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Research article
Zhonghai Ren
Shandong Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-0759-3668
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important regulatory components in biological growth and development. To date, there has been relatively little effort to systematically carry out comprehensive genomic and functional analyses of bHLH genes in cucumber ( Cucumis sativus L.).
Results: Here, a total of 142 bHLH genes were identified in the recently released cucumber genome and further classified into 32 subgroups based on the phylogenetic analysis, conserved motifs and gene structures. Multiple sequence alignment analyses showed that the sequences of CsbHLH proteins were highly conserved. The chromosomal distribution, synteny analysis, and gene duplications of these 142 CsbHLHs were further analysed. A cis-element analysis revealed many elements related to stress responsiveness and plant hormones in the promoter regions of CsbHLH genes. Phylogenetic comparison of the bHLH members between cucumber and Arabidopsis , revealed that cucumber bHLH proteins were clustered into the different functional clades of Arabidopsis bHLH members. The transcript abundance analysis of selected CsbHLHs under abiotic stresses (NaCl, ABA and low-temperature treatments) identified five CsbHLH genes that could simultaneously respond to the three abiotic stresses. Tissue-specific expression profiles of these five genes were also analysed. In addition, 35S : CsbHLH041 enhanced the tolerance to salt and ABA in transgenic Arabidopsis and in cucumber seedlings, suggesting CsbHLH041 is an important regulator in response to abiotic stresses. Finally, the functional interoperability network among the CsbHLH proteins was analysed.
Conclusion: This study provided a good foundation for further research into the functions and regulatory mechanisms of CsbHLH proteins and identified candidate genes for stress resistance in cucumber.
Keywords
Abiotic stresses, bHLH family, Cucumber, CsbHLH041, Expression patterns, Regulatory networks
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CURRENT STATUS: Published
View the published article at BMC Plant Biology.
No community comments so far
Editorial decision: Accept
On 11 May, 2020
No comments provided
Editorial decision: Minor revision
On 07 May, 2020
Submission checks complete
On 05 May, 2020
Version 2
Posted 26 Mar, 2020
No comments provided
Editorial decision: Minor revision
On 28 Apr, 2020
Review #1 received
Received 25 Apr, 2020
Reviewer #2 agreed
On 18 Apr, 2020
Review #2 received
Received 18 Apr, 2020
Reviewer #1 agreed
On 03 Apr, 2020
Reviewers invited
Invitations sent on 31 Mar, 2020
Editor assigned
On 24 Mar, 2020
Submission checks complete
On 23 Mar, 2020
Editor invited
On 23 Mar, 2020
No comments provided
Editorial decision: Major revision
On 03 Mar, 2020
Review #2 received
Received 01 Mar, 2020
Reviewer #3 agreed
On 16 Jan, 2020
Review #1 received
Received 12 Dec, 2019
Reviewer #2 agreed
On 05 Dec, 2019
Reviewers invited
Invitations sent on 24 Nov, 2019
Reviewer #1 agreed
On 24 Nov, 2019
Editor assigned
On 05 Nov, 2019
Submission checks complete
On 04 Nov, 2019
Editor invited
On 04 Nov, 2019
First submitted
On 03 Nov, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
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A new preprint design is coming!
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See the published version of this preprint at BMC Plant Biology.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Zhonghai Ren
Shandong Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-0759-3668
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Plant Biology.
No community comments so far
Editorial decision: Accept
On 11 May, 2020
No comments provided
Editorial decision: Minor revision
On 07 May, 2020
Submission checks complete
On 05 May, 2020
Version 2
Posted 26 Mar, 2020
No comments provided
Editorial decision: Minor revision
On 28 Apr, 2020
Review #1 received
Received 25 Apr, 2020
Reviewer #2 agreed
On 18 Apr, 2020
Review #2 received
Received 18 Apr, 2020
Reviewer #1 agreed
On 03 Apr, 2020
Reviewers invited
Invitations sent on 31 Mar, 2020
Editor assigned
On 24 Mar, 2020
Submission checks complete
On 23 Mar, 2020
Editor invited
On 23 Mar, 2020
No comments provided
Editorial decision: Major revision
On 03 Mar, 2020
Review #2 received
Received 01 Mar, 2020
Reviewer #3 agreed
On 16 Jan, 2020
Review #1 received
Received 12 Dec, 2019
Reviewer #2 agreed
On 05 Dec, 2019
Reviewers invited
Invitations sent on 24 Nov, 2019
Reviewer #1 agreed
On 24 Nov, 2019
Editor assigned
On 05 Nov, 2019
Submission checks complete
On 04 Nov, 2019
Editor invited
On 04 Nov, 2019
First submitted
On 03 Nov, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Plant Biology.
Background: The basic/helix-loop-helix (bHLH) transcription factor family exists in all three eukaryotic kingdoms as important regulatory components in biological growth and development. To date, there has been relatively little effort to systematically carry out comprehensive genomic and functional analyses of bHLH genes in cucumber ( Cucumis sativus L.).
Results: Here, a total of 142 bHLH genes were identified in the recently released cucumber genome and further classified into 32 subgroups based on the phylogenetic analysis, conserved motifs and gene structures. Multiple sequence alignment analyses showed that the sequences of CsbHLH proteins were highly conserved. The chromosomal distribution, synteny analysis, and gene duplications of these 142 CsbHLHs were further analysed. A cis-element analysis revealed many elements related to stress responsiveness and plant hormones in the promoter regions of CsbHLH genes. Phylogenetic comparison of the bHLH members between cucumber and Arabidopsis , revealed that cucumber bHLH proteins were clustered into the different functional clades of Arabidopsis bHLH members. The transcript abundance analysis of selected CsbHLHs under abiotic stresses (NaCl, ABA and low-temperature treatments) identified five CsbHLH genes that could simultaneously respond to the three abiotic stresses. Tissue-specific expression profiles of these five genes were also analysed. In addition, 35S : CsbHLH041 enhanced the tolerance to salt and ABA in transgenic Arabidopsis and in cucumber seedlings, suggesting CsbHLH041 is an important regulator in response to abiotic stresses. Finally, the functional interoperability network among the CsbHLH proteins was analysed.
Conclusion: This study provided a good foundation for further research into the functions and regulatory mechanisms of CsbHLH proteins and identified candidate genes for stress resistance in cucumber.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
This is a list of supplementary files associated with this preprint. Click to download.
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