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Background Lepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is available for the monarch butterfly ( Danaus plexippus ), but it lacks an in-depth transposable element (TE) annotation, presenting an opportunity to explore monarch TE dynamics and the impact of TEs on shaping the monarch genome. Results We find 6.21% of the monarch genome is comprised of TEs, a reduction of 6.85% compared to the original TE annotation performed on the draft genome assembly. Monarch TE content is low compared to two closely related species with available genomes,  Danaus chrysippus  (33.97% TE) and  Danaus melanippus  (11.87% TE). The biggest TE contributions to genome size in the monarch are LINEs and  Penelope -like elements, and three newly identified families,  r2-hero_dPle  (LINE),  penelope-1_dPle  ( Penelope -like), and  hase2-1_dPle  (SINE), collectively contribute 34.92% of total TE content. We find evidence of recent TE activity, with two novel Tc1 families rapidly expanding over recent timescales ( tc1-1_dPle ,  tc1-2_dPle ). LINE fragments show signatures of genomic deletions indicating a high rate of TE turnover. We investigate associations between TEs and wing colouration and immune genes and identify a three-fold increase in TE content around immune genes compared to other host genes. Conclusions We provide a detailed TE annotation and analysis for the monarch genome, revealing a considerably smaller TE contribution to genome content compared to two closely related  Danaus  species with available genome assemblies. We identify highly successful novel DNA TE families rapidly expanding over recent timescales, and ongoing signatures of both TE expansion and removal highlight the dynamic nature of repeat content in the monarch genome. Our findings also suggest that insect immune genes are promising candidates for future interrogation of TE-mediated host adaptation.

Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus