Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

Abstract

DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although variable in sequence length, molecular weight, and isoelectric point, all TaDof proteins contained conserved zinc-finger structures and were phylogenetically divided into 7 sub-groups. Exon/intron and motif analyses suggested that TaDof structures and conserved motifs were similar within sub-groups but diverse among sub-groups. Many segmental duplications were identified and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was main reason for increased number of TaDofs. Prediction and experimental confirmation revealed that TaDofs functioned as transcription factors in the nucleus. Expression pattern profiling showed that TaDofs specifically affected growth and development, and biotic and abiotic stress responses. Wheat miRNAs and cis-regulator were predicted as essential players in molding TaDofs expression patterns. qRT-PCR analysis revealed that TaDofs were induced by salt and drought stresses. Customized annotation revealed that TaDofs were widely involved in phytohormone response, defense, growth and development, and metabolism. Our study provided a comprehensive understanding to wheat TaDofs.

Alcohol dehydrogenase (ADH) genes family in wheat (Triticum aestivum): Genome-wide identification, characterization, phylogenetic relationship and expression patterns

“…The protein molecular weight and isoelectric point of the candidate genes were calculated by ExPASy website (https://web.expasy.org/compute_pi/). Plant-mPLoc (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi) was used to predict the subcellular location of the TaADH genes [44].…”

Evolutionary Expansion and Expression Analysis of the Oligopeptide Transporter Gene Family Between Cucurbita Moschata and Cucurbita Maxima

“…The molecular weight, isoelectric point and grand average hydropathy (GRAVY) values of each OPT gene were estimated using the ExPASy Proteomics Server (https://web.expasy.org/tools/protparam.html/) [40]. The subcellular location of OPTs gene was predicted using the Plant-mPLoc (http://www.csbio.sjtu.edu.cn/bioinf/plant-multi) [41].…”

Mining the Roles of Wheat (Triticum Aestivum) SnRK Gene Family in Biotic and Abiotic Responses

“…The conserved domain and gene structure analysis provide information regarding gene duplication and their functional conservation during evolution [30]. We analyzed TaSnRKs according to the following criteria: (1) one gene of the triads was retained, (2) only the rst variant was kept, the 65 representative TaSnRKs were chosen (Fig.…”

“…The computer-based method was used to identify SnRK gene family members from the wheat reference genome IWGSC RefSeq v1.1 assembly (https://wheat-urgi.versailles.inra.fr/Seq-Repository/Assemblies) [30].…”

“…Tandem duplication events were identi ed using the following evaluation criteria: (1) length of the aligned sequence > 80% of the length of each sequence; (2) identity > 80%; (3) threshold ≤ 10 −10 ; (4) only one duplication event could be admitted when genes were linked closely; (5) the intergenic distance was less than 25 kb. If genes satis ed criteria (1), (2), and (3) and located on different chromosomes, they were judged as segmental duplications [30][31]. The evolutionary rates (Ka, Ks, and Ka/Ksratio) were estimated by TBtools (https://github.com/CJ-Chen/TBtools) [71].…”