Genome-wide identification and expression analysis of Dof gene family members in mulberry trees (Morus notabilis L.) under drought stress

Abstract

Background: The DNA-binding with one finger (Dof) gene is a classical plant transcription factor with specific conserved structural domains, which plays an important role in the regulation of plant metabolism, root development, and stress defense mechanisms. In recent years, drought has severely jeopardized the growth and development of crops and is one of the main environmental factors limiting plant growth and reducing crop yields. Whether Dof family genes play a role in mulberry drought resistance is largely unknown.

Results: To investigate the characteristics of the Dof gene family members in mulberry trees, 24 members of the mulberry Dof gene family were identified in the whole mulberry genome, and bioinformatics tools were employed to analyze the protein physicochemical properties, gene structure, phylogenetic evolution, conserved sequences, interaction networks, promoter cis-acting elements, and expression levels of Dof genes in mulberry.

Conclusions: Most of the mulberry Dof proteins were unstable, all were hydrophilic. Subcellular localization prediction showed that all proteins were localized in the nucleus. The prediction of promoter cis-elements showed that the MnDof (Morus notabilis L. Dof) gene family contained 75 promoter cis-elements for growth and development, hormone, light, and stress responses. Amino acid sequence alignment and phylogenetic tree analysis showed that all 24 Dof transcription factors contained zinc finger structural proteins. MnDof genes were distributed on all chromosomes except chromosomes 1, 2, and 7. A portion of MnDof genes responded to drought stress. These results provide information on the Dof gene family in mulberry and provide new insights into the function of MnDof genes in perennial plants, laying the foundation for further analysis of the function of these genes.

Keywords: Bioinformatics analysis; Dof transcription factor; Drought stress; Mulberry.

Fig. 1

Cis-elements in the promoter regions of Dof genes in mulberry. Each colored block represents functionally similar promoter cis-acting elements

Fig. 2

Amino acid sequence alignment

Fig. 3

Phylogenetic (I), conservative motif (II), and conservative domain (III) prediction of mulberry Dof gene family. A, B, C, D, and E are the five groups of the Dof gene in mulberry

Fig. 4

Phylogenetic tree of mulberry Dof genes. The tree was produced using MEGA11.0 software. The full length of amino acid sequences of140 DOF proteins (24, Mn; 36, At; 30, Os; 25, Vv; 25, Pp) were used to generate the evolutionary tree by maximum likelihood method. The DOF proteins of all species were categorized into six groups according to their evolutionary relationships, among which the mulberry DOF proteins were categorized into five groups (Group I, Group II, Group III, Group IV, and Group V). Bootstrap values are labeled above the branches. Different colors in the figure indicate different subgroups, and group name are marked on the periphery. Species abbreviations used: Mn, mulberry; At, Arabidopsis; Os, rice; Vv, grape; Pp, peach

Fig. 5

Mulberry DOF transcription factor protein interactions

Fig. 6

Chromosomal localization of mulberry Dof genes

Fig. 7

The heatmap of pairwise ka/ks between Dof genes

Fig. 8

Expression of 9 Dof genes in mulberry tree under drought stress