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

Background – Structural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated for de-novo genome assemblies of 26 diverse inbred maize lines.
Results – We generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposab..., 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 ne..., , # Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

Structural differences between genomes are a major source of genetic variation. Transposable elements, or TEs, are mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes. TEs can generate structural variation as a result of their transposition. Advancements in long-read sequencing technologies and computation methods have enhanced our ability to characterize and investigate structural variation between genomes. Detailed characterization of multiple haplotypes for several loci in domestic maize (Zea mays ssp. mays) revealed extensive structural polymorphisms for TE content. Given the high TE content of the maize genome, it is likely that TEs are a major contributor to structural variants (SVs), but this has yet to be fully quantified.

Recently, high-quality TE annotations were recently generated for de-n...