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Fu C, Liao Z, Jiang N, Yang Y. Genome-wide identification and molecular evolution of Dof transcription factors in Cyperus esculentus. BMC Genomics 2024; 25:667. [PMID: 38961361 PMCID: PMC11223408 DOI: 10.1186/s12864-024-10565-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Dof transcription factor family in Cyperus esculentus genome was identified and analyzed using bioinformatics. The analysis results revealed that C.esculentus genome contains 29 Dof genes (CesDof), all of which are located in the nucleus according to subcellular localization prediction. CesDof proteinrs have a range of 124 to 512 amino acids, with most being basic proteins. Their secondary structure was mainly irregular curl. The promoter sequence of CesDof genes contains cis-acting elements that respond to light, drought, hormones, low temperature, and circadian rhythm. Codon preference analysis showed that CesDof genes' codon preference ends in T/A. Collinearity analysis revealed that C.esculentus had three pairs of collinear CesDof genes. Additionally, there were 15 pairs of collinear genes between C.esculentus and Arabidopsis thaliana. The genetic relationship between C.esculentus and Rhynchospora pubera was found to be the closest. Phylogenetic tree analysis revealed that 29 CesDof genes of C.esculentus can be classified into 4 subgroups. Additionally, 144 miRNAs were predicted to target these CesDof genes. Furthermore, protein interaction analysis indicated that 15 Dof proteins in C.esculentus had interactions. The qRT-PCR verification results of drought stress and salt stress treatment experiments showed that most CesDof genes were involved in drought stress and salt stress responses, and the gene expression trends under drought stress and salt stress conditions were consistent. These results lay a theoretical foundation for further studying the molecular functions of Dof gene family in C.esculentus and its molecular mechanisms in regulating the life activities of C.esculentus.
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Affiliation(s)
- Chun Fu
- Key Laboratory of Sichuan Province for Bamboo Pests Control and Resource Development, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan, 614000, China.
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan, 614000, China.
| | - ZiHui Liao
- Key Laboratory of Sichuan Province for Bamboo Pests Control and Resource Development, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan, 614000, China
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan, 614000, China
| | - Na Jiang
- College of Tourism and Geographical Science, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan, 614000, China
| | - YaoJun Yang
- Key Laboratory of Sichuan Province for Bamboo Pests Control and Resource Development, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan, 614000, China.
- College of Life Science, Leshan Normal University, No. 778 Binhe Road, Shizhong District, Leshan, Sichuan, 614000, China.
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Song H, Ji X, Wang M, Li J, Wang X, Meng L, Wei P, Xu H, Niu T, Liu A. 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.). Gene 2024; 910:148336. [PMID: 38447680 DOI: 10.1016/j.gene.2024.148336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
DNA binding with one finger (Dof), plant-specific zinc finger transcription factors, can participate in various physiological and biochemical processes during the life of plants. As one of the most important oil crops in the world, sunflower (Helianthus annuus L.) has significant economic and ornamental value. However, a systematic analysis of H. annuus Dof (HaDof) members and their functions has not been extensively conducted. In this study, we identified 50 HaDof genes that are unevenly distributed on 17 chromosomes of sunflower. We present a comprehensive overview of the HaDof genes, including their chromosome locations, phylogenetic analysis, and expression profile characterization. Phylogenetic analysis classified the 366 Dof members identified from 11 species into four groups (further subdivided into nine subfamilies). Segmental duplications are predominantly contributed to the expansion of sunflower Dof genes, and all segmental duplicate gene pairs are under purifying selection due to strong evolutionary constraints. Furthermore, we observed differential expression patterns for HaDof genes in normal tissues as well as under hormone treatment or abiotic stress conditions by analyzing RNA-seq data from previous studies and RT-qPCR data in our current study. The expression of HaDof04 and HaDof43 were not detected in any samples, which implied that they may be gradually undergoing pseudogenization process. Some HaDof genes, such as HaDof25 and HaDof30, showed responsiveness to exogenous plant hormones, such as kinetin, brassinosteroid, auxin or strigolactone, while others like HaDof15 and HaDof35 may participate in abiotic stress resistance of sunflower seedling. Our study represents the initial step towards understanding the phylogeny and expression characterization of sunflower Dof family genes, which may provide valuable reference information for functional studies on hormone response, abiotic stress resistance, and molecular breeding in sunflower and other species.
