Visualization Tools for Genomic Conservation.

SynVisio and Accusyn ( genomevis.usask.ca ) are freely available web-based tools for visualizing genomic conservation that provide easy-to-access visualizations for researchers to interact with their datasets and change parameters in real time to carry out synteny exploration and analysis through multiple coordinated visual representations. The tools use standard file formats and outputs from existing synteny detection systems such as MCScanX or DAGChainer, and provide several features that are valuable for large-scale genomic analysis: a range of visualization scales from full genomes down to single collinearity blocks; single-level and multiple-level plots that enable the analysis of more than two genomic regions; annotation tracks that can be loaded using standard BedGraph files; several techniques for reducing visual clutter in visualizations; the ability to download high-quality images of the visualizations; and a snapshot panel for storing configurations of the interface for later revisitation.

Multiple wheat genomes reveal global variation in modern breeding.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.