Genome-wide evolutionary characterization and analysis of bZIP transcription factors and their expression profiles in response to multiple abiotic stresses in Brachypodium distachyon.

Xiang Liu,Zhaoqing Chu

doi:10.1186/s12864-015-1457-9

Abstract

BackgroundPlant basic leucine zipper (bZIP) transcription factors are one of the largest and most diverse gene families and play key roles in regulating diverse stress processes. Brachypodium distachyon is emerging as a widely recognized model plant for the temperate grass family and the herbaceous energy crops, however there is no comprehensive analysis of bZIPs in B. distachyon, especially those involved in stress tolerances.ResultsIn this study, 96 bZIP genes (BdbZIPs) were identified distributing unevenly on each chromosome of B. distachyon, and most of them were scattered in the low CpG content regions. Gene duplications were widespread throughout B. distachyon genome. Evolutionary comparisons suggested B. distachyon and rice’s bZIPs had the similar evolutionary patterns. The exon splicing in BdbZIP motifs were more complex and diverse than those in other plant species. We further revealed the potential close relationships between BdbZIP gene expressions and items including gene structure, exon splicing pattern and dimerization features. In addition, multiple stresses expression profile demonstrated that BdbZIPs exhibited significant expression patterns responding to 14 stresses, and those responding to heavy metal treatments showed opposite expression pattern comparing to the treatments of environmental factors and phytohormones. We also screened certain up- and down-regulated BdbZIP genes with fold changes ≥2, which were more sensitive to abiotic stress conditions.ConclusionsBdbZIP genes behaved diverse functional characters and showed discrepant and some regular expression patterns in response to abiotic stresses. Comprehensive analysis indicated these BdbZIPs’ expressions were associated not only with gene structure, exon splicing pattern and dimerization feature, but also with abiotic stress treatments. It is possible that our findings are crucial for revealing the potentialities of utilizing these candidate BdbZIPs to improve productivity of grass plants and cereal crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1457-9) contains supplementary material, which is available to authorized users.

Highlights

Plant basic leucine zipper transcription factors are one of the largest and most diverse gene families and play key roles in regulating diverse stress processes
Some plant species maintained the high number of basic leucine zipper (bZIP) genes, which might contribute to their numerous tandem duplications and large-scale segmental duplications [52]
Except Zea mays had a little bit more (126). bZIP genes, the plant species sub-grouped in monocot clades had approximately the close numbers (95–104), which might due that the species in this clade shared the common ancestor of Poaceae and had similar whole genome duplication [53]

Summary

Introduction

Plant basic leucine zipper (bZIP) transcription factors are one of the largest and most diverse gene families and play key roles in regulating diverse stress processes. The intron patterns within the basic and the hinge region are very important for their functional evolution due to different status of exon splicing in these regions In plant species such as rice, maize and Arabidopsis, the patterns of those motifs exhibited regular conservation and diversity [10,11]. Depend upon the basis of the presence of attractive or repulsive interhelical g↔e electrostatic interactions and the presence of polar or charged amino acids in the a and d positions of the hydrophobic interface of the leucine zipper region, dimerization specificity of bZIP proteins in plant species such as Arabidopsis, maize and rice have been predicted [10,11,15]

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