GourdBase: a genome-centered multi-omics database for the bottle gourd (Lagenaria siceraria), an economically important cucurbit crop

Scientific Reports
Ying WangGuojing Li

Abstract

GourdBase is an integrative data platform for the bottle gourd to examine its multifarious intuitive morphology and annotated genome. GourdBase consists of six main modules that store and interlink multi-omic data: the genome (with transcriptomic data integrated) module, the phenome module, the markers/QTLs module, the maps (genetic, physical and comparative) module, the cultivars module, and the publications module. These modules provide access to various type of data including the annotated reference genome sequence, gene models, transcriptomic data from various tissues, physical and comparative genome maps, molecular markers in different types, phenotypic data for featuring traits including fruit shape and umami taste, and quantitative trait loci (QTLs) that underlie these traits. GourdBase is intuitive, user-friendly and interlinked and is designed to allow researchers, breeders and trained farmers to browse, search and fetch information on interests and assist in genomics-driven studies and breeding. The knowledge base and web interface can be accessed at http://www.gourdbase.cn/ .

References

Sep 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jiping LiuSteven D Tanksley
Dec 15, 2005·Proceedings of the National Academy of Sciences of the United States of America·David L EricksonNoreen Tuross
Jun 15, 2007·Journal of Agricultural and Food Chemistry·Maria-Jose Oruna-ConchaDonald S Mottram
Apr 5, 2008·Science·Timothy D HarrisZheng Xie
Jun 24, 2010·Nucleic Acids Research·Kevin J TraversStephen W Turner
Mar 16, 2011·BMC Plant Biology·Aphrodite TsaballaAthanasios S Tsaftaris
Dec 11, 2013·The Plant Journal : for Cell and Molecular Biology·Pei XuGuojing Li
Jun 7, 2014·Frontiers in Plant Science·Esther van der KnaapShan Wu

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Citations

Jun 24, 2019·The New Phytologist·Guillaume ChomickiSusanne S Renner
Aug 16, 2019·Database : the Journal of Biological Databases and Curation·Nan LuJunhui Wang
May 28, 2021·The Plant Journal : for Cell and Molecular Biology·Pei XuGuojing Li

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Methods Mentioned

BETA
dissect
RNA-seq
RAD-Seq
Chip-Seq

Software Mentioned

Search
GourdBase genome browser
GourdBase
Basic Local Alignment Search Tool ( BLAST )
Genome Browser

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