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. 2014 Apr 23;9(4):e96014.
doi: 10.1371/journal.pone.0096014. eCollection 2014.

Genome-wide analysis of the bZIP transcription factors in cucumber

Mehmet Cengiz Baloglu  1 , Vahap Eldem  2 , Mortaza Hajyzadeh  3 , Turgay Unver  3
Affiliations

Genome-wide analysis of the bZIP transcription factors in cucumber

Mehmet Cengiz Baloglu et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: Turgay Unver is currently serving as an academic editor for PLOS ONE and this does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1
Figure 1. Distribution of 64 CsbZIP genes onto seven cucumber chromosomes.
(A) Percentage of bZIP genes on each cucumber chromosome to show their distribution abundance. (B) Graphical (scaled) representation of physical locations for each CsbZIP gene on cucumber chromosomes (numbered 1–7). Tandem-duplicated genes on a particular chromosome are indicated in the box. Chromosomal distances are given in Mbp.
Figure 2
Figure 2. Phylogenetic relationships of cucumber bZIP proteins.
The sequences were aligned by CLUSTALW at MEGA5 and the unrooted phylogenetic tree was deduced by neighbor-joining method. The proteins were classified into six distinct clusters. Each family was assigned a different color according to well-known members in other species.
Figure 3
Figure 3. Gene Ontology (GO) distributions for the bZIP proteins.
The Blast2Go program defines the gene ontology under three categories (A) biological processes, (B) molecular functions and (C) cellular component.
Figure 4
Figure 4. Time of duplication and divergence (MYA) based on synonymous substitution rate (Ks), which estimated using duplicated bZIP gene pairs of cucumber and orthologous bZIP gene pairs between cucumber and poplar (49) or Arabidopsis (42) or rice (28).
Figure 5
Figure 5. Predicated structures of bZIP proteins.
The structure of 9 bZIP proteins with >90% confidence level are shown.
Figure 6
Figure 6. Heatmap of the differentially expressed CsbZIP genes in different tissues.
The image summarizes the tissue-specific expression pattern of 64 bZIP transcription factors. Note that expression values mapped to a color gradient from low (plain green) to high expression (dark blue).
Figure 7
Figure 7. PCA score plots of different tissues.
The graph shows a clear separation between flower and other tissues.
Figure 8
Figure 8. Expression profiles of selected cucumber bZIP genes under drought stress.
Relative expression levels of the genes upon 0, 3, 12, and 24(a, c, e, g, i, k, m, o, r and t) and leaf (b, d, f, h, j, l, n, p, s and u) tissues are shown.
See this image and copyright information in PMC

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