library_construction_protocol: Leaf and root samples were extracted using a Qiagen Dneasy plant mini kit according to manufacturers instructions. DNA from Pollen and Endosperm samples were extracted using a modified CTAB DNA extraction protocol (see methods). All DNA samples were then sheared to a mean of 1000 bp using a Covaris E220 Evolution. Libraries were constructed for all samples by first ligating a custom Museq Adapter, and then subsequent PCR reactions to selectively amplify genomic regions adjacent to Mu insertions. See Methods for details