Abstract
BackgroundLepidoptera (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.ResultsWe 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.ConclusionsWe 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.
Highlights
Lepidoptera are an important model system in ecology and evolution
When examining the source of this variation, the major difference in transposable element (TE) content can be attributed to unclassified elements, for which we find coverage is reduced by 16.31 Mb (6.6% of total genome size) (Table S1; Additional File 1)
This difference is likely due to two issues: (i) improvements in TE annotation tools over the last decade, where improved knowledge of TE structure has led to exclusion of erroneous sequences previously annotated as putatively TE, given that the original annotation used similar tools and databases to those applied in this study [36]; (ii) We apply a conservative approach to TE annotation that excludes very short fragments which cannot be confidently identified as TE sequence, and we remove overlapping TE annotations
Summary
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. TEs are present in most eukaryotes and are important in shaping their genomes [1,2,3,4,5,6,7,8]. Due to the great diversity and dynamic nature of TEs, species-specific TE libraries and accompanying TE annotations are required to provide an understanding of their evolution and impact. From a practical perspective, accurate and reliable repeat annotation is essential to provide high-quality genome annotations, and to help avoid repeat sequences being incorrectly annotated as host genes and vice versa, especially given the vast numbers of genomes currently being sequenced across the tree of life
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