Genome-wide selection on transposable elements in maize

While most evolutionary research has focused on single nucleotide polymorphisms (SNPs), transposable elements (TEs) represent a major but understudied source of mutations that can influence organismal fitness. Previous studies on TEs often overlook the mechanisms and rates of transposition, rely on short-read sequencing that limits TE detection, or focus on small genomes such as Arabidopsis or Drosophila. In this study, we leveraged high-quality, long-read genome assemblies from 26 maize inbreds to investigate natural selection on TEs. We developed a novel and interpretable method, {Phi}SFS, which incorporates TE age and improves resolution for detecting selection. Using this approach, we identified key factors influencing selection on TEs: (1) the distance to the nearest gene, (2) the pre-insertion DNA methylation level at the insertion site, and (3) intrinsic TE characteristics, including copy number and expression level. This work represents the first application of long-read genome assemblies to study TE selection in a major crop species with a typical plant genome size. Our {Phi}SFSmethod offers a broadly applicable framework for detecting selection on TEs, and the factors uncovered provide new insights into the evolutionary dynamics and trade-offs between TEs and host genes.