Assessing structural variations of the hexaploid wheat genome

Structural variations (SVs) represent a type of polymorphisms affecting genomes related to rearrangements such as insertions, deletions, duplications, inversions and translocations. In an attempt to decipher the extent of SVs in the hexaploid wheat genome, we have established strategies combining the whole-genome draft assembly of cv. Chinese Spring, the pseudomolecules of chromosomes 3B and 1B (under construction), and resequencing data from cultivated and wild wheat accessions, including whole genome shotgun from13 bread wheat accessions as well as whole-chromosome shotgun of flow-sorted chromosomes 3B from 44 hexaploid and tetraploid wheat accessions. Our results revealed high levels of SVs affecting genes and transposable elements (TEs) and reflecting the phylogeny. Local variations of the extent of SVs follow the structural and functional partitioning of chromosome 3B observed previously, with the chromosomal extremities having accumulated much more polymorphisms than the central part of the chromosome