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

dc.contributor.authorBaril, T
dc.contributor.authorHayward, A
dc.date.accessioned2022-02-11T14:10:47Z
dc.date.issued2022-02-16
dc.date.updated2022-02-11T12:03:09Z
dc.description.abstractBackground 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.en_GB
dc.description.sponsorshipBiotechnology & Biological Sciences Research Council (BBSRC)en_GB
dc.identifier.citationVol. 13, article 5en_GB
dc.identifier.doihttps://doi.org/10.1186/s13100-022-00263-5
dc.identifier.grantnumberBB/N020146/1en_GB
dc.identifier.grantnumberBB/M009122/1en_GB
dc.identifier.urihttp://hdl.handle.net/10871/128773
dc.identifierORCID: 0000-0002-5936-7531 (Baril, Toby)
dc.language.isoenen_GB
dc.publisherBMCen_GB
dc.rights© The Author(s) 2022. Open Access This 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/. The Creative Commons Public Domain Dedication waiver (http://creativeco mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.en_GB
dc.subjectTransposonen_GB
dc.subjectTE Annotationen_GB
dc.subjectLepidopteraen_GB
dc.subjectDanaus plexippusen_GB
dc.subjectButterflyen_GB
dc.subjectgenomic deletionen_GB
dc.subjectrepeaten_GB
dc.subjectgenome evolutionen_GB
dc.titleMigrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippusen_GB
dc.typeArticleen_GB
dc.date.available2022-02-11T14:10:47Z
dc.identifier.issn1759-8753
dc.descriptionThis is the final version. Available on open access from BMC via the DOI in this recorden_GB
dc.descriptionAvailability of Data and Materials: All data generated or analysed during this study are included in this article and its supplementary information files.en_GB
dc.identifier.journalMobile DNAen_GB
dc.relation.ispartofMobile DNA
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/  en_GB
dcterms.dateAccepted2022-02-06
rioxxterms.versionVoRen_GB
rioxxterms.licenseref.startdate2022-02-06
rioxxterms.typeJournal Article/Reviewen_GB
refterms.dateFCD2022-02-11T12:03:13Z
refterms.versionFCDAM
refterms.dateFOA2022-02-18T12:08:34Z
refterms.panelAen_GB


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© The Author(s) 2022. Open Access This 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/. The Creative Commons Public Domain Dedication waiver (http://creativeco mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Except where otherwise noted, this item's licence is described as © The Author(s) 2022. Open Access This 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/. The Creative Commons Public Domain Dedication waiver (http://creativeco mmons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.