Genome-wide analysis of wheat DNAbinding with one finger (Dof) transcription factor genes: Evolutionary characteristics and diverse abiotic stress responses

- Although genome-wide identification and analysis of the DOF transcription factor family has been reported in other species, no relevant studies have emerged in wheat.
- The aim of this study was to investigate the evolutionary and functional characteristics associated with plant growth and abiotic stress responses by genome-wide analysis of the wheat Dof transcription factor gene family..
- Gene duplication analysis revealed a broad and heterogeneous distribution of TaDofs on the chromosome groups 1 to 7, and obvious tandem duplication genes were present on chromosomes 2 and 3.Members of the same gene subfamily had similar exon-intron structures, while members of different subfamilies had obvious differences.
- Functional divergence analysis indicated that type-II functional divergence played a major role in the differentiation of the TaDof gene family.
- Conclusions: The genome-wide analysis and identification of wheat DOF transcription factor family and the discovery of important amino acid sites are expected to provide new insights into the structure, evolution and function of the plant Dof gene family..
- Full list of author information is available at the end of the article.
- OBPl specifically increased the binding of the OBF proteins to octopine synthase (‘ocs’) element sequences [7].
- Wheat PBF could trans- activate the transcription of the native alpha-gliadin pro- moter by binding to the intact prolamin-box [28]..
- The completion of the sequencing of the wheat genome will accelerate the studies on the structure, evolution and function of the wheat Dof gene family..
- In this study, using common wheat genome database (IWGSC RefSeq v1.0), we conducted a comprehensive genome-wide analysis on the structural characterization, molecular evolution and expression profiling of the wheat Dof gene family, which can provide new informa- tion for further understanding the evolution characteris- tics and function of plant Dof genes..
- Ultimately, a total of 96 members of the Dof transcription factor gene family were identified from wheat.
- The number of amino acids of the TaDof encoding proteins varied from 152 to 539 amino acids, their pI values ranged from 4.66 to 10.46 with an average of 8.05 and weakly alkaline, and their molecular weights were from 15.77 to 58.13 kDa, with an average of 33.38 kDa..
- Based on the IWGSC database, the physical locations of the TaDof genes on the corresponding chromosomes are depicted in Fig.
- In particular, chromo- some 3 with 27 TaDof members from TaDof38 to TaDof64 had the highest density, and they were closely arranged at the lower part of the chromosomes, but chromosome 7 only contained three TaDof genes (TaDof94, TaDof95 and TaDof96).
- Interestingly, we found that the genes located on chromosome 4A were opposite to the position of the homologous genes lo- cated on chromosome 4B and chromosome 4D.
- The results showed that strong green fluorescent signals of the three GFP fusion proteins were observed in the nucleus (Fig.
- Multiple sequence alignments of the 162 Dof proteins were performed to construct a Bayesian phylogenetic tree (Fig.
- The exon-intron structures of the 96 TaDof gene members were analyzed by comparing the CDSs and the complete gene sequences using the GSDSv2.0, and the results are shown in Fig.
- The number of introns in the TaDof genes was extremely small, with 0–2 introns in each gene.
- In addition, the members of the same subfamily generally had similar number of introns.
- The DIVERGE v3.0 software combined with the poster- ior probability analysis method [42–44] was used to esti- mate the type-I and type-II functional divergences of the.
- gene group in the Dof family.
- Among them, likelihood ratio test (LRT) values of the subfamily pairs Group A/Group E, Group C/Group E and Group D/Group E were significantly dif- ferent (p <.
- 1 Distribution and duplication of TaDof genes in Triticum aestivum L.
- In order to distinguish the intersecting lines, one of the red dotted lines was replaced with blue.
- divergence played a major role in the differentiation of the TaDof gene family.
- By comparing M0 and M3 models, we found that the twice log-likelihood difference of the models (2△lnL) was 883.03, indicating that certain amino acid sites might be undergone strong positive selection pressure.
- The estimated ω value of the M8 model was 2.55223, which is much higher than 1, indicating that some TaDof amino acid sites were strongly affected by positive selection.
