CottonFGD: an integrated functional genomics database for cotton

Tao Zhu,Guoqing Sun,Rui Zhang,Chengzhen Liang,Zhaoghong Meng,Zhigang Meng,Sandui Guo

doi:10.1186/s12870-017-1039-x

Tao Zhu, Guoqing Sun + Show 5 more

Open Access

https://doi.org/10.1186/s12870-017-1039-x

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Abstract

BackgroundCotton (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.DescriptionWe 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.ConclusionEquipped 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.

Highlights

Cotton (Gossypium spp.) is the most important fiber and oil crop in the world
The polyploidy of currently cultivated cottons, and its close relationship with ancestral diploid donor species makes it an excellent model organism for studies of polyploidization. These two aspects have resulted in demand for an integrated genomics database that provides gene information resources for researchers engaged in molecular breeding and in evolutionary studies
After checking the annotation consistency between the General Feature Format (GFF) files and the provided Coding DNA Sequence (CDS) or protein sequences, we found that the HAU assembly (v1.0) and annotation (v1.0) of G. barbadense [6] contain systemic errors; it was not included in CottonFGD (Additional file 1)

Summary

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.

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