title: Genome-wide evolutionary characterization and analysis of bZIP transcription factors and their expression profiles in response to multiple abiotic stresses in Brachypodium distachyon.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  BdbZIP 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.
authors.affiliation: Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, 201602, Shanghai, Songjiang, China. xiang_liu@hotmail.com.
authors.forename: Xiang
authors.initials: X
authors.lastname: Liu
authors.affiliation: Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 3888 Chenhua Road, 201602, Shanghai, Songjiang, China. zqchu@sibs.ac.cn.
authors.forename: Zhaoqing
authors.initials: Z
authors.lastname: Chu
mesh_terms: D050976:Basic-Leucine Zipper Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D058431:Brachypodium / Q000235:genetics* / Q000378:metabolism*; D004777:Environment; D019143:Evolution, Molecular; D005091:Exons; D020869:Gene Expression Profiling; D018745:Genome, Plant; D019216:Metals, Heavy / Q000378:metabolism; D009928:Organ Specificity; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000378:metabolism; D055503:Protein Multimerization; D013312:Stress, Physiological
chemical_list: D050976:Basic-Leucine Zipper Transcription Factors; D019216:Metals, Heavy; D010937:Plant Growth Regulators