- 5b-c), which were mainly located at the N-terminal of the Dof protein..
- In total, seven types of cis-acting elements were found in the promoter region of the TaDof genes, as shown in Table S4..
- The localization of the nuclei was detected by 4 ′ ,6-diamidino-2-phenylindole (DAPI) staining.
- Blue fluorescence indicates the location of the nucleus stained by DAPI.
- Merged: emergence of the GFP fluorescence signal, chlorophyll autofluorescence signal and bright light field.
- Only 17 members of the TaDof gene family did not contain G-box while the remaining members had at least one G-box copy.
- Some TaDof genes.
- Additionally, CCGTCC-box, CAT-box and O2-site accounted for and 21.7% of the total number of development related elements, respectively.
- Except for the promoter of TaDof86 that had no TATA-box, the other members of the wheat TaDof protein family all contained these two types of cis-acting elements related to transcriptional regulation..
- Among the development related elements, subfam- ily A had the largest number of CCGTCC-box, while sub- family D had 59.3% of the total number of O2-site.
- The number of AREs in the environmental stress-related elements in sub- family D accounted for 51.5% of the total.
- Expression of TaDof genes in different organs and developmental stages.
- b Exon-intron structures of the TaDof genes.
- Table 1 Functional divergence between subfamilies of the TaDof gene family.
- 5 Protein sequences and model building of the 3D structure of TaDof6.
- genes that were significantly expressed in all stages of the stem growth, and generally with a low expression in root and high expression in seeds at two and 14 days post anthesis (DPA).
- Further analysis found that some TaDof genes which clustered in the same sub- family of the phylogenetic tree (Fig.
- In particular, the homologous genes TaDof2, TaDof3, and TaDof6 clustered in a small branch of the phylogenetic tree showed a high expression in the endo- sperm, but the corresponding expression values detected in the qRT-PCR experiment were particularly low in other tissues (Fig.
- Expression profiling of TaDof genes in response to various abiotic stresses.
- The publicly available RNA-seq data of wheat leaves under polyethylene glycol (PEG)-simulated drought and heat stresses were used to show the expression profile of the TaDof genes (Table S6 and Fig.
- 2 △ lnL, twice the log-likelihood difference of the models.
- According to the results of RNA-seq datas and qRT-PCR, the expression levels of the most homologous genes in response to abiotic stress.
- a Heat map of the expression profiling of wheat TaDof genes at seedling, vegetative and reproductive stages.
- b Heat map of the expression profiling of wheat TaDof genes at seedling under heat or PEG stress.
- The gray represents the value of 0 in the original RNA-seq data, and the cluster software automatically recognizes this part of the data as “ missing.
- The effects of nitrogen stress on the expression of the TaDof3 and TaDof6 genes were more obvious during grain development (Fig.
- Under drought stress, three TaDof genes were significantly upregulated in the early developmental stages of the wheat cultivars Zhongmai 175 and Jimai 22 (Fig.
- In addition, the structural conservation of the TaDof genes in subfamilies was consistent with other plants such as Arabidopsis and rice [32], barley [33], sorghum [34] and B.
- Expression of the wheat Ubiqutin gene was used as a reference gene.
- (Table 1), demonstrating the important roles of the physical and chemical property changes of amino acids in the diversification among the subfamilies.
- All seven type-II functional divergence sites (47E, 52 K, 55 N, 66 M, 71Y, 75A and 94G) are located in the Dof domain (Fig.
- 5), indicating that they may be the main driving force promoting the variation of the Dof domain and the functional divergence of the wheat Dof family.
- These coevolu- tionary sites may not only perform an important function, but also play a key role in the evolution of the wheat Dof gene family.
- In this study, we detected a large number of the meristem-specific activation-related element CCGTCC-box in the TaDof gene promoter regions of Group E, and each gene con- tained more than 2.3 copies (Table S5), indicating that these TaDof genes may also function in various vascular development processes..
- Expression and functions of TaDof genes in response to abiotic stresses.
