15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Abstract The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The...

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Vydáno v:	Nucleic acids research Ročník 47; číslo D1; s. D1137 - D1145
Hlavní autoři:	Jung, Sook, Lee, Taein, Cheng, Chun-Huai, Buble, Katheryn, Zheng, Ping, Yu, Jing, Humann, Jodi, Ficklin, Stephen P, Gasic, Ksenija, Scott, Kristin, Frank, Morgan, Ru, Sushan, Hough, Heidi, Evans, Kate, Peace, Cameron, Olmstead, Mercy, DeVetter, Lisa W, McFerson, James, Coe, Michael, Wegrzyn, Jill L, Staton, Margaret E, Abbott, Albert G, Main, Dorrie
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England Oxford University Press 08.01.2019
Témata:	applied research Computational Biology - methods Computational Biology - statistics & numerical data crops data collection Database Issue Databases, Genetic Gene Expression Profiling - methods Genes, Plant - genetics genome assembly Genome, Plant - genetics genomics Genomics - methods information management Information Storage and Retrieval - methods Internet management systems phenotype Plant Breeding - methods Quantitative Trait Loci - genetics quantitative traits Rosaceae Rosaceae - classification Rosaceae - genetics single nucleotide polymorphism Species Specificity Synteny Time Factors transcriptome User-Computer Interface
ISSN:	0305-1048, 1362-4962, 1362-4962
On-line přístup:	Získat plný text
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Shrnutí:	Abstract The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0305-1048 1362-4962 1362-4962
DOI:	10.1093/nar/gky1000