Abstract
BackgroundThe bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar.ResultsIn this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic.ConclusionsUsing comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.
Highlights
The basic leucine zipper (bZIP) gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses
Identification and characterization of the bZIP transcription factor family in poplar In this study, we identified 86 proteins from the bZIP family, by use of HMMER analysis (E-value < 1 × 10− 5)
Evidence from verification by Pfam and SMART indicated that the 86 poplar proteins shared the bZIP domain, which is congruent to our predictions
Summary
The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. Systems biology is powerful for mechanistic understanding of gene functions. Such studies have not yet been reported in poplar. The basic leucine zipper (bZIP) represents a super gene family that encodes transcription factors. This gene family is widely distributed in eukaryotes. Transcription factor proteins coded by the bZIP gene family contain a highly conserved bZIP domain. The structure is composed of 60–80 amino acids, including a basic DNA binding region and adjacent leucine zipper [2]. The leucine zipper region is composed of heptad repeats of leucine or other large hydrophobic amino acids, and the number of repeats in
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
