The natural history of transposons in plant pangenomes and panepigenomes

Transposons are DNA sequences capable of self-mobilization, which occupy large fractions of plant genomes. Due to their repetitive nature, complete maps of transposon diversity have been challenging to obtain. The advent of long-read sequencing now provides high-quality pangenomic assemblies, revealing transposon diversity within and between species. Transposons are major targets of epigenetic and post-transcriptional silencing, which provide the capacity for cryptic transmission, and facilitate environmental and developmental regulation. Transposon distributions are highly structured along plant chromosomes and we examine genomic niches that specific families are adapted to occupy. Here, we review new insights into transposon core and accessory proteins, and how these can regulate activity in vivo. Finally, we consider the role of transposons in host genome adaptation and evolution, as well as how they are selected on their own terms.