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Research article
Shuxun Yu
Chinese Academy of Agricultural Sciences Cotton Research Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0002-9715-3462
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. As the superfamily of HDACs, RPD3/HDA1-type HDACs were most studied and reported that RPD3 genes played crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on RPD3/HDA1 gene family in cotton.
Results: In this research, 9, 9, 18 and 18 RPD3 genes were determined by genome-wide analysis in Gossypium raimondii, G. arboreum, G. hirsutum and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motifs analysis exhibited high conservation in each branch of cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the GhRPD3 gene family. There was at least one presumed cis-element related to plant hormone existing in the promoter regions of all the GhRPD3 genes, especially MeJA and ABA responsive elements, owning more members than other hormone-relevant elements. Characterizations of expression patterns showed that most GhRPD3 genes performed relative high expression in floral organs and possessed the higher expression in early-maturity cotton compared with the late-maturity cotton during flower bud differentiation period. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA and ABA.
Conclusions: Our findings revealed that GhRPD3 genes might be involved in flower bud differentiation and resistance to abiotic stresses, which provided a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.
Keywords
Cotton, RPD3/HDA1 gene family, Expression patterns, Abiotic stress, Early maturity
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Peer Review Timeline
CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Editorial decision: Accept
On 10 Sep, 2020
Editor assigned
On 27 Aug, 2020
Submission checks complete
On 26 Aug, 2020
Editor invited
On 26 Aug, 2020
Version 1
Posted 19 Dec, 2019
No comments provided
Editorial decision: Major revision
On 28 Jul, 2020
Review #3 received
Received 04 Jul, 2020
Review #2 received
Received 04 Jul, 2020
Reviewer #4 agreed
On 06 Jun, 2020
Reviewer #3 agreed
On 04 Jun, 2020
Reviewer #2 agreed
On 04 Jun, 2020
Review #1 received
Received 28 Jan, 2020
Reviewer #1 agreed
On 31 Dec, 2019
Reviewers invited
Invitations sent on 26 Dec, 2019
Editor assigned
On 10 Dec, 2019
First submitted
On 09 Dec, 2019
Submission checks complete
On 09 Dec, 2019
Editor invited
On 09 Dec, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
See the published version of this preprint at BMC Genomics.
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
Shuxun Yu
Chinese Academy of Agricultural Sciences Cotton Research Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0002-9715-3462
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 Genomics.
No community comments so far
Editorial decision: Accept
On 10 Sep, 2020
Editor assigned
On 27 Aug, 2020
Submission checks complete
On 26 Aug, 2020
Editor invited
On 26 Aug, 2020
Version 1
Posted 19 Dec, 2019
No comments provided
Editorial decision: Major revision
On 28 Jul, 2020
Review #3 received
Received 04 Jul, 2020
Review #2 received
Received 04 Jul, 2020
Reviewer #4 agreed
On 06 Jun, 2020
Reviewer #3 agreed
On 04 Jun, 2020
Reviewer #2 agreed
On 04 Jun, 2020
Review #1 received
Received 28 Jan, 2020
Reviewer #1 agreed
On 31 Dec, 2019
Reviewers invited
Invitations sent on 26 Dec, 2019
Editor assigned
On 10 Dec, 2019
First submitted
On 09 Dec, 2019
Submission checks complete
On 09 Dec, 2019
Editor invited
On 09 Dec, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. As the superfamily of HDACs, RPD3/HDA1-type HDACs were most studied and reported that RPD3 genes played crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on RPD3/HDA1 gene family in cotton.
Results: In this research, 9, 9, 18 and 18 RPD3 genes were determined by genome-wide analysis in Gossypium raimondii, G. arboreum, G. hirsutum and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motifs analysis exhibited high conservation in each branch of cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the GhRPD3 gene family. There was at least one presumed cis-element related to plant hormone existing in the promoter regions of all the GhRPD3 genes, especially MeJA and ABA responsive elements, owning more members than other hormone-relevant elements. Characterizations of expression patterns showed that most GhRPD3 genes performed relative high expression in floral organs and possessed the higher expression in early-maturity cotton compared with the late-maturity cotton during flower bud differentiation period. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA and ABA.
Conclusions: Our findings revealed that GhRPD3 genes might be involved in flower bud differentiation and resistance to abiotic stresses, which provided a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 11
This is a list of supplementary files associated with this preprint. Click to download.
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