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BMC plant biology
06 08, 2017;17 (1): 101.

CottonFGD: an integrated functional genomics database for cotton.

Tao Zhu, Chengzhen Liang, Zhigang Meng, Guoqing Sun, Zhaoghong Meng, Sandui Guo, Rui Zhang
Author Information
  1. Tao Zhu: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  2. Chengzhen Liang: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  3. Zhigang Meng: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  4. Guoqing Sun: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  5. Zhaoghong Meng: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
  6. Sandui Guo: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. guosandui@caas.cn.
  7. Rui Zhang: Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. zhangrui@caas.cn.
PMID: 28595571 DOI: 10.1186/s12870-017-1039-x

Abstract

BACKGROUND: Cotton (Gossypium spp.) is the most important fiber and oil crop in the world. With the emergence of huge -omics data sets, it is essential to have an integrated functional genomics database that allows worldwide users to quickly and easily fetch and visualize genomic information. Currently available cotton-related databases have some weakness in integrating multiple kinds of -omics data from multiple Gossypium species. Therefore, it is necessary to establish an integrated functional genomics database for cotton.
DESCRIPTION: We developed CottonFGD (Cotton Functional Genomic Database, https://cottonfgd.org ), an integrated database that includes genomic sequences, gene structural and functional annotations, genetic marker data, transcriptome data, and population genome resequencing data for all four of the sequenced Gossypium species. It consists of three interconnected modules: search, profile, and analysis. These modules make CottonFGD enable both single gene review and batch analysis with multiple kinds of -omics data and multiple species. CottonFGD also includes additional pages for data statistics, bulk data download, and a detailed user manual.
CONCLUSION: Equipped with specialized functional modules and modernized visualization tools, and populated with multiple kinds of -omics data, CottonFGD provides a quick and easy-to-use data analysis platform for cotton researchers worldwide.

Keywords

Cotton Database Functional annotation Genetic marker RNA-seq Variation

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MeSH Term

Databases, Genetic
Forecasting
Genetic Markers
Genetic Variation
Genome, Plant
Gossypium
Information Storage and Retrieval
Internet
Molecular Sequence Annotation

Chemicals

Genetic Markers
Journal Article Research Support, Non-U.S. Gov't

Links to CNCB-NGDC Resources

Database Commons: DBC003680 (CottonFGD)
Article has an altmetric score of 2

Word Cloud

Created with Highcharts 10.0.0datafunctionalmultiple-omicsintegrateddatabaseCottonFGDCottonGossypiumgenomicskindsspeciescottonanalysisworldwidegenomicFunctionalDatabaseincludesgenemarkermodulesBACKGROUND:sppimportantfiberoilcropworldemergencehugesetsessentialallowsusersquicklyeasilyfetchvisualizeinformationCurrentlyavailablecotton-relateddatabasesweaknessintegratingThereforenecessaryestablishDESCRIPTION:developedGenomichttps://cottonfgdorgsequencesstructuralannotationsgenetictranscriptomepopulationgenomeresequencingfoursequencedconsiststhreeinterconnectedmodules:searchprofilemakeenablesinglereviewbatchalsoadditionalpagesstatisticsbulkdownloaddetailedusermanualCONCLUSION:Equippedspecializedmodernizedvisualizationtoolspopulatedprovidesquickeasy-to-useplatformresearchersCottonFGD:annotationGeneticRNA-seqVariation

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