Genome-Wide Identification of DNA Binding with One Finger (Dof) Gene Family in Tartary Buckwheat (Fagopyrum tataricum) and Analysis of Its Expression Pattern after Exogenous Hormone Stimulation

Abstract

DNA binding with one finger (Dof) proteins have been proven to be involved in multiple biological processes. However, genome-wide identification of the Dof gene family has not been reported for Tartary buckwheat (Fagopyrum tataricum). In this study, 35 FtDof proteins were identified, and they could be divided into nine phylogenetic subgroups. Proteins within the same subgroup had similar gene structure and motif composition. Moreover, abundant cis-acting elements were present in the promoter regions of FtDof genes. Segmental duplication was the primary driving force for the evolution of the FtDof gene family. Synteny analysis indicated that Tartary buckwheat was closer to dicotyledons, and more orthologous Dof genes existed among them. The expression pattern of FtDofs in different tissues and at different fruit developmental stages varied. Different tissues contained several genes that were specifically expressed. FtDof expression was mainly upregulated under methyl jasmonate treatment and downregulated under other hormone treatments. Taken together, FtDofs may play important roles in the growth and development of Tartary buckwheat and in response to abiotic and biotic stresses. Therefore, the genome-wide identification and expression pattern analysis of the Tartary buckwheat Dof gene family lays a foundation for further exploration of the functional characteristics of FtDofs in the future.

Keywords: Dof; Tartary buckwheat; cis-acting elements; hormone; motif; synteny analysis.

Figure 1

Schematic of chromosomal distribution of Tartary buckwheat Dof genes.

Figure 2

Phylogenetic tree constructed with Dof proteins from Tartary buckwheat and Arabidopsis thaliana by MEGA X (version 10.0.4) based on maximum likelihood method.

Figure 3

Gene structure, motif composition and cis-acting element distribution of Dof genes in Tartary buckwheat. (a) Exon–intron structures of Dof genes in Tartary buckwheat. The green box represents the untranslated region, the yellow box represents the coding sequence, and the red box represents the Dof domain. (b) Motif composition of Dof proteins in Tartary buckwheat. As shown in the legend on the right, Motifs 1–10 are marked with different colours. (c) Distribution of cis-acting elements in the promoter region of Tartary buckwheat Dof genes. Different types of cis-elements are marked with different colours, as indicated in the legend to the right.

Figure 4

Schematic of interchromosomal relationship of Tartary buckwheat Dof proteins. Red lines represent segmental duplication events.

Figure 5

Synteny analysis between the Dof proteins of Tartary buckwheat with four dicotyledonous plants (Arabidopsis thaliana, Solanum lycopersicum, Glycine max and Vitis vinifera) and three monocotyledonous plants (Oryza sativa, Setaria italica and Sorghum bicolor) by MCScanX.

Figure 6

Heatmap of tissue specificity of Tartary buckwheat Dof genes and expression pattern after stimulation with exogenous hormones. (a) Expression pattern of FtDofs in Tartary buckwheat roots, stems, leaves and four developmental stages of fruit (F_S1, F_S2, F_S3 and F_S4). With the increase in gene expression, the colour of the bar shifts from white to red, as shown in the bar on the right. (b) Expression pattern of FtDofs after stimulation with exogenous hormones. The asterisk on the heatmap indicates a significant difference between the treatment and the control (Student’s t-test). * and ** represent 0.05 and 0.01 significance levels, respectively. With the increase in gene expression, the colour of the bar shifts from blue to red, as shown in the bar on the right.

Figure 7

Enrichment analysis of FtDofs. (a) Gene ontology (GO) enrichment analysis of FtDofs. Blue, red and yellow represent three ontologies of GO, namely, molecular function, cellular component and biological process, respectively. (b) Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of FtDofs.