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

Abstract

Background DNA binding with one finger (Dof) transcription factors play important roles in plant growth and 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. Results Using the recently released wheat genome database (IWGSC RefSeq v1.1), we identified 96 wheat Dof gene family members, which were phylogenetically clustered into five distinct subfamilies. 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. Positive selection analysis revealed that the Dof gene family experienced different degrees of positive selection pressure during the process of evolution, and five significant positive selection sites (30A, 31T, 33A, 102G and 104S) were identified. Additionally, nine groups of coevolving amino acid sites, which may play a key role in maintaining the structural and functional stability of Dof proteins, were identified. The results from the RNA-seq data and RT-qPCR analysis revealed that TaDof genes exhibited obvious expression preference or specificity in different organs and developmental stages, as well as in diverse abiotic stress responses. Most TaDof genes were significantly upregulated by heat, PEG and heavy metal stresses. 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.

Identification and Characterization of PLATZ Transcription Factors in Wheat

“…The TaPLATZ s were unequally distributed in sub-genomes A, B, and D, which included 24, 16, and 20 members, respectively ( Table S1 , Figure 2 ). This suggests that homologous genes on the B genome may be absent or become pseudogenes in the lineage leading to wheat [ 31 ]. During the evolutionary process of wheat, rapid alterations and sporadic changes in wheat genome took place due to hybridization, polyploidization, domestication, and mutation, resulting in some modifications and a high level of gene loss [ 32 ].…”

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

“…The DOF TFs are plant-specific transcription factors, first identified in maize in 1995, and were shown to play an essential role in regulating carbon metabolism-related and light-regulated genes [ 3 , 4 , 5 ]. Subsequently, a diverse number of DOF TFs have been identified in several plants, including 36, 30, and 96 in Arabidopsis, rice, and wheat, respectively [ 6 , 7 , 8 ]. In Arabidopsis, the first protein–protein interaction of DOF domain protein with bZIP protein associated with the stress response was reported, indicating the potential role of DOF TFs in complex regulatory networks [ 9 ].…”

Expression Profiling of the Dof Gene Family Under Abiotic Stresses in Spinach

“…4). The quantity of SoDofs is lower than that of Arabidopsis (36) 27 , tomato (34) 33 , wheat (96) 34 , rice (30) 27 , potato (35) 35 , soybean (78) 28 , and sugarcane (29) 31 . This is because spinach separated with Arabidopsis just after the ancient whole genome triplicationand there was no whole genome replication in spinach genome 1 .…”

“…The intron-exon structure in each subgroup is conserved except for that in the subgroup D1. The distribution of motifs is indicative of evolutionary relationship 34 . The protein sequence analysis of the 22 SoDof genes revealed that only Dof motifs of these 22 protein sequences are conserved (Fig.…”

“…The spinach genome data came from SpinachBase (http://www.spinachbase.org/?q=download). Then predicted proteins were con rmed by performing NCBI Conserved Domain Database (CDD) 33 Pfam 34 and SMART 35 to make sure the presence of the conserved Dof domain in the existence of putative SoDof members in the spinach genome. Similarly, Arabidopsis Dof genes had been identi ed by scanning Arabidopsis database (ftp://ftp.ensemblgenomes.org/pub/plants/release-42/fasta/arabidopsis_thaliana/) using HMM and CDD.…”