Background: Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be diverse transcriptional regulators, playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. Results: In this study, we identified 428 bZIP genes encoding 585 distinct proteins in six legumes, Glycine max, Medicago truncatula,Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Lotus japonicus. The legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. Four kinds of intron patterns (a–d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. We predicted the DNA-binding patterns and the dimerization properties, based on the characteristic features in the basic and hinge regions and the Leu zipper, respectively, which indicated that some highly conserved amino acid residues existed across each major group. The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. We also detected several key legume bZIP genes involved in drought- and salt-responses by comparing fold changes of expression values in drought-stressed or salt-stressed roots and leaves. Conclusions: In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses.

Raw protein sequences of all identified bZIPs in six legume genomesThis file includes the bZIPs protein sequences from Arabidopsis thaliana and six legume genomes (Glycine max,Medicago truncatula,Cajanus cajan,Cicer arietinum,Phaseolus vulgaris and Lotus japonicus). All these proteins were used to construct phylogenetic tree which correspondence to Figure 1 and Additional file 3 of publication.Raw protein sequences of bZIPs from Arabidopsis thaliana and six legume genomes.txtAligned protein sequences of bZIPs from Arabidopsis thaliana and six legume genomesThis file includes the aligned bZIPs protein sequences from Arabidopsis thaliana and six legume genomes (Glycine max,Medicago truncatula,Cajanus cajan,Cicer arietinum,Phaseolus vulgaris and Lotus japonicus). The sequences were aligned using ClustalX 2.0. All these proteins were used to construct phylogenetic tree which correspondence to Figure 1 and Additional file 3 of publication.The newick format of phylogenetic tree of all bZIP proteins from Arabidopsis thaliana and six legume genomesThe file was the tree file which was formated as .newick. The file could be opend by software MEGA to view or edit the phylogenetic tree. The tree file was correspoding to the Figure 1 and Additional file 3 in publication.Phylogenetic tree of all bZIP proteins from Arabidopsis thaliana and six legume genomes.newickPhylogenetic tree of all bZIP proteins from Arabidopsis thaliana and six legume genomesThe PDF file was the phylogenetic tree of all bZIP proteins from Arabidopsis thaliana and six legume genomes, which corresponds to the Figure 1 and Additional file 3 in publication