Improved Gossypium raimondii genome using a Hi-C-based proximity-guided assembly

Abstract Introduction Genome sequence plays an important role in both basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of upland cotton (G. hirsutum), highlights the need to improve the genome quality rapidly and efficiently. Methods We performed Hi-C sequencing of G. raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds. We also compared the reassembled genome sequence with the previously published G. raimondii genomes for gene and genome sequence collinearity. Result A total of 98.42% of scaffold sequences were clustered successfully, among which 99.72% of the clustered sequences were ordered and 99.92% of the ordered sequences were oriented with high-quality. Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than the previous one (Nat Genet 44:98–1103, 2012). Conclusion This improvement in G. raimondii genome not only provides a better reference to increase study efficiency but also offers a new way to assemble cotton genomes. Furthermore, Hi-C data of G. raimondii may be used for 3D structure research or regulating analysis.

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Improved Gossypium Raimondii Genome Using a Hi-C-based Proximity-Guided Assembly

10.21203/rs.3.rs-63005/v1 ◽

2020 ◽

Author(s):

Huoli Song ◽

Qiuhong Yang ◽

Dongyun Zuo ◽

Qiaolian Wang ◽

Hailiang Cheng ◽

...

Keyword(s):

Genome Sequence ◽

Upland Cotton ◽

Reference Genome ◽

3D Structure ◽

High Quality ◽

Heat Map ◽

Gossypium Raimondii ◽

Guided Assembly ◽

Structure Research

Abstract Genome sequence plays an important role both in basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of Upland cotton (G. hirsutum), highlights the need to improve the genome quality in a rapid and efficient way. Here, we performed Hi-C sequencing of G. raimondii and reassembled its genome based on new Hi-C data and previously published scaffolds. We identified and corrected errors of initial scaffolds before reassembled into chromosomes. In total 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. This improvement in G. 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 G. raimondii may be used for 3D structure research or regulating analysis.

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Improved Gossypium raimondii Genome Using a Hi-C-based Proximity-Guided Assembly

10.21203/rs.3.rs-63005/v2 ◽

2020 ◽

Author(s):

Guoli Song ◽

Qiuhong Yang ◽

Dongyun Zuo ◽

Qiaolian Wang ◽

Hailiang Cheng ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Genome Sequence ◽

Upland Cotton ◽

Reference Genome ◽

3D Structure ◽

High Quality ◽

Heat Map ◽

Gossypium Raimondii ◽

Guided Assembly ◽

Structure Research

Abstract 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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Improved Gossypium raimondii Genome Using a Hi-C-based Proximity-Guided Assembly

10.21203/rs.3.rs-63005/v3 ◽

2021 ◽

Author(s):

Guoli song ◽

Qiuhong Yang ◽

Dongyun Zuo ◽

Hailiang Cheng ◽

Youping Zhang ◽

...

Keyword(s):

Genome Sequence ◽

Upland Cotton ◽

Reference Genome ◽

3D Structure ◽

High Quality ◽

Heat Map ◽

Gossypium Raimondii ◽

Guided Assembly ◽

Structure Research

Abstract Introduction: Genome sequence plays an important role in both basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of Upland cotton (G. hirsutum), highlights the need to improve the genome quality rapidly and efficiently. Methods: We performed Hi-C sequencing of G. raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds. We also compared the reassembled genome sequence with the previous published G. raimondii genomes for gene and genome sequence collinearity. Result: A total of 98.42% of scaffold 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 the previous one (Wang et al. 2012). Conclusion: This improvement in G. 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 G. raimondii may be used for 3D structure research or regulating analysis.

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High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae

Standards in Genomic Sciences ◽

10.1186/1944-3277-9-9 ◽

2014 ◽

Vol 9 (1) ◽

Cited By ~ 20

Author(s):

Oleg Mediannikov ◽

Thi-Thien Nguyen ◽

Lesley Bell-Sakyi ◽

Roshan Padmanabhan ◽

Pierre-Edouard Fournier ◽

...

