“…More structural changes (deletions) were found in the two Gm15 intervals, where there was higher transposon density, suggesting a correlation between structural changes and transposable elements. It is known that transposons can induce major genome rearrangements, including deletions, duplications, inversions, macrotransposition, and reciprocal translocations (Gray, 2000;Caceres et al, 2001;Lonnig and Saedler, 2002;Huang and Dooner, 2008;Lee et al, 2008;Zhang et al, 2009). We hypothesize that Gm15, with a higher transposon density, underwent more extensive structural changes (i.e., higher density of LTR retrotransposon, solo LTRs, and lower gene retention rate) and that transposable elements were likely an active force in this remodeling of a homoeologous chromosome in soybean (see Supplemental Figure 17 online).…”