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. 2014 Jan;42(Database issue):D1229-36.
doi: 10.1093/nar/gkt1064. Epub 2013 Nov 6.

CottonGen: a genomics, genetics and breeding database for cotton research

Jing Yu  1 , Sook Jung, Chun-Huai Cheng, Stephen P Ficklin, Taein Lee, Ping Zheng, Don Jones, Richard G Percy, Dorrie Main
Affiliations

CottonGen: a genomics, genetics and breeding database for cotton research

Jing Yu et al. Nucleic Acids Res. 2014 Jan.

Abstract

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, visualization and data retrieval of cotton research data. CottonGen contains annotated whole genome sequences, unigenes from expressed sequence tags (ESTs), markers, trait loci, genetic maps, genes, taxonomy, germplasm, publications and communication resources for the cotton community. Annotated whole genome sequences of Gossypium raimondii are available with aligned genetic markers and transcripts. These whole genome data can be accessed through genome pages, search tools and GBrowse, a popular genome browser. Most of the published cotton genetic maps can be viewed and compared using CMap, a comparative map viewer, and are searchable via map search tools. Search tools also exist for markers, quantitative trait loci (QTLs), germplasm, publications and trait evaluation data. CottonGen also provides online analysis tools such as NCBI BLAST and Batch BLAST.

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Figures

Figure 1.
Figure 1.
Gene/Sequence search site in CottonGen. (A) Genes/sequences can be searched using various categories, such as by name, GO terms, InterPro protein domain name or KEGG pathway term. The example shows the InterPro term search site. (B) The search result page has links to the download, gene/sequence detail page and external database. (C) The Gene detail page has various tabs to show the data. The annotated sequence page is highlighted. (D) The alignment tab of the gene detail page shows the position in the whole genome with link to GBrowse. (E) The GBrowse page linked from the alignment tab of the gene detail page. Users can go back to the gene detail page from GBrowse.
Figure 2.
Figure 2.
Marker search site in CottonGen. (A) Multiple markers search sites are available based on the type of information users are interested in. (B) An example search interface where users can view and search for marker source information. (C) A Marker details page with various links to detailed information. (D) The Map position tab of the marker page shows all the maps where the marker has been mapped. (E) From the marker page users can go to the CMap. (F) For the markers that are anchored to the genome, CMap provides hyperlinks to GBrowse. From GBrowse users can follow the links to go back to Cmap, the marker detail page or the Sequence Retrieval Tool.
Figure 3.
Figure 3.
Germplasm search site in CottonGen. (A) Multiple germplasm search sites are available based on the type of information users are interested in. (B) An example search where users can view and search for germplasm and their collection centre. (C) A germplasm details page with various tabs to show the detailed information. (D) The Map tab of a germplasm page shows all the maps for which the germplasm has been used. (E) From the map page users can open CMap for further exploration.
See this image and copyright information in PMC

References

    1. Brubaker CL, Wendel JF. Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs) Am. J. Bot. 1994;81:1309–1326.
    1. Brubaker CL, Bourland FM, Wendel JF. The origin and domestication of cotton. In: Smith CW, Cothren JT, editors. ‘Cotton: Origin, History, Technology and Production’. New York: Wiley; 1999. pp. 3–31.
    1. Percy RG, Wendel JF. Allozyme evidence for the origin and diversification of Gossypium barbadense L. Theor. Appl. Genet. 1990;79:529–542. - PubMed
    1. Wendel JF. New World tetraploid cottons contain Old World cytoplasm. Proc. Natl Acad. Sci. USA. 1989;86:4132–4136. - PMC - PubMed
    1. Wendel JF, Small RL, Cronn RC, Brubaker CL. Genes, jeans, and genomes: reconstructing the history of cotton. In: van Raamsdonk LWD, den Nijs JCM, editors. Plant Evolution in Man-Made Habitats. Proceedings of the VIIth International Symposium of the International Organization of Plant Biosystematists. Amsterdam, The Netherlands: Hugo de Vries Laboratory; 1999. pp. 133–161.

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