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.
Highlights
Rapid advances in plant genomics have enabled the development of various tools for crop improvement, including molecular markers, genetic maps, genomic data, plant resources and novel information about traits and statistics
In addition to assembly of the draft genome (Rs1.0), we developed a large collection of genotypes and a broad array of available genomic resources such as molecular markers, genetic maps and omics data including the transcriptome, methylome and variome [5, 6, 17, 18]
Through a combination of programbased prediction using Fgenesh+, AUGUSTUS [20] and SNAP [21] with parameters trained on the radish matrix, sequence similarity-based prediction using Basic Local Alignment Search Tool (BLAST) search [22], transcriptome-based prediction using Genomic Short-read Nucleotide Alignment Program (GSNAP) [23] and Program to Assemble Spliced Alignments [24] and consensus gene structure prediction using EVidenceModeler [24], we identified a total of 46 514 protein-coding genes encoding 67 016 proteins in 84 967 transcripts
Summary
Rapid advances in plant genomics have enabled the development of various tools for crop improvement, including molecular markers, genetic maps, genomic data, plant resources and novel information about traits and statistics. A unified information platform integrating the available genomic data and tools would serve as a fundamental resource for research and breeding of crop species of interest. In addition to assembly of the draft genome (Rs1.0), we developed a large collection of genotypes (mapping populations and germplasm accessions) and a broad array of available genomic resources such as molecular markers, genetic maps and omics data including the transcriptome, methylome and variome [5, 6, 17, 18].
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