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Improved Gossypium raimondii Genome Using a Hi-C-based Proximity-Guided Assembly
Guoli Song
Chinese Academy of Agricultural Sciences Cotton Research Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0003-3236-9286
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Background: Genome sequence plays an important role in both the basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of Upland cotton (Gossypium. hirsutum), highlights the need to improve the genome quality in a rapid and efficient way.
Methods: we performed Hi-C sequencing of Gossypium raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds. We identified and corrected errors of initial scaffolds before reassembled into chromosomes.
Result: A total of 98.42% of sequence was clustered successfully, among which 99.72% of the clustered sequence was ordered and 99.92% of the ordered sequence was oriented with high-quality. Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than previous one.
Conclusion: This improvement in Gossypium raimondii genome not only provides a better reference genome to increase study efficiency, but also offers a new way to assemble cotton genomes. Furthermore, Hi-C data of Gossypium raimondii may be used for 3D structure research or regulating analysis.
Keywords
Gossypium raimondii, Hi-C, genome assembly, heatmap and collinearity
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- errorbin.bed.xls
Supplemental 1: Table of error bins.
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CURRENT STATUS: Under Revision
No community comments so far
Editorial decision: Major revision
On 17 Feb, 2021
Review #1 received
Received 13 Feb, 2021
Review #2 received
Received 10 Feb, 2021
Reviewer #2 agreed
On 31 Jan, 2021
Reviewer #1 agreed
On 27 Jan, 2021
Reviewers invited
Invitations sent on 25 Jan, 2021
Editor assigned
On 17 Jan, 2021
Submission checks complete
On 17 Jan, 2021
Editor invited
On 17 Jan, 2021
Version 2
Posted 21 Oct, 2020
No comments provided
Review #1 received
Received 16 Nov, 2020
Review #2 received
Received 14 Nov, 2020
Reviewer #2 agreed
On 19 Oct, 2020
Reviewers invited
Invitations sent on 18 Oct, 2020
Reviewer #1 agreed
On 18 Oct, 2020
Editor assigned
On 13 Oct, 2020
Submission checks complete
On 12 Oct, 2020
Editor invited
On 12 Oct, 2020
No comments provided
Editorial decision: Revise before peer review
On 25 Aug, 2020
First submitted
On 20 Aug, 2020
Editor assigned
On 20 Aug, 2020
Submission checks complete
On 19 Aug, 2020
Editor invited
On 19 Aug, 2020
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This preprint is under consideration at Journal of Cotton Research. A preprint is 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
Improved Gossypium raimondii Genome Using a Hi-C-based Proximity-Guided Assembly
Guoli Song
Chinese Academy of Agricultural Sciences Cotton Research Institute
Corresponding Author
ORCiD: https://orcid.org/0000-0003-3236-9286
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: Under Revision
No community comments so far
Editorial decision: Major revision
On 17 Feb, 2021
Review #1 received
Received 13 Feb, 2021
Review #2 received
Received 10 Feb, 2021
Reviewer #2 agreed
On 31 Jan, 2021
Reviewer #1 agreed
On 27 Jan, 2021
Reviewers invited
Invitations sent on 25 Jan, 2021
Editor assigned
On 17 Jan, 2021
Submission checks complete
On 17 Jan, 2021
Editor invited
On 17 Jan, 2021
Version 2
Posted 21 Oct, 2020
No comments provided
Review #1 received
Received 16 Nov, 2020
Review #2 received
Received 14 Nov, 2020
Reviewer #2 agreed
On 19 Oct, 2020
Reviewers invited
Invitations sent on 18 Oct, 2020
Reviewer #1 agreed
On 18 Oct, 2020
Editor assigned
On 13 Oct, 2020
Submission checks complete
On 12 Oct, 2020
Editor invited
On 12 Oct, 2020
No comments provided
Editorial decision: Revise before peer review
On 25 Aug, 2020
First submitted
On 20 Aug, 2020
Editor assigned
On 20 Aug, 2020
Submission checks complete
On 19 Aug, 2020
Editor invited
On 19 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The most recent version of this article is available here.
Background: Genome sequence plays an important role in both the basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of Upland cotton (Gossypium. hirsutum), highlights the need to improve the genome quality in a rapid and efficient way.
Methods: we performed Hi-C sequencing of Gossypium raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds. We identified and corrected errors of initial scaffolds before reassembled into chromosomes.
Result: A total of 98.42% of sequence was clustered successfully, among which 99.72% of the clustered sequence was ordered and 99.92% of the ordered sequence was oriented with high-quality. Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than previous one.
Conclusion: This improvement in Gossypium raimondii genome not only provides a better reference genome to increase study efficiency, but also offers a new way to assemble cotton genomes. Furthermore, Hi-C data of Gossypium raimondii may be used for 3D structure research or regulating analysis.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5