- We detected a nu- merous phytohormone regulation-related elements in the promoter region of the 96 TaDof family members, such as the TCA-element, GARE-motif, TGA-element, ABRE and CGTCA-motif (Table S4).
- Most of the Dof genes in Chinese cabbage were also quickly upregulated by salt, drought, heat, and cold stress treatments [56]..
- In this study, most TaDof genes were up- regulated under heat stress, and the RNA-Seq data also revealed that the majority of the TaDof genes were re- sponsive to heat and PEG stresses (Fig.
- Introduction of the maize ZmDof1 gene into rice can in- crease nitrogen assimilation and enhance plant growth under low-nitrogen conditions [67].
- Consistent with previous studies, in this study, the expression of the TaDof2, TaDof3 and TaDof6 genes was upregulated under drought and nitrogen stresses (Fig.
- These results suggest the potential roles of TaDof genes in the response to abiotic stresses..
- The mem- bers of the TaDof family almost had no introns and all contained a conserved Dof domain.
- The Dof gene family underwent different degrees of positive selection pressure in the evolutionary process.
- Our study provides valuable information for further understanding the mo- lecular evolutionary mechanism and functional traits of the plant Dof gene family..
- Chromosome location and gene duplication analysis of TaDof genes.
- The duplication gene pairs in the Dof gene family were identified based on the criteria of the previous studies [52, 72].
- Based on the similarity and arrangement of the genes on the chromosomes near the two genes, it was determined whether the two genes were segment.
- Multiple sequence alignment of the amino acid se- quences of Dof proteins were performed based on MUSCLE program (http://www.ebi.ac.uk/Tools/msa/.
- Furthermore, maximum like- lihood and minimal evolution methods were applied for the tree construction to validate the results of the N-J method in MEGA5.0..
- webtools/plantcare/html/) was used to analyze cis-acting elements in the 1500 bp promoter region upstream of the TaDofs [47].
- Conserved motifs of the TaDof pro- tein sequences were detected by MEME website (http://.
- Molecular evolution analysis of the TaDofs gene family DIVERGE 3.0 software package was used to detect the presence of type I and type II functional divergence sites in different subfamilies, and the critical value of poster- ior probability (Qk) was set to 0.8 [43].
- The positive se- lection analysis of the Dof protein family was performed using site model in the PAML4.4 software package .
- The RNA-seq data of the TaDof genes were downloaded from the expVIP website (http://www.wheat-expression..
- The expression levels of the target genes were determined according to the expression changes relative to the reference gene.
- At the beginning of the experi- ment, the relative stability of the reference gene was tested by using various organs and wheat materials treated with different abiotic stress treatments..
- Cis-element analysis of 1500 bp nucleotide sequences data upstream of the translation initiation codon of TaDof genes.
- The RNA-Seq atlas data of the TaDof genes..
- The funders had no role in the study process including preparation of the manuscript..
- The RNA-seq data of the 96 wheat Dof genes with specific accession numbers from En- semble Plants (http://plants.ensembl.org/Triticum_aestivum/Info/Index) are available on the expVIP website (http://www.wheat-expression.com.
- Functional dissections between GAMYB and Dof transcription factors suggest a role for protein-protein associations in the gibberellin- mediated expression of the RAmy1A gene in the rice aleurone.
- Members of the Dof transcription factor family in Triticum aestivum are associated with light- mediated gene regulation.
- Genomewide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families.
- Identification and characterisation of Dof transcription factors in the cucumber genome..
- Genome-wide identification and analysis of the AP2 transcription factor gene family in wheat (Triticum aestivum L.
- Identification of genes bordering breakpoints of the pericentric inversions on 2B, 4B, and 5A in bread wheat (Triticum aestivum L.
- Transcriptome-wide identification and expression profiling of the DOF transcription factor gene family in Chrysanthemum morifolium.
- The DNA binding site of the Dof protein NtBBF1 is essential for tissuespecific and auxin-regulated expression of the rolB oncogene in plants.
- Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions.
- 20 years of the SMART protein domain annotation resource.
- Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.
- Genome-wide analysis of the cellulose synthase-like (Csl) gene family in bread wheat (Triticum aestivum L

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