aim of this study was to identify Dof genes in two rice subspecies, indica and japonica, and screen for Dof genes that may be involved in cold tolerance during plant growth. Results A total of 30 rice Dofs (OsDofs) were identified using bioinformatics and genome-wide analyses and phylogenetically analyzed. The 30 OsDOFs were classified into six subfamilies, and 24 motifs were identified based on protein sequence alignment. The chromosome locations of OsDofs were determined and nine gene duplication events were identified. A joint phylogenetic analysis was performed on DOF protein sequences obtained from four monocotyledon species to examine the evolutionary relationship of DOF proteins. Expression profiling of OsDofs from two japonica cultivars (Longdao5, which is cold-tolerant, and Longjing11, which is cold-sensitive) revealed that OsDof1 and OsDof19 are cold-inducible genes. We examined the seed setting rates in OsDof1- and OsDof19-overexpression and RNAi lines and found that OsDof1 showed a response to cold stress. Conclusions Our investigation identified OsDof1 as a potential target for genetic breeding of rice with enhanced cold tolerance.

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“…Earlier studies identified 37 DOF members in Arabidopsis thaliana, one of which is a pseudogene (Yanagisawa, 2002), while 30 DOF members were identified in rice (Oryza sativa) (Lijavetzky et al, 2003). With the analysis of the whole genomes of many species, an increasing number of DOF members have been identified in different species (Table 1), including 26 DOF genes in birch (Betula platyphylla) (Sun et al, 2021), 36 in watermelon (Citrullus lanatus) (Zhou et al, 2020), 35 in foxtail millet (Setaria italica) (Zhang et al, 2017), 22 in spinach (Spinacia oleracea) (Yu et al, 2021a) and 24 in rose (Rosa chinensis) (Nan et al, 2021). Despite the species differences, the functions of DOF members in the monocot model plant rice are still questioned.…”

Section: Origin and Evolution Of Dof Tfsmentioning

confidence: 99%

DOF transcription factors: Specific regulators of plant biological processes

Zou

Sun

2023

Front. Plant Sci.

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Plant biological processes, such as growth and metabolism, hormone signal transduction, and stress responses, are affected by gene transcriptional regulation. As gene expression regulators, transcription factors activate or inhibit target gene transcription by directly binding to downstream promoter elements. DOF (DNA binding with One Finger) is a classic transcription factor family exclusive to plants that is characterized by its single zinc finger structure. With breakthroughs in taxonomic studies of different species in recent years, many DOF members have been reported to play vital roles throughout the plant life cycle. They are not only involved in regulating hormone signals and various biotic or abiotic stress responses but are also reported to regulate many plant biological processes, such as dormancy, tissue differentiation, carbon and nitrogen assimilation, and carbohydrate metabolism. Nevertheless, some outstanding issues remain. This article mainly reviews the origin and evolution, protein structure, and functions of DOF members reported in studies published in many fields to clarify the direction for future research on DOF transcription factors.

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Genome-Wide Analysis of Dof Genes and Their Response to Abiotic Stress in Rose (Rosa chinensis)

Cited by 19 publications

References 56 publications

Genome-wide survey and expression analysis of Dof transcription factor family in sweetpotato shed light on their promising functions in stress tolerance

Genome-wide survey and expression analysis of Dof transcription factor family in sweetpotato shed light on their promising functions in stress tolerance

Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.)

DOF transcription factors: Specific regulators of plant biological processes

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