Comprehensive analysis of bZIP transcription factors uncovers their roles during dimorphic floret differentiation and stress response in Cleistogenes songorica

Qi Yan,Fan Wu,Qian Ma,Yufeng Zhao,Tiantian Ma,Jiyu Zhang,Yanrong Wang,Xifang Zong,Jie Li

doi:10.1186/s12864-019-6092-4

Qi Yan, Fan Wu + Show 7 more

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https://doi.org/10.1186/s12864-019-6092-4

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Abstract

BackgroundTranscription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. However, no information is available for the bZIP family in Cleistogenes songorica, which is an important xerophytic and allotetraploid grass in desert grasslands.ResultsIn this study, 86 CsbZIPs were identified in the allotetraploid C. songorica genome. For location analysis, CsbZIPs were distributed evenly across two subgenomes of C. songorica. Phylogenetic tree analysis among three species indicated that CsbZIPs were evolutionarily more closely related to OsbZIPs than AtbZIPs. Syntenic and phylogenetic analyses confirmed that the CsbZIPs were mainly expanded by whole-genome duplication events. Furthermore, it was determined that rice and C. songorica might have undergone purified selection during their long evolutionary history by calculating the Ks values and Ka/Ks ratios of orthologous gene pairs. By analysing the expression patterns of CsbZIPs in different tissues and under abiotic stresses, 21 CsbZIP genes were differentially expressed between chasmogamous (CH) and cleistogamous (CL) flowers, including two FLOWERING LOCUS D (FD) genes. In shoots and roots, 79.1 and 87.2% of the CsbZIP genes, respectively, displayed transcript changes under at least one stress treatment, such as heat, cold, drought and salt. Strikingly, 17 common CsbZIP genes showed differential expression under stress response and during CL flowering. Co-expression network, GO annotation and real-time quantitative reverse transcription PCR (qRT-PCR) analyses revealed a close relationship between CL flowering-associated genes and abiotic stress-related genes.ConclusionsBZIP TFs were comprehensively analysed and identified in allotetraploid C. songorica. Our results provide insights into the evolutionary history of the bZIP family in C. songorica and provide abiotic stress-responsive and CL-associated candidate CsbZIP genes for potential applications in the genetic improvement of plants.

Highlights

Transcription factors act as important regulators of transcription networks
Genome-wide identification of Basic leucine zipper (bZIP) family genes in C. songorica In this study, 86 predicted CsbZIP genes were identified from the C. songorica genome, named CsbZIP1 to CsbZIP86 (Additional file 1: Table S1)
The 86 CsbZIP proteins varied from 122 (CsbZIP68) to 1032 (CsbZIP79) amino acid residues, the CDSs were distributed from 377 to 3175 bp, the relative molecular weights (Mws) ranged from 13.8 (CsbZIP19) to 113.4 (CsbZIP79) KDa, the grand average of hydropathicity (GRAVY) values ranged from − 1.194 (CsbZIP30) to 0.483 (CsbZIP69), and the pIs ranged from 4.81 (CsbZIP68) to 11.7 (CsbZIP47; Additional file 1: Table S1)

Summary

Introduction

Transcription factors act as important regulators of transcription networks. Basic leucine zipper (bZIP) transcription factors have been shown to be involved in multiple biological processes in plants. BZIP TFs have been demonstrated to be involved in many important biological processes in plants, such as flowering, lateral root development, biomass, lipid productivity, pollen germination and seed maturation [10,11,12,13,14]. The OsbZIP71 RNAi knockdown transgenic plants were highly sensitive to salt and polyethylene glycol stress [26]. Together, these studies showed that bZIPs are widely involved in biological processes and various stresses in plants

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