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Affiliation(s)
- Huifang Song
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Xuchao Ji
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Mingyang Wang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Juan Li
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Xi Wang
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Liying Meng
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Peipei Wei
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Haiyan Xu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Tianzeng Niu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China.
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China.
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Li Y, Tian M, Feng Z, Zhang J, Lu J, Fu X, Ma L, Wei H, Wang H. GhDof1.7, a Dof Transcription Factor, Plays Positive Regulatory Role under Salinity Stress in Upland Cotton. PLANTS (BASEL, SWITZERLAND) 2023; 12:3740. [PMID: 37960096 PMCID: PMC10649836 DOI: 10.3390/plants12213740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Salt stress is a major abiotic stressor that can severely limit plant growth, distribution, and crop yield. DNA-binding with one finger (Dof) is a plant-specific transcription factor that plays a crucial role in plant growth, development, and stress response. In this study, the function of a Dof transcription factor, GhDof1.7, was investigated in upland cotton. The GhDof1.7 gene has a coding sequence length of 759 base pairs, encoding 252 amino acids, and is mainly expressed in roots, stems, leaves, and inflorescences. Salt and abscisic acid (ABA) treatments significantly induced the expression of GhDof1.7. The presence of GhDof1.7 in Arabidopsis may have resulted in potential improvements in salt tolerance, as suggested by a decrease in H2O2 content and an increase in catalase (CAT) and superoxide dismutase (SOD) activities. The GhDof1.7 protein was found to interact with GhCAR4 (C2-domain ABA-related 4), and the silencing of either GhDof1.7 or GhCAR4 resulted in reduced salt tolerance in cotton plants. These findings demonstrate that GhDof1.7 plays a crucial role in improving the salt tolerance of upland cotton and provide insight into the regulation of abiotic stress response by Dof transcription factors.
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Affiliation(s)
- Yi Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Miaomiao Tian
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Zhen Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Jingjing Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Jianhua Lu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Xiaokang Fu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Liang Ma
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Hengling Wei
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
| | - Hantao Wang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of CAAS, Anyang 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
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Zhang C, Dong T, Yu J, Hong H, Liu S, Guo F, Ma H, Zhang J, Zhu M, Meng X. Genome-wide survey and expression analysis of Dof transcription factor family in sweetpotato shed light on their promising functions in stress tolerance. FRONTIERS IN PLANT SCIENCE 2023; 14:1140727. [PMID: 36895872 PMCID: PMC9989284 DOI: 10.3389/fpls.2023.1140727] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
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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Affiliation(s)
- Chengbin Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jing Yu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Haiting Hong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Siyuan Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Fen Guo
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Hongting Ma
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jianling Zhang
- Laboratory of Plant Germplasm Innovation and Utilization, School of Life Sciences, Liaocheng University, Liaocheng, China
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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Zou X, Sun H. DOF transcription factors: Specific regulators of plant biological processes. FRONTIERS IN PLANT SCIENCE 2023; 14:1044918. [PMID: 36743498 PMCID: PMC9897228 DOI: 10.3389/fpls.2023.1044918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/03/2023] [Indexed: 06/12/2023]
Abstract
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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Affiliation(s)
- Xiaoman Zou
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang, China
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Wang Z, Wong DCJ, Chen Z, Bai W, Si H, Jin X. Emerging Roles of Plant DNA-Binding With One Finger Transcription Factors in Various Hormone and Stress Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2022; 13:844201. [PMID: 35668792 PMCID: PMC9165642 DOI: 10.3389/fpls.2022.844201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/25/2022] [Indexed: 05/24/2023]
Abstract
Coordinated transcriptional regulation of stress-responsive genes orchestrated by a complex network of transcription factors (TFs) and the reprogramming of metabolism ensure a plant's continued growth and survival under adverse environmental conditions (e.g., abiotic stress). DNA-binding with one finger (Dof) proteins, a group of plant-specific TF, were identified as one of several key components of the transcriptional regulatory network involved in abiotic stress responses. In many plant species, Dofs are often activated in response to a wide range of adverse environmental conditions. Dofs play central roles in stress tolerance by regulating the expression of stress-responsive genes via the DOFCORE element or by interacting with other regulatory proteins. Moreover, Dofs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid, jasmonate, SA and redox signaling in response to many abiotic stresses. Taken together, we highlight a unique role of Dofs in hormone and stress signaling that integrates plant response to adverse environmental conditions with different aspects of plant growth and development.
