Genome-wide analysis and evolution of the bZIP transcription factor gene family in six Fragaria species

Abstract

Basic leucine zipper (bZIP) transcription factor gene family is one of the largest and most conserved plant-specific gene families and plays key roles in regulating diverse biological processes. The recent completion of genome sequences of the woodland strawberry (F. vesca), cultivated strawberry (F. × ananassa), and its four wild relatives (F. iinumae, F. nipponica, F. nubicola, and F. orientalis) provides the opportunity to study the micro-evolution of bZIP genes among six Fragaria genomes. In this study, we presented the first genome-wide identification and characterization of bZIP genes in six Fragaria genomes using bioinformatics. The total of 51, 36, 34, 33, 26, and 50 bZIP genes were detected in the genomes of F. × ananassa, F. iinumae, F. nipponica, F. nubicola, F. orientalis, and F. vesca, respectively, which were divided into eight sub-families according to the phylogenetic relationship with those in Arabidopsis thaliana. Diverse gene structures were found in Fragaria bZIPs, including eight major motif patterns. Interestingly, two sub-families consisted intron-less genes only, except FvbZIP19 and FnibZIP28. Paralogs had greater Ks values than those of orthologs, which indicated that the most duplication events of Fragaria bZIP genes occurred prior to the divergence of the six Fragaria species plant. In addition, orthologs are subject to weaker functional constraints and faster evolutionary processes than paralogs based on the Ka/Ks values. The great variation was also detected in the promoter region. This study provided insight into the micro-evolution of bZIP gene family within genus Fragaria.