Genome-wide analysis of Dof transcription factors reveals functional characteristics during development and response to biotic stresses in pepper

Abstract

The DNA-binding with one zinc finger proteins (Dofs) are a plant-specific family of transcription factors. The Dofs are involved in a variety of biological processes such as phytohormone production, seed development, and environmental adaptation. Dofs have been previously identified in several plants, but not in pepper. We identified 33 putative Dof genes in pepper (CaDofs). To gain an overview of the CaDofs, we analyzed phylogenetic relationships, protein motifs, and evolutionary history. We divided the 33 CaDofs, containing 25 motifs, into four major groups distributed on eight chromosomes. We discovered an expansion of the CaDofs dated to a recent duplication event. Segmental duplication that occurred before the speciation of the Solanaceae lineages was predominant among the CaDofs. The global gene-expression profiling of the CaDofs by RNA-seq analysis showed distinct temporal and pathogen-specific variation during development and response to biotic stresses (two TMV strains, PepMoV, and Phytophthora capsici), suggesting functional diversity among the CaDofs. These results will provide the useful clues into the responses of Dofs in biotic stresses and promote a better understanding of their multiple function in pepper and other species.

CYCLING DOF FACTOR 1 represses transcription through the TOPLESS co‐repressor to control photoperiodic flowering in Arabidopsis

“…To explore the possible mechanisms through which CDF transcription factors are able to confer repression on CO and FT transcription, we first looked for regions of high conservation at the amino acid level, as this would imply a retained function. We constructed an amino acid alignment of CDF proteins from Arabidopsis, functionally characterized CDFs from other plant species, as well as CDF‐related DOF transcription factors from a variety of green plant lineages (Lijavetzky et al ., ; Yang et al ., ; Hernando‐Amado et al ., ; Sugiyama et al ., ; Kloosterman et al ., ; Corrales et al ., ; Lucas‐Reina et al ., ; Kang et al ., ; Ridge et al ., ). We found several stretches of amino acid conservation in CDF proteins (Figure S1).…”

Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications

“…The gene structures (exon–intron) of CaChi were obtained by aligning the CDS sequences with their corresponding genomic sequences, and their structures were shaped by using online Gene-Structure-Display Server 2.0 as described by Kang et al (2016) [83]. Conserved motifs of the CaChi genes were recognized using MEME tool (4.12.0) (Available online: ) as described by Guo et al (2016) [84] with maximum number of motifs = 10.…”

Genome-Wide Identification and Characterization of the <i>Dof</i> Transcription Factor Gene Family in <i>Phaseolus vulgaris</i> L.

“…Identification of each of these motifs is also illustrated in Figure 2, in which motif 1 is represented by the Dof domain that is uniformly found in all bean protein sequences ( Table 3). The motifs 12,16,19,20,23,24, and 25 were observed in subclass A; motifs 2, 3, 5, 6, 7, 8, 12, 14, 15, 22, 23, and 24, were observed in subclass B1, which contained the highest number of motifs; motifs 7, 12, 16, 19, 20, 23, and 24 were observed in subclass B2; motifs 4,10,15,17,18,21, and 23 were observed in subclass C1; motifs 4, 9, 10, 11, 13, 18, 19, and 25 were observed in subclass C2; and the subclasses D1 and D2 contained two motifs each, consisting of 5 and 21 and 8 and 9, respectively. From these results, it can be seen that the majority of the members …”

“…Dof TFs are involved in several important functions [18], such as root light signaling [19], germination [20], regulation of stomatal development [21], development of the vascular system [22], and responses to biotic [23] and abiotic [24] [25] stress. As such, identification and classification of the Dof family in common beans is useful for future research on plant gene expression, as to date no study has been performed on identifying members of the Dof family in common bean.…”