Abstract
The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.
Highlights
The International Wheat Genome Sequencing Consortium (IWGSC) [1] is an international collaborative group of growers, academic scientists, and public and private breeders that was established to generate a high-quality reference genome sequence of the hexaploid bread wheat, and to provide breeders with state-of-the-art tools for wheat improvement
The vision of the consortium is that the high-quality, annotated ordered genome sequence integrated with physical maps will serve as a foundation for the accelerated development of improved varieties and will empower all aspects of basic and applied wheat science to address the important challenge of food security
The repository has been designed in accordance with the “FAIR” principles [3] to ensure that the data are Findable, Accessible, Interoperable, and Reusable
Summary
The International Wheat Genome Sequencing Consortium (IWGSC) [1] is an international collaborative group of growers, academic scientists, and public and private breeders that was established to generate a high-quality reference genome sequence of the hexaploid bread wheat, and to provide breeders with state-of-the-art tools for wheat improvement. Sequence assemblies and annotations The IWGSC wheat genome sequence assemblies available for download, BLAST [11], and display in genome browsers include the draft survey sequence assemblies released in 2014 (IWGSC Chromosome Survey Sequencing (CSS) v1) and two improved versions (CSS v2 and v3) [12] and the chromosome 3B reference sequence (the first reference-quality chromosome sequence obtained by the consortium) [13] Associated with these assemblies are the virtual gene order map generated for the CSS (Genome Zipper), the population sequencing (POPSEQ) data used to order sequence contigs on chromosomes [14], and mapped marker sets. The “markers track” provides links to additional genetic information stored in GnpIS-coreDB which includes access to the position of the marker in centimorgans (cM) on genetic maps and to the overlapping QTLs. The most popular tool of the IWGSC data repository is the BLAST search tool (476,000 BLAST searches launched in 2017, Additional file 1: Table S1, Additional file 1: Figure S1).
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