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Research article
Wuwei Ye
Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4757-1057
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: U-box gene is gene of ubiquitin ligase, which contain U-box domain. Plant U-box gene (PUB) plays an important role in the response to stresses, but less reports about PUBs in cotton were issued. Therefore research of PUBs in cotton will be of great importance and necessity to study the mechanism of tolerance-resistance of the cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from the three sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. arbadense (AD2), respectively. Subcellular localization analysis showed that the PUBs in cotton were distributed in various parts of the cells, mainly in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) by phylogenetic analysis, and intron/exon structure was comparatively conserved within the subfamily. Location analysis showed cotton PUBs were unevenly anchored on all the chromosomes varying from 1 to 14. It was found that there are 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs between A2 and D5, through multiple sequence alignment, but that the tandem duplication region of A2 or D5 was not found. It was also found that, there were 105, 14 and 17 homologous gene pairs in intra-subgenome of At and Dt, At subgenome, Dt subgenome of allotetraploid cotton, respectively. Among the PUBs family, totally 106, 116, 85 and 81 homologous gene pairs were found in A2-At, A2-Dt, D5-At and D5-Dt. Function analysis of GhPUB85A and GhPUB45D showed they positively responded the abiotic stresses, but the expression patterns were different. Besides, although the expressions of these two homologous genes were similar, their contributions were different when responding to stresses, showing different response differences to abiotic stresses and function division of two subgenomes of G. hirsutum. Conclusion: This study provided the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs was highly conserved in evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses at varying degrees.
Keywords
U-box domain, PUB gene, cotton, evolution, Collinearity, homologous gene pairs
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A new preprint design is coming!
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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
Wuwei Ye
Institute of Cotton Research, Chinese Academy of Agricultural Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4757-1057
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
Editor assigned
On 26 Feb, 2020
Submission checks complete
On 25 Feb, 2020
Editor invited
On 25 Feb, 2020
No comments provided
Submission checks complete
On 20 Feb, 2020
Editorial decision: Minor revision
On 20 Feb, 2020
No comments provided
Editorial decision: Minor revision
On 18 Feb, 2020
Editor assigned
On 03 Feb, 2020
Submission checks complete
On 02 Feb, 2020
Editor invited
On 02 Feb, 2020
No comments provided
Editorial decision: Major revision
On 21 Jan, 2020
Review #1 received
Received 17 Jan, 2020
Reviewers invited
Invitations sent on 16 Jan, 2020
Reviewer #1 agreed
On 16 Jan, 2020
Editor assigned
On 14 Jan, 2020
Submission checks complete
On 13 Jan, 2020
Editor invited
On 13 Jan, 2020
No comments provided
Editorial decision: Major revision
On 08 Jan, 2020
Review #1 received
Received 07 Jan, 2020
Reviewers invited
Invitations sent on 02 Jan, 2020
Reviewer #1 agreed
On 02 Jan, 2020
Editor assigned
On 27 Dec, 2019
Submission checks complete
On 26 Dec, 2019
Editor invited
On 26 Dec, 2019
No comments provided
Editorial decision: Major revision
On 16 Nov, 2019
Review #2 received
Received 13 Nov, 2019
Reviewer #2 agreed
On 11 Nov, 2019
Review #1 received
Received 14 Oct, 2019
Reviewer #1 agreed
On 03 Oct, 2019
Reviewers invited
Invitations sent on 03 Oct, 2019
Editor assigned
On 11 Jul, 2019
Submission checks complete
On 10 Jul, 2019
Editor invited
On 10 Jul, 2019
Version 1
Posted 01 Aug, 2019
No comments provided
Editorial decision: Revise before sending to peer reviewers
On 08 Jul, 2019
Submission checks complete
On 19 Jun, 2019
Editor invited
On 17 Jun, 2019
Editor assigned
On 17 Jun, 2019
First submitted
On 13 Jun, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: U-box gene is gene of ubiquitin ligase, which contain U-box domain. Plant U-box gene (PUB) plays an important role in the response to stresses, but less reports about PUBs in cotton were issued. Therefore research of PUBs in cotton will be of great importance and necessity to study the mechanism of tolerance-resistance of the cotton. Results: In this study, we identified 93, 96, 185 and 208 PUBs from the three sequenced cotton species G. raimondii (D5), G. arboreum (A2), G. hirsutum (AD1) and G. arbadense (AD2), respectively. Subcellular localization analysis showed that the PUBs in cotton were distributed in various parts of the cells, mainly in the nucleus. The PUBs in cotton were divided into six subfamilies (A-F) by phylogenetic analysis, and intron/exon structure was comparatively conserved within the subfamily. Location analysis showed cotton PUBs were unevenly anchored on all the chromosomes varying from 1 to 14. It was found that there are 3 tandem duplications and 28 segmental duplications in cotton genome D5, 2 tandem duplications and 25 segmental duplications in A2, and 143 homologous gene pairs between A2 and D5, through multiple sequence alignment, but that the tandem duplication region of A2 or D5 was not found. It was also found that, there were 105, 14 and 17 homologous gene pairs in intra-subgenome of At and Dt, At subgenome, Dt subgenome of allotetraploid cotton, respectively. Among the PUBs family, totally 106, 116, 85 and 81 homologous gene pairs were found in A2-At, A2-Dt, D5-At and D5-Dt. Function analysis of GhPUB85A and GhPUB45D showed they positively responded the abiotic stresses, but the expression patterns were different. Besides, although the expressions of these two homologous genes were similar, their contributions were different when responding to stresses, showing different response differences to abiotic stresses and function division of two subgenomes of G. hirsutum. Conclusion: This study provided the genome-wide identification, structure, evolution and expression analysis of PUBs in cotton, and the results showed that the PUBs was highly conserved in evolutionary history of cotton. All PUB genes were involved in response to abiotic stresses at varying degrees.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
This is a list of supplementary files associated with this preprint. Click to download.
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