Vol.:(0123456789) 1 3 Plant Growth Regulation https://doi.org/10.1007/s10725-018-0465-6 ORIGINAL PAPER Comparative identifcation, characterization, and expression analysis of bZIP gene family members in watermelon and melon genomes Necdet Mehmet Unel 1  · Fadime Cetin 1  · Yasin Karaca 1  · Yasemin Celik Altunoglu 1  · Mehmet Cengiz Baloglu 1 Received: 20 May 2018 / Accepted: 30 November 2018 © Springer Nature B.V. 2018 Abstract The family of basic leucine zipper (bZIP) transcription factors plays diverse crucial roles in numerous biological processes. Despite the identifcation of bZIP genes in several plants, to our knowledge, bZIP members in watermelon and melon are yet to be comprehensively investigated. The genomes of watermelon and melon encode 59 ClabZIP and 75 CmbZIP putative genes, respectively. Both bZIP protein family members were phylogenetically grouped into seven subfamilies. The majority of bZIP genes in the same subfamily shared similar gene structures and conserved motifs. Chromosome distribution and genetic analysis revealed that 21 duplication events between ClabZIP genes and 106 duplication events between CmbZIP genes have occurred. Further, the three-dimensional structure and functional annotation of bZIP proteins was predicted. For evaluating the expression patterns of ClabZIP and CmbZIP genes, RNA-seq data available in public databases were analyzed. The expression profles of selected ClabZIP and CmbZIP genes in root and leaf tissues of drought-stressed watermelon and melon were also examined using qRT-PCR. ClabZIP-57, CmbZIP-52, and CmbZIP-31 genes exhibited the highest expression levels after stress exposure in leaf and root tissues. Gene identifcation studies like the present study ofer new perspectives in the analysis of bZIP protein family members and their functions in plants. Keywords Cucumis melo · Citrullus lanatus · bZIP transcription factor genes · Bioinformatics analysis · Drought stress · Gene expression analysis Introduction Melon (Cucumis melo) and watermelon (Citrullus lanatus) belong to Cucurbits or the Cucurbitaceae family. They are economically highly valuable as fresh produce worldwide; approximately 111 and 29 million tons of watermelons and melons have been produced, respectively, and their culti- vated area is measured at a total of approximately 4.7 million hectares (ha) throughout the world (Food and Agriculture Organization 2014). According to FAO reports, Turkey is the second-largest producer of watermelons (3.9 million tons) and melons (1.7 million tons) after China. Transcription factors (TFs) play regulatory roles for their downstream target genes, which they may induce or repress. They comprise of two structures, namely sequence-specifc DNA-binding and activation domains. Based on their 3D structures and DNA-binding sequence properties, TFs can be classifed into 40–60 families in plants (Wingender et al. 2001; Yilmaz et al. 2009). The basic leucine zipper (bZIP) TF family is one of the most diverse TFs families in plants (Wang et al. 2015). They are described as contain- ing a highly conserved bZIP domain, which is 60–80 amino acids in length, and which comprises a basic region and a leucine zipper dimerization motif (Wang et al. 2011). The basic region is responsible for nuclear localization and DNA binding, whereas the leucine zipper controls the homo- and/ or hetero-dimerization of bZIP proteins (Jakoby et al. 2002; Nijhawan et al. 2008). Like other TFs, bZIP TFs play signifcant roles in devel- opmental and diferentiation processes in plants. The roles of the family members encompass organ and tissue difer- entiation (Shen et al. 2007; Silveira et al. 2007), cell elon- gation (Fukazawa et al. 2000), nitrogen/carbon and energy Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10725-018-0465-6) contains supplementary material, which is available to authorized users. * Mehmet Cengiz Baloglu mcbaloglu@gmail.com 1 Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey