Articles
Genome Database for Vaccinium: a community resource for genetics, genomics, and breeding research
Article number
1440_10
Pages
71 – 78
Language
English
Abstract
The Genome Database for Vaccinium (GDV, https://www.vaccinium.org/) is an online, community database that enables translational Vaccinium research in genetics, genomics, and breeding by providing tools and published data in one central resource.
The database contains curated genetic maps, genetic markers, quantitative trait loci, and genome data from published manuscripts which are searchable through customizable interfaces.
GDV includes tools to view genetic maps (MapViewer), genome annotations (JBrowse), synteny (Synteny Viewer) metabolic pathways (PathwayTools), gene expression levels (Expression Heatmap Tool), as well as a BLAST tool for searching genome, transcriptome, and marker sequences.
Structural graph data, along with the genome sequences from the Vaccinium Pangenome Project are also available to view and search using tools on GDV. Embedded in GDV is the Breeding Information Management System (BIMS). It can be used to view and search the Vaccinium USDA-GRIN phenotype data and manage private breeding programs.
GDV also serves as a community information hub through access to the VacCAP project (https://www.vacciniumcap.org/). The tools and resources available on GDV are based on user input and needs of the research community.
Community feedback is always welcome.
The database contains curated genetic maps, genetic markers, quantitative trait loci, and genome data from published manuscripts which are searchable through customizable interfaces.
GDV includes tools to view genetic maps (MapViewer), genome annotations (JBrowse), synteny (Synteny Viewer) metabolic pathways (PathwayTools), gene expression levels (Expression Heatmap Tool), as well as a BLAST tool for searching genome, transcriptome, and marker sequences.
Structural graph data, along with the genome sequences from the Vaccinium Pangenome Project are also available to view and search using tools on GDV. Embedded in GDV is the Breeding Information Management System (BIMS). It can be used to view and search the Vaccinium USDA-GRIN phenotype data and manage private breeding programs.
GDV also serves as a community information hub through access to the VacCAP project (https://www.vacciniumcap.org/). The tools and resources available on GDV are based on user input and needs of the research community.
Community feedback is always welcome.
Publication
Authors
J.L. Humann, C.-H. Cheng, T. Lee, K. Buble, P. Zheng, S. Jung, J. Yu, K. Gasic, S. Ru, N.V. Bassil, M. Iorizzo, D. Main
Keywords
BIMS, genome synteny, gene functional annotation, pangenome
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