Improved Gossypium raimondii Genome Using a Hi-C-based Proximity-Guided Assembly
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.
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This is a list of supplementary files associated with this preprint. Click to download.
Supplemental 1: Table of error bins.
On 17 Feb, 2021
Received 13 Feb, 2021
Received 10 Feb, 2021
On 31 Jan, 2021
On 27 Jan, 2021
Invitations sent on 25 Jan, 2021
On 17 Jan, 2021
On 17 Jan, 2021
On 17 Jan, 2021
Posted 21 Oct, 2020
Received 16 Nov, 2020
Received 14 Nov, 2020
On 19 Oct, 2020
Invitations sent on 18 Oct, 2020
On 18 Oct, 2020
On 13 Oct, 2020
On 12 Oct, 2020
On 12 Oct, 2020
On 25 Aug, 2020
On 20 Aug, 2020
On 20 Aug, 2020
On 19 Aug, 2020
On 19 Aug, 2020
Improved Gossypium raimondii Genome Using a Hi-C-based Proximity-Guided Assembly
On 17 Feb, 2021
Received 13 Feb, 2021
Received 10 Feb, 2021
On 31 Jan, 2021
On 27 Jan, 2021
Invitations sent on 25 Jan, 2021
On 17 Jan, 2021
On 17 Jan, 2021
On 17 Jan, 2021
Posted 21 Oct, 2020
Received 16 Nov, 2020
Received 14 Nov, 2020
On 19 Oct, 2020
Invitations sent on 18 Oct, 2020
On 18 Oct, 2020
On 13 Oct, 2020
On 12 Oct, 2020
On 12 Oct, 2020
On 25 Aug, 2020
On 20 Aug, 2020
On 20 Aug, 2020
On 19 Aug, 2020
On 19 Aug, 2020
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