Genome-wide identification of bZIP transcription factors and their expression analysis in Platycodon grandiflorus under abiotic stress

Abstract

The Basic Leucine Zipper (bZIP) transcription factors (TFs) family is among of the largest and most diverse gene families found in plant species, and members of the bZIP TFs family perform important functions in plant developmental processes and stress response. To date, bZIP genes in Platycodon grandiflorus have not been characterized. In this work, a number of 47 PgbZIP genes were identified from the genome of P. grandiflorus, divided into 11 subfamilies. The distribution of these PgbZIP genes on the chromosome and gene replication events were analyzed. The motif, gene structure, cis-elements, and collinearity relationships of the PgbZIP genes were simultaneously analyzed. In addition, gene expression pattern analysis identified ten candidate genes involved in the developmental process of different tissue parts of P. grandiflorus. Among them, Four genes (PgbZIP5, PgbZIP21, PgbZIP25 and PgbZIP28) responded to drought and salt stress, which may have potential biological roles in P. grandiflorus development under salt and drought stress. Four hub genes (PgbZIP13, PgbZIP30, PgbZIP32 and PgbZIP45) mined in correlation network analysis, suggesting that these PgbZIP genes may form a regulatory network with other transcription factors to participate in regulating the growth and development of P. grandiflorus. This study provides new insights regarding the understanding of the comprehensive characterization of the PgbZIP TFs for further exploration of the functions of growth and developmental regulation in P. grandiflorus and the mechanisms for coping with abiotic stress response.

Keywords: Platycodon grandiflorus; abiotic stress; bZIP transcription factor; evolutionary analyses; expression profiling.

Figure 1

The distribution information of PgbZIP genes on chromosomes and gene replication events in the P.grandiflorus. (A) Information on the location of the PgbZIP genes on the P.grandiflorus. (B) Gene duplication events of bZIP genes in P.grandiflorus. Black lines indicate gene segmental duplication events in the PgbZIP gene, and gray lines show that collinear pairs of all P.grandiflorus genes. The yellow lines and red bar indicate the genes density in each chromosome.

Figure 2

The phylogenetic relationship and classification of the of the bZIP proteins in P. grandiflorus, I. indigotica and A. thaliana. The bootstrap value were set to 1000 replications. Subfamilies are marked with distinct colors. The red star, blue triangle and black dots point out the bZIP proteins of P. grandiflorus, I. indigotica and A. thaliana, respectively.

Figure 3

Phylogenetic analysis motifs, conserved domains and cis-element analysis of the PgbZIP genes. (A) Distribution of motifs within each PgbZIP protein. (B) Conserved domains of PgbZIP proteins. (C) Distribution of different types of cis-elements in the promoter region of the PgbZIP genes. (D) PgbZIP gene structures, lines indicate introns. (D) Distribution of different types of cis-elements in the promoter region of the PgbZIP genes.

Figure 4

Synteny analysis of bZIP genes between P.grandiflorus and M. domestica, V. vinifera, S. lycopersicum, C. sativa, C. lanceolata, and O. sativa. Gray lines symbolize the colinear blocks within P.grandiflorus and other genomes, Purple lines represent the syntenic bZIP gene pairs.

Figure 5

Heatmap of bZIP gene expression profiles in eight tissues of P. grandifloru. Data represent FPKM values from transcriptome data come from 8 tissues, including seed, leaf, petal, pistil, root, sepal, stamen and stem. Gene expression using Log₂(FPKM+1) logarithmic transformation treatment.

Figure 6

qRT–PCR analysis of PgbZIP genes in five different tissues of P. grandiflorus. Different colors represent different tissues. Use of the PgGAPDH gene as a reference gene.

Figure 7

qRT-PCR analysis of PgbZIP genes under drought and salt stress. CK: normal growth group; Salt stress and drought stress simulated using NaCl and PEG. The PgGAPDH gene was used as a reference gene. The significance analysis was carried out the use of a t-test. *, **, *** indicate significant difference in p < 0.05, p < 0.01, and p < 0.001.

Figure 8

PgbZIP genes correlation network established using RNA-seq data from 8 tissues of P.grandiflorus. Circles represent co-expressed transcription factors, and diamonds represent the PgbZIP genes. Positive and negative correlations are indicated by solid and dashed lines, respectively. The shade of the color indicates the amount of genes correlated.

Figure 9

The GO annotation and KEGG pathway enrichment analysis of TFs in correlation networks. (A) The GO annotation of TFs in correlation networks. (B) The GO enrichment analysis of TFs in correlation networks. (C) The KEGG pathway enrichment analysis of TFs in correlation networks.