Department of Life Science, The Catholic University of Korea, Bucheon, Korea.
Department of Bioscience and Bioinformatics, Myongji University, Yongin, Korea.
Database (Oxford). 2019 Jan 1;2019:baz009. doi: 10.1093/database/baz009.
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.
萝卜（Raphanus sativus L.）是十字花科的一种重要根茎类蔬菜作物，为人体健康提供了多样化的营养物质，与芸薹属作物密切相关。最近，我们将萝卜基因组测序并组装成九个染色体假染色体。此外，我们还开发了多样化的基因组资源，包括遗传图谱、分子标记、转录组、全基因组甲基化和变异性数据。在这项研究中，我们描述了萝卜基因组数据库（RadishGD），包括我们生成的数据集的详细信息以及允许访问这些数据的网络界面。RadishGD 包括六个主要单元，使研究人员和普通用户能够以集成的方式搜索、浏览和分析萝卜基因组数据。搜索单元通过关键字或 BLAST 搜索提供基因结构和基因模型的序列。基因组浏览器以图形方式显示各种基因型的基因模型、mRNA、重复序列、全基因组甲基化和变异性。功能注释单元为基因模型提供基因本体、植物本体、途径和基因家族信息。遗传图谱单元使用两种类型的遗传图谱提供有关标记及其遗传位置的信息。表达单元呈现 18 种组织中每个基因的转录特征和甲基化水平。RadishGD 中包含的所有序列数据都可以从数据资源单元下载。RadishGD 将不断更新，作为萝卜基因组学和育种研究的社区资源。
