Exploring Wheat Physical Maps and Genomic Data Using URGI Browsers

The wheat genome is complex and its analysis is a key challenge for agronomy and modern bioinformatics. To enable analysis of this important crop, the URGI (INRA research unit in genomics and bioinformatics dedicated to plants and crop parasites) developed customized browsers (GMOD tools) to display physical maps and reference sequence annotation data.

The IWGSC (International Wheat Genome Sequencing Consortium) sequences (survey sequences and 3B reference sequence) and physical maps data of each chromosome are hosted by the URGI Sequence Repository (http://wheat-urgi.versailles.inra.fr/Seq-Repository).

Using our physical maps browser (https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_phys_pub/), the scientific community can browse contigs, BACs, markers, deletion bins, and WGP tag sequences as they become available.

We also host the wheat survey sequence annotation browser with polymorphism data and gene models (https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_survey_sequence_annotation/). One can reach the wheat survey sequence annotation from our BLAST page (https://urgi.versailles.inra.fr/blast/).

Moreover, we setup a JBrowse to display 3B reference sequence annotation data such as mRNA, transposable elements, markers, QTLs, etc., and will be incorporating similar data for for reference sequences of other chromosomes as they are completed.  

We provide a strong interoperability between data sources by linking the 3B annotation JBrowse to the 3B physical map. There are also many external links to complete searches: toward GnpIS (https://urgi.versailles.inra.fr/gnpis/, Steinbach et al. 2013 doi: 10.1093/database/bat058), a multi-species integrative information system that we developed at URGI or toward Wheat3BMine (http://urgi.versailles.inra.fr/Wheat3BMine/), a data warehouse dedicated to the wheat 3B chromosome.