soybean Exome resequences
Structural variation hotspots in the soybean genome localize to clusters of biotic stress response genes
In this study, we sought to define the range of structural variation between four diverse soybean cultivars, Archer, Minsoy, Noir 1 and the genotype that provided the reference genome sequence Williams 82 (Schmutz et al. 2010).  We were able to resolve course structural differences using CGH technology and identify some specific gene content variants (i.e., gene PAVs) using exome resequencing analyses.  We were able to use this data to catalog the genes located within structural variation hotspots, giving us new insight into the mechanisms and forces that may be driving structural variation in soybean.
Genome-wide structural and gene content variation were assessed among four diverse soybean cultivars using both hybridization and resequencing approaches.  Many chromosomes exhibited relatively low rates of structural variation, however several copy number variation hotspots were observed in specific regions, most prominently on chromosomes 3, 6, 7, 16 and 18.  Structural variation hotspots localized to gene-rich regions that were enriched for clustered multi-gene families.  The most abundant gene families associated with these hotspots were the Nucleotide Binding (NB) and Receptor-Like Protein (RLP) classes, which are important for plant biotic defense responses.  Implications for these findings are discussed.