Shujun Ou1,2,3,4, Armin Scheben5, Tyler Collins3, Yinjie Qiu2, Arun S. Seetharam1,6, Claire C. Menard2, Nancy Manchanda1, Jonathan I. Gent7, Michael C. Schatz3, Sarah N. Anderson6, Matthew B. Hufford1 and Candice N. Hirsch2 1Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011, USA; 2Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108, USA; 3Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA; 4Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA; 5Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA; 6Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA; 7Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA Corresponding authors: mhuffordiastate.edu, cnhirschumn.edu Abstract

Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms reveals that 64.7% of the variability is contributed by LTR families that are young, less methylated, and more expressed in tropical maize, whereas 18.5% is driven by LTR families with removal or loss in temperate maize. Additionally, we find enrichment for Young LTR families adjacent to nucleotide-binding and leucine-rich repeat (NLR) clusters of varying copy number across lines, suggesting TE activity may be associated with disease resistance in maize.

Received May 26, 2023. Accepted August 12, 2024.