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

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 ex...

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Autores principales: Baril, Tobias, Hayward, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8848866/
https://www.ncbi.nlm.nih.gov/pubmed/35172896
http://dx.doi.org/10.1186/s13100-022-00263-5
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author Baril, Tobias
Hayward, Alexander
author_facet Baril, Tobias
Hayward, Alexander
author_sort Baril, Tobias
collection PubMed
description 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13100-022-00263-5.
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spelling pubmed-88488662022-02-18 Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus Baril, Tobias Hayward, Alexander Mob DNA Research 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13100-022-00263-5. BioMed Central 2022-02-16 /pmc/articles/PMC8848866/ /pubmed/35172896 http://dx.doi.org/10.1186/s13100-022-00263-5 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Baril, Tobias
Hayward, Alexander
Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus
title Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus
title_full Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus
title_fullStr Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus
title_full_unstemmed Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus
title_short Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus
title_sort migrators within migrators: exploring transposable element dynamics in the monarch butterfly, danaus plexippus
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8848866/
https://www.ncbi.nlm.nih.gov/pubmed/35172896
http://dx.doi.org/10.1186/s13100-022-00263-5
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