Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus

Lohani, Neeta; Babaei, Saeid; Singh, Mohan B.; Bhalla, Prem L.

doi:10.3390/plants10040709

Cited by 23 publications

(21 citation statements)

References 99 publications

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“…Ethylene induces specific increased expression of several MaDofs in bananas during fruit ripening [ 53 ]. More than half of the A and B1 Dof group members in Brassica napus were more highly expressed in the stems and young roots, respectively [ 54 ]. CsDof33 was highly expressed in the terminal buds of tea plants, whereas the expression in young leaves was reversed [ 55 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of Dof Transcription Factors in Lotus (Nelumbo nucifera Gaertn.)

Xiaohan

Wenyang²,

Mao³

et al. 2022

Plants

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Lotus (Nelumbo nucifera Gaertn.) is a traditional Chinese aquatic flower with high ornamental and economic value, but water salinity seriously affects lotus cultivation and distribution. The Dof transcription factors (TFs) play a crucial function in the regulatory network of growth and defense in plants. However, no systematic investigations of the Dof TFs in lotus have been performed. In this study, comprehensive searches of the lotus genome yielded 29 potential NnDofs. We carried out a series of standardized analyses, which include physical properties, multiple sequence alignment, phylogenetic analysis, gene structure, motif composition, cis-acting element prediction, chromosome distribution, and synteny analysis. The results showed that segment duplication probably caused the NnDofs gene family expansion. The potential functions of NnDofs in lotus development and stress conditions are speculated by promoter analysis. Furthermore, a complete expression investigation of NnDofs utilizing an RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) was performed. The majority of the NnDofs exhibit tissue-specific expression patterns, and many genes have been identified as being extremely sensitive to salt stressors. Overall, this study is the first to report a genome-wide assessment of the Dof family in lotus, and the findings offer vital insights for prospective functional studies on lotus salinity stress.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of Dof Transcription Factors in Lotus (Nelumbo nucifera Gaertn.)

Xiaohan

Wenyang²,

Mao³

et al. 2022

Plants

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“…The Dof domain is considered as a bifunctional region: DNA-protein and protein-protein interactions ( Krohn et al., 2002 ; Gupta et al., 2015 ). The first Dof gene, ZmDof1 , was found in maize ( Yanagisawa and Izui, 1993 ), and gradually expended into diverse taxonomic groups ranging from ferns and mosses to vascular plants ( Kushwaha et al., 2011 ; Lohani et al., 2021 ). Presently, genome-wide isolation of Dof TFs are emerging from sundry plants, for example, 30, 30, 119, 74 and 114 Dofs were found in monocots such as Oryza sativa ( Khan et al., 2021 ), Sorghum bicolor ( Xiao et al., 2022 ), Saccharum officinarum ( Gupta et al., 2014 ), Musa nana ( Dong et al., 2016 ), and Gossypium hirsutum ( Li et al., 2018 ), respectively.…”

Section: Introductionmentioning

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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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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“…The DNA binding with one zinc finger (DOF) family of transcription factors is a plant-specific family, and genome-wide identification of Dofs has been reported for many species, including Arabidopsis and crops such as oilseeds rape, wheat, and cotton [25][26][27][28]. This gene family has not been detected in Gongylonema pulchrum, Drosophila melanogaster, or Saccharomyces cerevisiae.…”

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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Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus

Cited by 23 publications

References 99 publications

Genome-Wide Identification and Expression Analysis of Dof Transcription Factors in Lotus (Nelumbo nucifera Gaertn.)

Genome-Wide Identification and Expression Analysis of Dof Transcription Factors in Lotus (Nelumbo nucifera Gaertn.)

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.)

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