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CottonGen JBrowse

dataset
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

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 JBrowse link in the Tools menu.

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.


Resources in this dataset:

  • Resource Title: CottonGen JBrowse and User Manual.

    File Name: Web Page, url: https://www.cottongen.org/node/8287911

    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 JBrowse link in the Tools menu. 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.

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

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

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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.

Usage metrics

    Categories

    Keywords

    CottonGenNP301cottongenomicschloroplastOnline databasedata.govARS

    Licence

    U.S. Public Domain

    Exports

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