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Genome-wide analysis of the bZIP transcription factors in cucumber.
PLoS One. 2014; 9(4):e96014.Plos

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.

Authors+Show Affiliations

Kastamonu University, Faculty of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey.Istanbul University, Faculty of Science, Department of Biology, Istanbul, Turkey.Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey.Cankırı Karatekin University, Faculty of Science, Department of Biology, Cankiri, Turkey.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24760072

Citation

Baloglu, Mehmet Cengiz, et al. "Genome-wide Analysis of the bZIP Transcription Factors in Cucumber." PloS One, vol. 9, no. 4, 2014, pp. e96014.
Baloglu MC, Eldem V, Hajyzadeh M, et al. Genome-wide analysis of the bZIP transcription factors in cucumber. PLoS One. 2014;9(4):e96014.
Baloglu, M. C., Eldem, V., Hajyzadeh, M., & Unver, T. (2014). Genome-wide analysis of the bZIP transcription factors in cucumber. PloS One, 9(4), e96014. https://doi.org/10.1371/journal.pone.0096014
Baloglu MC, et al. Genome-wide Analysis of the bZIP Transcription Factors in Cucumber. PLoS One. 2014;9(4):e96014. PubMed PMID: 24760072.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of the bZIP transcription factors in cucumber. AU - Baloglu,Mehmet Cengiz, AU - Eldem,Vahap, AU - Hajyzadeh,Mortaza, AU - Unver,Turgay, Y1 - 2014/04/23/ PY - 2014/02/26/received PY - 2014/03/31/accepted PY - 2014/4/25/entrez PY - 2014/4/25/pubmed PY - 2015/6/20/medline SP - e96014 EP - e96014 JF - PloS one JO - PLoS One VL - 9 IS - 4 N2 - 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. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/24760072/Genome_wide_analysis_of_the_bZIP_transcription_factors_in_cucumber_ L2 - https://dx.plos.org/10.1371/journal.pone.0096014 DB - PRIME DP - Unbound Medicine ER -