The radish genome database (RadishGD): an integrated information resource for radish genomics. (5th February 2019)

• Record Type: Journal Article
• Authors: Yu, Hee-Ju; Baek, Seunghoon; Lee, Young-Joon; Cho, Ara; Mun, Jeong-Hwan
• Is Part Of: Database. Volume 2019(2019)
• Publication Date: 2019-02-05
• Subjects: Biology -- Databases -- Periodicals; Bioinformatics -- Periodicals; 570.285
• DOI: 10.1093/database/baz009
• Languages: English
• ISSNs: 1758-0463

Abstract

Abstract: Radish ( Raphanus sativus L.) is an important root vegetable crop in the family Brassicaceae, which provides diverse nutrients for human health and is closely related to the Brassica crop species. Recently, we sequenced and assembled the radish genome into nine chromosome pseudomolecules. In addition, we developed diverse genomic resources, including genetic maps, molecular markers, transcriptome, genome-wide methylation and variome data. In this study, we describe the radish genome database (RadishGD), including details of data sets that we generated and the web interface that allows access to these data. RadishGD comprises six major units that enable researchers and general users to search, browse and analyze the radish genomic data in an integrated manner. The Search unit provides gene structures and sequences for gene models through keyword or BLAST searches. The Genome browser displays graphic representations of gene models, mRNAs, repetitive sequences, genome-wide methylation and variomes among various genotypes. The Functional annotation unit offers gene ontology, plant ontology, pathway and gene family information for gene models. The Genetic map unit provides information about markers and their genetic locations using two types of genetic maps. The Expression unit presents transcriptional characteristics and methylation levels for each gene in 18 tissues. All sequence data incorporated into RadishGD can be downloaded from the Data resources unit. RadishGD will be continually updated to serve as a community resource for radish genomics and breeding research.