Genome-wide identification, molecular evolution and expression analysis of the B-box gene family in mung bean (Vigna radiata L.)

Abstract

Background: Mung bean (Vigna radiata L.) is an important warm-season grain legume. Adaptation to extreme environmental conditions, supported by evolution, makes mung bean a rich gene pool for stress tolerance traits. The exploration of resistance genes will provide important genetic resources and a theoretical basis for strengthening mung bean breeding. B-box (BBX) proteins play a major role in developmental processes and stress responses. However, the identification and analysis of the mung bean BBX gene family are still lacking.

Results: In this study, 23 VrBBX genes were identified through comprehensive bioinformatics analysis and named based on their physical locations on chromosomes. All the VrBBXs were divided into five groups based on their phylogenetic relationships, the number of B-box they contained and whether there was an additional CONSTANS, CO-like and TOC1 (CCT) domain. Homology and collinearity analysis indicated that the BBX genes in mung bean and other species had undergone a relatively conservative evolution. Gene duplication analysis showed that only chromosomal segmental duplication contributed to the expansion of VrBBX genes and that most of the duplicated gene pairs experienced purifying selection pressure during evolution. Gene structure and motif analysis revealed that VrBBX genes clustered in the same group shared similar structural characteristics. An analysis of cis-acting elements indicated that elements related to stress and hormone responses were prevalent in the promoters of most VrBBXs. The RNA-seq data analysis and qRT-PCR of nine VrBBX genes demonstrated that VrBBX genes may play a role in response to environmental stress. Moreover, VrBBX5, VrBBX10 and VrBBX12 are important candidate genes for plant stress response.

Conclusions: In this study, we systematically analyzed the genomic characteristics and expression patterns of the BBX gene family under ABA, PEG and NaCl treatments. The results will help us better understand the complexity of the BBX gene family and provide valuable information for future functional characteristics of specific genes in this family.

Keywords: B-box gene family; Abiotic stresses; Evolution; Expression profiles; Mung bean.

Fig. 1

The diagrams of conserved domains for the VrBBX proteins. The length of each protein sequence is represented by the black bar. The colored boxes refer to the conserved domains: red box, B-box1 domain; green box, B-box2 domain; blue box, CCT domain. The sequence length of each protein is represented at the bottom and the scale bar represents 100 amino acids

Fig. 2

Multiple sequence alignments of the B-box1 (a), B-box2 (b) and CCT (c) domains. The identical amino acids, conserved amino acids and similar amino acid residues are shaded in black, charcoal gray and gray, respectively

Fig. 3

The conserved domains in the VrBBX proteins. Logos of the protein alignment of the B-box1 (a), B-box2 (b) and CCT domains (c) are shown. The x-axis represents the conservative sequences of the domains. The height of each letter represents the conservation of each residue across all proteins. The y-axis is the scale of the relative entropy that reflects the conservation rate of each amino acid

Fig. 4

Phylogenetic tree of BBXs. The full-length amino acid sequences of BBX in mung bean, soybean and Arabidopsis are used for Neighbor-joining (NJ) phylogeny reconstruction with 1000 bootstrap replicates and the bootstrap values are indicated at each node. The green circles, red triangles and blue stars represent VrBBXs, AtBBXs and GmBBXs, respectively. The BBX proteins are divided into five groups (I-V) with different colors

Fig. 5

Synteny analysis of BBX genes between mung bean and monocotyledonous rice (a), monocotyledonous Arabidopsis (b) and soybean (c). V. radiata, O. sativa, A. thaliana and G. max represent Vigna radiata, Oryza sativa, Arabidopsis thaliana and Glycine max, respectively. Gray lines in the background are the duplicated gene pairs between mung bean and other plant genomes, while the red lines indicate the syntenic BBX gene pairs. The colored bars represent chromosomes or scaffolds, and their numbering is displayed at the top or bottom of the colored bars

Fig. 6

Synteny analysis of VrBBX genes on mung bean chromosomes. The light purple lines in the background indicate all synteny blocks in the mung bean genome between each chromosome, and the thick red lines indicate duplicate VrBBX gene pairs. The colored boxes indicate the different chromosomes or scaffolds and their numbering is shown on the outside of boxes. The scale bar marked on the chromosome is the length of the chromosome (Mb)

Fig. 7

Phylogenetic tree, exon–intron structure and motif analysis of the BBX gene family in mung bean. a Structure analysis of VrBBX genes. Exons and introns are represented by yellow boxes and black lines, respectively. The untranslated regions (UTRs) are represented by blue boxes. The numbers (0, 1 and 2) indicate the intron phase. b Conserved motif analysis of VrBBX proteins. Each motif is represented by a number in a colored box

Fig. 8

Predicted cis-elements in the promoter regions of VrBBX genes. The scale bar at the bottom indicates the length of promoter sequence (− 1500 bp). The cis-acting elements were represented by colored boxes

Fig. 9

Heatmap expression profiles of VrBBX genes under drought stress. Red color indicates up-regulated gene expression, yellow color indicates no significant change in gene expression, and blue color indicates down-regulated gene expression under drought stress

Fig. 10

Expression profile of nine selected VrBBX genes in response to ABA (a), PEG (b) and NaCl (c) treatments. The mean value was calculated from three independent replicates. Vertical bars indicate the standard deviation. Asterisks indicate corresponding genes that were significantly upregulated or downregulated compared with the control (* p < 0.05; ** p < 0.01)