Genome-wide identification and expression characterization of the DoG gene family of moso bamboo (Phyllostachys edulis)

Abstract

Background: The DoG (Delay of Germination1) family plays a key regulatory role in seed dormancy and germination. However, to date, there is no complete genomic overview of the DoG gene family of any economically valuable crop, including moso bamboo (Phyllostachys edulis), and no studies have been conducted to characterize its expression profile. To identify the DoG gene members of moso bamboo (PeDoG) and to investigate their family structural features and tissue expression profile characteristics, a study was conducted. Based on the whole genome and differential transcriptome data, in this investigation, we have scrutinized the physicochemical properties, gene structure, cis-acting elements, phylogenetic relationships, conserved structural (CS) domains, CS motifs and expression patterns of the PeDoG1 family of moso bamboo.

Results: The DoG family genes of moso bamboo were found distributed across 16 chromosomal scaffolds with 24 members. All members were found to carry DoG1 structural domains, while 23 members additionally possessed basic leucine zipper (bZIP) structural domains. We could divide the PeDoG genes into three subfamilies based on phylogenetic relationships. Covariance analysis revealed that tandem duplication was the main driver of amplification of the PeDoG genes. The upstream promoter of these genes containing several cis-acting elements indicates a plausible role in abiotic stress and hormone induction. Gene expression pattern according to transcriptome data revealed participation of the PeDoG genes in tissue and organ development. Analysis using Short Time-series Expression Miner (STEM) tool revealed that the PeDoG gene family is also associated with rapid early shoot growth. Gene ontology (GO) and KEGG analyses showed a dual role of the PeDoG genes. We found that PeDoGs has a possible role as bZIP transcription factors by regulating Polar like1 (PL1) gene expression, and thereby playing a disease response role in moso bamboo. Quantitative gene expression of the PeDoG genes revealed that they were abundantly expressed in roots and leaves, and could be induced in response to gibberellin (GA).

Conclusion: In this study, we found that the PeDoG genes are involved in a wide range of activities such as growth and development, stress response and transcription. This forms the first report of PeDoG genes and their potential roles in moso bamboo.

Keywords: BZIP transcription factor; Bioinformatics; DoG gene family; Gene expression; Phyllostachys edulis.

Fig. 1

Analysis of chromosome distribution and intra-syntenic relationship of DoG family in P. edulis (Moso bamboo). A: The chromosomal distribution of the DoG gene in P. edulis. Gray lines indicate collinear relationship of all the members of P. edulis, blue lines represent collinear relationship between the members of DoG family and yellow areas show the gene density; S: chromosome Scaffold of moso bamboo. B: Interlinear analysis of P. edulis (Pe), Arabidopsis thaliana (At) and Oryza sativa (Os). CHR, Chr: chromosome

Fig. 2

Phylogenetic analysis of DoG gene family from P. edulis (Pe) (Moso bamboo) and O. sativa (Os). A: Solid circles represent DOG family proteins of P. edulis (Pe); solid rectangles represent Oryza sativa’s (Os) DOG family proteins. B: solid circles denote bZIP family proteins, solid triangles denote DOG family proteins, where some renamed bZIP families are named with DOG. C: Evolutionary tree of bZIP family subfamily C. Solid black circles indicate bZIP family proteins and solid purple circles indicate DOG family proteins, where some renamed bZIP families are named after DOG

Fig. 3

Analysis of Cis-acting elements on promoters of DoG gene family in P. edulis (Moso bamboo). The color scale on the right side indicates the number of Cis-acting elements per gene

Fig. 4

Analysis of conserved structural domains and conserved motifs of PeDoGs in P. edulis (Moso bamboo). A: Domains of PeDoGs predicted by NCBI-CD D. B: Motifs of PeDoGs predicted by MEME. C: The yellow amino acids in Motif indicate the amino acid sequences that match the structural features of bZIP, while the red and blue amino acids indicate the motif3 and motif4 feature sequences, respectively

Fig. 5

3D homology modeling of protein sequences analysis of DoG gene family in P. edulis (Moso bamboo). A: PeDoG1. B: PeDoG3; The purple orbs in A and B indicate the leucine positions

Fig. 6

Differential expression of genes involved in hormone signaling pathways and bubble diagram of gene ontology (GO) terms. A: Differential expression of PeDoG genes in vitro, colors indicate the expression values of the genes. Expression values are presented as TPM values lg10 transformed counts, red boxes indicate genes in which family members are involved, yellow indicates monomers in which family genes are not involved. B: GO enrichment analysis of PeDoG genes in the top 20; vertical axis indicates GO terms; horizontal axis indicates Rich factor. the larger the Rich factor, the stronger the enrichment. The size of the dots indicates the number of genes in the GO terms

Fig. 7

Protein–protein interaction (PPI) network of the PeDOGs. The nodes are all the core proteins of the hormone signaling pathway, and the gray connecting lines represent the predicted protein interactions, with the color gradually increasing from dark (blue) to light (red), indicating a gradual increase in the number of interacting genes

Fig. 8

Transcriptome expression of DoG family in different stages and different organs of P. edulis (Moso bamboo). The scale value is from low to high, and the color changes from blue to red, which represents the expression from low to high

Fig. 9

Quantitative Real-time PCR analysis from a part of DoG family in different organs (different tissues from field samples) of P. edulis (Moso bamboo)

Fig. 10

Seedling's relative expression levels in gibberellin treatment of P. edulis (Moso bamboo). A: Relative expression of each gene of PeDoG in GA treatment; B: GA-treated red bars with red boxed lines indicate an increase in the expression of the gene to GA and black boxed lines blue bars indicate a decrease in the expression of the gene to GA; *, p < 0.05; **, p < 0.01; ****, p < 0.0001. Three biological and three technical replicates were used for each real-time PCR

Fig. 11

The Short Time-series Expression Miner (STEM) analysis of PeDoG family. A: trend graph of 10 genes with changed expression trends, red trend graph indicates that the temporal pattern of the profile conforms to the significant change trend; colorless trend graph indicates that the temporal pattern of the profile is a statistically non-significant change trend; B: trend graph of all genes under the profile with a p-value of 2.1E⁻⁶

Fig. 12

Subcellular localization of GFP-PeDOG14 by transient expression in the cells of tobacco leaves. A: Schematic diagram of the DNA construct used for PeDOG14 subcellular localization. LB, T-DNA left border. MAS, cauliflower mosaic virus MAS promoter; GFP, green fluorescent protein; NOS, nopaline synthase gene terminator; RB, T-DNA right border. B-C: Subcellular localization of GFP-tagged PeDOG14. D: Subcellular localization of GFP control