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CottonGen JBrowse

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posted on 2024-02-13, 13:45 authored by Taein Lee, Sook Jung, Ksenija Gasic, Todd Campbell, Jing Yu, Jodi Humann, Heidi Hough, Dorrie Main
<p>CottonGen has an instance of the JBrowse genome browser for viewing genome data. A list of the genomes available in CottonGen can be accessed by clicking the <a href="https://www.cottongen.org/tools/jbrowse">JBrowse link in the Tools menu</a>.</p> <p>Whole Genomes</p> <ul> <li>2019-03: Gossypium barbadense AD2 Hai-7124 genome ZJU v1.1_a1</li> <li>2018-12: Gossypium barbadense AD2 3-79 genome HAU v2_a1</li> <li>2015-12: Gossypium barbadense AD2 3-79 genome HAU v1_a1</li> <li>2019-03: Gossypium hirsutum AD1 genome ZJU-Improved v2.1_a1</li> <li>2018-12: Gossypium hirsutum AD1 genome HAU v1_a1</li> <li>2017-09: Gossypium hirsutum AD1 genome TX-JGI v1.1_a1</li> <li>2015-04: Gossypium hirsutum AD1 genome NAU-NBI v1.1_a1.1</li> <li>2015-04: Gossypium hirsutum AD1 genome CGP-BGI v1_a1</li> <li>2018-05: Gossypium arboreum A2 genome CRI-Updated v1_a1</li> <li>2014-05: Gossypium arboreum A2 genome CGP-BGI v2_a1</li> <li>2012-12: Gossypium raimondii D5 genome JGI v2_a2.1</li> <li>2012-08: Gossypium raimondii D5 genome CGP-BGI v1_a1</li> </ul> <p>Chloroplast Genomes</p> <ul> <li>Gossypium arboreum chloroplast</li> <li>Gossypium barbadense chloroplast</li> <li>Gossypium hirsutum chloroplast</li> <li>Gossypium raimondii chloroplast</li> </ul> <p>Please watch the JBrowse tutorial for more details about how to navigate and use JBrowse.</p> <div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: CottonGen JBrowse and User Manual.</p> <p>File Name: Web Page, url: <a href="https://www.cottongen.org/node/8287911" target="_blank">https://www.cottongen.org/node/8287911</a> </p><p>CottonGen has an instance of the JBrowse genome browser for viewing genome data. A list of the genomes available in CottonGen can be accessed by clicking the <a href="https://www.cottongen.org/tools/jbrowse" target="_blank">JBrowse link in the Tools menu</a>. Whole Genomes * 2019-03: Gossypium barbadense AD2 Hai-7124 genome ZJU v1.1_a1 * 2018-12: Gossypium barbadense AD2 3-79 genome HAU v2_a1 * 2015-12: Gossypium barbadense AD2 3-79 genome HAU v1_a1 * 2019-03: Gossypium hirsutum AD1 genome ZJU-Improved v2.1_a1 * 2018-12: Gossypium hirsutum AD1 genome HAU v1_a1 * 2017-09: Gossypium hirsutum AD1 genome TX-JGI v1.1_a1 * 2015-04: Gossypium hirsutum AD1 genome NAU-NBI v1.1_a1.1 * 2015-04: Gossypium hirsutum AD1 genome CGP-BGI v1_a1 * 2018-05: Gossypium arboreum A2 genome CRI-Updated v1_a1 * 2014-05: Gossypium arboreum A2 genome CGP-BGI v2_a1 * 2012-12: Gossypium raimondii D5 genome JGI v2_a2.1 * 2012-08: Gossypium raimondii D5 genome CGP-BGI v1_a1 Chloroplast Genomes * Gossypium arboreum chloroplast * Gossypium barbadense chloroplast * Gossypium hirsutum chloroplast * Gossypium raimondii chloroplast Please watch the JBrowse tutorial for more details about how to navigate and use JBrowse.</p></li></ul>

Funding

Cotton Incorporated

USDA-ARS: Crop Germplasm Research Unit, College Station, TX

Bayer CropScience

Dow Chemical Company

Monsanto Company

Washington State University

USDA-NIFA: 2009-51181-06036

USDA-NIFA: 2009-51181-05808

History

Related Materials

  1. 1.
    DOI - Is supplement to Yu, J., Jung, S., Cheng, C.-H., Ficklin, S. P., Lee, T., Zheng, P., Jones, D., Percy, R. G., & Main, D. (2013). CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Research, 42(D1), D1229–D1236. https://doi.org/10.1093/nar/gkt1064
  2. 2.
    URL - Is part of CottonGen: Cotton Database Resources
  3. 3.
    DOI - Is supplemented by Yu, J., Jung, S., Cheng, C.-H., Lee, T., Zheng, P., Buble, K., Crabb, J., Humann, J., Hough, H., Jones, D., Campbell, J. T., Udall, J., & Main, D. (2021). CottonGen: The Community Database for Cotton Genomics, Genetics, and Breeding Research. Plants, 10(12), 2805. https://doi.org/10.3390/plants10122805
  4. 4.
    URL - Is compiled by Tripal infrastructure

Data contact name

Main, Dorrie

Data contact email

dorrie@wsu.edu

Publisher

MainLab, Washington State University

Intended use

CottonGen has an instance of the JBrowse genome browser for viewing Gossypium spp. genome data.

Temporal Extent Start Date

2012-08-01

Temporal Extent End Date

2019-03-01

Theme

  • Not specified

Geographic Coverage

ISO Topic Category

  • biota
  • farming

National Agricultural Library Thesaurus terms

Internet; databases; genomics; breeding; translation (genetics); applied research; cotton; infrastructure; quantitative trait loci; pathogens; germplasm conservation; pedigree; unigenes; expressed sequence tags; loci; taxonomy; germplasm; Gossypium; genetic markers; publications; genetic databases; plant breeding; plant genetics; computer software; genotype; genome; transcriptome; nucleotide sequences

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 301

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Lee, Taein; Jung, Sook; Gasic, Ksenija; Campbell, Todd; Yu, Jing; Humann, Jodi; Hough, Heidi; Main, Dorrie (2019). CottonGen JBrowse. MainLab, Washington State University.

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    Categories

    Keywords

    CottonGenNP301cottongenomicschloroplastOnline databasedata.govARS

    Licence

    U.S. Public Domain

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