Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

High-quality genome assemblies for the 26 Nested Association Mapping (NAM) inbred founder lines were downloaded from MaizeGDB (https://www.maizegdb.org/genome). AnchorWave v1.0.1 was used to perform pairwise whole genome alignments to compare each of the NAM inbred genomes to the B73 reference genome (included in the NAM founder line set) for a total of 25 pairwise whole-genome alignments via the 'genoAli' command and '-IV' parameter. The MAFToGVCF plugin of tassel v5.2.82 was used to reformat genome alignments in MAF format into variant calling records in GVCF format. Both the MAF and GVCF formats are provided here. TE annotations, gene annotations, and gene synteny calls were downloaded from MaizeGDB. TE and gene annotations were downloaded from https://maizegdb.org/NAM_project, while synteny classifications for the NAM genes were downloaded from https://ars-usda.app.box.com/v/maizegdb-public/folder/186350887665. Scripts used to filter publicly available datasets and to generate new data can be found on GitHub at https://github.com/mam737/PolymorphicTEs_NAM along with a README detailing what each script does.