Abstract
bZIP proteins are one of the largest transcriptional regulators playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of recently published draft genome sequence of Cucumis sativus, no comprehensive investigation of these family members has been presented for cucumber. We have identified 64 bZIP transcription factor-encoding genes in the cucumber genome. Based on structural features of their encoded proteins, CsbZIP genes could be classified into 6 groups. Cucumber bZIP genes were expanded mainly by segmental duplication rather than tandem duplication. Although segmental duplication rate of the CsbZIP genes was lower than that of Arabidopsis, rice and sorghum, it was observed as a common expansion mechanism. Some orthologous relationships and chromosomal rearrangements were observed according to comparative mapping analysis with other species. Genome-wide expression analysis of bZIP genes indicated that 64 CsbZIP genes were differentially expressed in at least one of the ten sampled tissues. A total of 4 CsbZIP genes displayed higher expression values in leaf, flowers and root tissues. The in silico micro-RNA (miRNA) and target transcript analyses identified that a total of 21 CsbZIP genes were targeted by 38 plant miRNAs. CsbZIP20 and CsbZIP22 are the most targeted by miR165 and miR166 family members, respectively. We also analyzed the expression of ten CsbZIP genes in the root and leaf tissues of drought-stressed cucumber using quantitative RT-PCR. All of the selected CsbZIP genes were measured as increased in root tissue at 24th h upon PEG treatment. Contrarily, the down-regulation was observed in leaf tissues of all analyzed CsbZIP genes. CsbZIP12 and CsbZIP44 genes showed gradual induction of expression in root tissues during time points. This genome-wide identification and expression profiling provides new opportunities for cloning and functional analyses, which may be used in further studies for improving stress tolerance in plants.
Highlights
Cucumber (Cucumis sativus L.), a major vegetable crop consumed worldwide, belongs to Cucurbitaceae family commonly known as cucurbits
The released genome sequence of the cucumber encouraged the scientific research community for further study related with its structural and functional genomics, which has resulted in crop improvement and ensuring food security [4]
The basic leucine zipper transcription factor family is one of the largest and most diverse families. bZIP transcription factors have conserved bZIP domain which is composed of two structural features; a basic region that binds DNA and a leucine zipper dimerization motif [14]
Summary
Cucumber (Cucumis sativus L.), a major vegetable crop consumed worldwide, belongs to Cucurbitaceae family commonly known as cucurbits. BZIP transcription factors have conserved bZIP domain which is composed of two structural features; a basic region that binds DNA and a leucine zipper dimerization motif [14]. The genome-wide survey and identification studies from Arabidopsis [10], castor bean [11], maize [12], rice [13], sorghum [14], algae, mosses, ferns, gymnosperms and angiosperms [15] are a few examples for bZIP TFs. On the other hand, a draft of the Cucumis sativus L. genome sequence was reported recently [1]. We analyzed the expression patterns of these family members by using the publicly available expression and experimental data This extended analysis is the first comprehensive study of the bZIP gene family in cucumber and provides valuable information for further exploration into the functions of this significant gene family in cucumber. These results provide information about the relationship between evolution and functional divergence in the bZIP family
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