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Research article
Hantao Wang
Chinese Academy of Agricultural Sciences Cotton Research Institute
Corresponding Author
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. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton.
Results: In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes 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 motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA.
Conclusions: Our findings reveal that GhRPD3 genes might be involved in flower bud differentiation and resistance to abiotic stresses, which provides 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
Gossypium, Histone deacetylases, Expression patterns, Abiotic stress, Early maturity
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This is a list of supplementary files associated with this preprint. Click to download.
- TableS1.xlsx
Additional file 1: Table S1: Detailed parameters of the RPD3 proteins in nine species.
- TableS2.xlsx
Additional file 2: Table S2: Location of Hist_deacetyl domain in cotton RPD3 proteins.
- FigureS1.tif
Additional file 3: Figure S1: The conserved Hist_deacetyl domain of cotton RPD3 proteins. (a) Phylogenetic relationships of cotton RPD3 proteins and subfamilies of these proteins are exhibited using MEGA 7.0 with the neighbor-joining (NJ) method; (b) Conserved domains of 54 cotton RPD3 proteins. The green boxes represent the Hist_deacetyl domain.
- TableS3.xlsx
Additional file 4: Table S3: Numbers of introns and exons of cotton RPD3 genes.
- TableS4.xlsx
Additional file 5: Table S4: Chromosomal location of RPD3 genes in G. arboreum, G. raimondii, G. barbadense and G. hirsutum.
- TableS5.xlsx
Additional file 6: Table S5: Ka/Ks ratios and occurrence times of segmentally duplicated RPD3 gene pairs of three cotton species. When Ks was equal to 0, Ka/Ks ratios was marked as Ka>>Ks.
- TableS6.xlsx
Additional file 7: Table S6: Cis-acting elements in the promoters of GhRPD3 genes.
- FigureS2.tif
Additional file 8: Figure S2: The ratios of 5 kinds of plant hormone-related cis-elements. Five different kinds of plant hormone-related cis-elements are represented by different colors.
- TableS7.xlsx
Additional file 9: Table S7: The FPKM value of GhRPD3 genes in different tissues and under four different abiotic stresses.
- TableS8.xlsx
Additional file 10: Table S8: Specific primers of GhRPD3 genes for qRT-PCR.
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CURRENT STATUS: Published
View the published article at BMC Genomics.
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Posted 31 Aug, 2020
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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
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
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Subject Areas
Epigenetics & Genomics
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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
Hantao Wang
Chinese Academy of Agricultural Sciences Cotton Research Institute
Corresponding Author
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.
Version 2
Posted 31 Aug, 2020
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
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. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton.
Results: In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes 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 motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA.
Conclusions: Our findings reveal that GhRPD3 genes might be involved in flower bud differentiation and resistance to abiotic stresses, which provides 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
This is a list of supplementary files associated with this preprint. Click to download.
- TableS1.xlsx
Additional file 1: Table S1: Detailed parameters of the RPD3 proteins in nine species.
- TableS2.xlsx
Additional file 2: Table S2: Location of Hist_deacetyl domain in cotton RPD3 proteins.
- FigureS1.tif
Additional file 3: Figure S1: The conserved Hist_deacetyl domain of cotton RPD3 proteins. (a) Phylogenetic relationships of cotton RPD3 proteins and subfamilies of these proteins are exhibited using MEGA 7.0 with the neighbor-joining (NJ) method; (b) Conserved domains of 54 cotton RPD3 proteins. The green boxes represent the Hist_deacetyl domain.
- TableS3.xlsx
Additional file 4: Table S3: Numbers of introns and exons of cotton RPD3 genes.
- TableS4.xlsx
Additional file 5: Table S4: Chromosomal location of RPD3 genes in G. arboreum, G. raimondii, G. barbadense and G. hirsutum.
- TableS5.xlsx
Additional file 6: Table S5: Ka/Ks ratios and occurrence times of segmentally duplicated RPD3 gene pairs of three cotton species. When Ks was equal to 0, Ka/Ks ratios was marked as Ka>>Ks.
- TableS6.xlsx
Additional file 7: Table S6: Cis-acting elements in the promoters of GhRPD3 genes.
- FigureS2.tif
Additional file 8: Figure S2: The ratios of 5 kinds of plant hormone-related cis-elements. Five different kinds of plant hormone-related cis-elements are represented by different colors.
- TableS7.xlsx
Additional file 9: Table S7: The FPKM value of GhRPD3 genes in different tissues and under four different abiotic stresses.
- TableS8.xlsx
Additional file 10: Table S8: Specific primers of GhRPD3 genes for qRT-PCR.
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