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Affiliation(s)
- Zemin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Darren Chern Jan Wong
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Zhengliang Chen
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wei Bai
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xin Jin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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The Butterfly Effect: Mild Soil Pollution with Heavy Metals Elicits Major Biological Consequences in Cobalt-Sensitized Broad Bean Model Plants. Antioxidants (Basel) 2022; 11:antiox11040793. [PMID: 35453478 PMCID: PMC9028058 DOI: 10.3390/antiox11040793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
Among the heavy metals (HMs), only cobalt induces a polymorphic response in Vicia faba plants, manifesting as chlorophyll morphoses and a ‘break-through’ effect resulting in the elevated accumulation of other HMs, which makes Co-pretreated broad bean plants an attractive model for investigating soil pollution by HMs. In this study, Co-sensitized V. faba plants were used to evaluate the long-term effect of residual industrial pollution by examining biochemical (H2O2, ascorbic acid, malondialdehyde, free proline, flavonoid, polyphenols, chlorophylls, carotenoids, superoxide dismutase) and molecular (conserved DNA-derived polymorphism and transcript-derived polymorphic fragments) markers after long-term exposure. HM-polluted soil induced a significantly higher frequency of chlorophyll morphoses and lower levels of nonenzymatic antioxidants in Co-pretreated V. faba plants. Both molecular markers effectively differentiated plants from polluted and control soils into distinct clusters, showing that HMs in mildly polluted soil are capable of inducing changes in DNA coding regions. These findings illustrate that strong background abiotic stressors (pretreatment with Co) can aid investigations of mild stressors (slight levels of soil pollution) by complementing each other in antioxidant content reduction and induction of DNA changes.
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Liu J, Meng Q, Xiang H, Shi F, Ma L, Li Y, Liu C, Liu Y, Su B. Genome-wide analysis of Dof transcription factors and their response to cold stress in rice (Oryza sativa L.). BMC Genomics 2021; 22:800. [PMID: 34742240 PMCID: PMC8572462 DOI: 10.1186/s12864-021-08104-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 10/19/2021] [Indexed: 11/18/2022] Open
Abstract
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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08104-0.
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Affiliation(s)
- Jia Liu
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Qinglin Meng
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China.
| | - Hongtao Xiang
- Institute of Farming and Cultivation, Heilongjiang Academy of Agricultural Sciences, 150086, Harbin, China
| | - Fengmei Shi
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Ligong Ma
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Yichu Li
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Chunlai Liu
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Yu Liu
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
| | - Baohua Su
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Nangang District, 150086, Harbin, China
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Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus. PLANTS 2021; 10:plants10040709. [PMID: 33916912 PMCID: PMC8067633 DOI: 10.3390/plants10040709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
Abstract
DNA binding with one finger (DOF) proteins are plant-specific transcription factors that play roles in diverse plant functions. However, little is known about the DOF protein repertoire of the allopolyploid crop, Brassica napus. This in silico study identified 117 Brassica napus Dof genes (BnaDofs) and classified them into nine groups (A, B1, B2, C1, C2.1, C2.2, C3, D1, and D2), based on phylogenetic analysis. Most members belonging to a particular group displayed conserved gene structural organisation and protein motif distribution. Evolutionary analysis exemplified that the divergence of the Brassica genus from Arabidopsis, the whole-genome triplication event, and the hybridisation of Brassica oleracea and Brassica rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of the Dof transcription factor (TF) gene family in B. napus. So far, this is the largest number of Dof genes reported in a single eudicot species. Functional annotation of BnaDof proteins, cis-element analysis of their promoters, and transcriptomic analysis suggested potential roles in organ development, the transition from the vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness, as well as potential regulatory roles in abiotic stress. Overall, our results provide a comprehensive understanding of the molecular structure, evolution, and possible functional roles of Dof genes in plant development and abiotic stress response.
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