Abstract
This study identified 57 basic leucine zipper (bZIP) genes from the pineapple genome, and the analysis of these bZIP genes was focused on the evolution and divergence after multiple duplication events in relation to the pineapple genome fusion. According to bioinformatics analysis of a phylogenetic tree, the bZIP gene family was divided into 11 subgroups in pineapple, Arabidopsis, and rice; gene structure and conserved motif analyses showed that bZIP genes within the same subgroup shared similar intron-exon organizations and motif composition. Further synteny analysis showed 17 segmental duplication events with 27 bZIP genes. The study also analyzed the pineapple gene expression of bZIP genes in different tissues, organs, and developmental stages, as well as in abiotic stress responses. The RNA-sequencing data showed that AcobZIP57 was upregulated in all tissues, including vegetative and reproductive tissues. AcobZIP28 and AcobZIP43 together with the other 25 bZIP genes did not show high expression levels in any tissue. Six bZIP genes were exposed to abiotic stress, and the relative expression levels were detected by quantitative real-time PCR. A significant response was observed for AcobZIP24 against all kinds of abiotic stresses at 24 and 48 h in pineapple root tissues. Our study provides a perspective for the evolutionary history and general biological involvement of the bZIP gene family of pineapple, which laid the foundation for future functional characterization of the bZIP genes in pineapple.
Highlights
Transcription factors (TFs) play important roles in the growth and development of plants [1]
A considerably significant response was observed for AcobZIP24 against all kinds of abiotic stress at 24 and 48 h in pineapple root tissues, followed by AcobZIP36, which was upregulated against abiotic stress at high-level treatments
We identified 57 basic leucine zipper (bZIP) gene sequences and performed an analysis of genome data sets, considering phylogeny (Arabidopsis, rice and pineapple), gene structures, and conserved motifs, followed by gene location on chromosomes by synteny analysis
Summary
Transcription factors (TFs) play important roles in the growth and development of plants [1]. When plants are subjected to low temperature, drought, salt stress, or exogenous hormones, TFs are induced to bind to their corresponding cis-elements through a series of signal transduction steps to activate or inhibit gene expression [2]. Genes in the ERF family encode transcriptional regulators with a variety of functions involved in the developmental and physiological processes in plants [3]. WRKY70 and WRKY54 cooperate as negative regulators of stomatal closure and osmotic stress tolerance in Arabidopsis, suggesting that they have an important role in plant defense and abiotic stress signaling [5]. OsbZIP62 is involved in the ABA signaling pathways and positively regulates rice drought tolerance by regulating the International Journal of Genomics expression of genes associated with stress [6]. The identification and functional depiction of TFs are essential for the reconstruction of transcriptional regulatory networks [7]
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