Keyword(s):

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

High Quality ◽

The Family

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High-Quality Draft Genome Sequence of Biocontrol Strain Pantoea sp. OXWO6B1

Genome Announcements ◽

10.1128/genomea.00582-16 ◽

2016 ◽

Vol 4 (3) ◽

Author(s):

Jennifer Town ◽

Patrice Audy ◽

Susan M. Boyetchko ◽

Tim J. Dumonceaux

Keyword(s):

Phytophthora Infestans ◽

Genome Sequence ◽

Draft Genome ◽

Draft Genome Sequence ◽

High Quality ◽

Biocontrol Strain

Pantoea sp. strain OXWO6B1 inhibits the growth of the potato pathogen Phytophthora infestans . We determined the 5.2-Mbp genome sequence of this strain, which featured at least 3 confirmed plasmids of up to 250 kbp. The genome sequence of OXWO6B1 is different from that of all previously sequenced strains of Pantoea .

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High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5T)

Standards in Genomic Sciences ◽

10.4056/sigs.3537045 ◽

2013 ◽

Vol 8 (1) ◽

pp. 37-46 ◽

Cited By ~ 5

Author(s):

Erko Stackebrandt ◽

Olga Chertkov ◽

Alla Lapidus ◽

Matt Nolan ◽

Susan Lucas ◽

...

Keyword(s):

Genome Sequence ◽

Type Strain ◽

Draft Genome ◽

Draft Genome Sequence ◽

High Quality

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The Gossypium stocksii genome as a novel resource for cotton improvement

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab125 ◽

2021 ◽

Author(s):

Corrinne E Grover ◽

Daojun Yuan ◽

Mark A Arick ◽

Emma R Miller ◽

Guanjing Hu ◽

...

Keyword(s):

Genome Sequence ◽

De Novo ◽

Pest Resistance ◽

Cotton Leaf ◽

High Quality ◽

Cotton Leaf Curl Virus ◽

Cotton Species ◽

Wild Cotton ◽

Leaf Curl Virus ◽

Insight Into

Abstract Cotton is an important textile crop whose gains in production over the last century have been challenged by various diseases. Because many modern cultivars are susceptible to several pests and pathogens, breeding efforts have included attempts to introgress wild, naturally resistant germplasm into elite lines. Gossypium stocksii is a wild cotton species native to Africa, which is part of a clade of vastly understudied species. Most of what is known about this species comes from pest resistance surveys and/or breeding efforts, which suggests that G. stocksii could be a valuable reservoir of natural pest resistance. Here we present a high-quality de novo genome sequence for G. stocksii. We compare the G. stocksii genome with resequencing data from a closely related, understudied species (G. somalense) to generate insight into the relatedness of these cotton species. Finally, we discuss the utility of the G. stocksii genome for understanding pest resistance in cotton, particularly resistance to cotton leaf curl virus.

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High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea

Genome Announcements ◽

10.1128/genomea.00383-18 ◽

2018 ◽

Vol 6 (19) ◽

pp. e00383-18 ◽

Cited By ~ 4

Author(s):

David K. Ngugi ◽

Ulrich Stingl

Keyword(s):

Single Cell ◽

Lake Sediments ◽

Red Sea ◽

Genome Sequence ◽

Soda Lake ◽

Genome Sequences ◽

High Quality ◽

Candidate Division ◽

Cell Genome ◽

Single Cell Genome

ABSTRACT Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in deep hypersaline anoxic brines around the globe. Recently, the genome sequences of two cultivated representatives from hypersaline soda lake sediments were published. Here, we present a single-cell genome sequence from Nereus Deep in the Red Sea that represents a putatively novel family within SA1.

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High-Quality Draft Genome Sequence of the Multidrug-Resistant Clinical Isolate Enterococcus faecium VRE16

Genome Announcements ◽

10.1128/genomea.00992-16 ◽

2016 ◽

Vol 4 (5) ◽

Cited By ~ 2

Author(s):

Suelen Scarpa de Mello ◽

Daria Van Tyne ◽

Andrei Nicoli Gebieluca Dabul ◽

Michael S. Gilmore ◽

Ilana L. B. C. Camargo

Keyword(s):

Antibiotic Resistance ◽

Virulence Factors ◽

Genome Sequence ◽

Enterococcus Faecium ◽

Draft Genome ◽

Antibiotic Resistance Genes ◽

Multidrug Resistant ◽

Draft Genome Sequence ◽

Commensal Bacterium ◽

High Quality

Specific lineages of the commensal bacterium Enterococcus faecium belonging to CC17, especially ST412, have been isolated from patients in several hospitals worldwide and harbor antibiotic resistance genes and virulence factors. Here, we report a high-quality draft genome sequence and highlight features of E. faecium VRE16, a representative of this ST.

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