Stepwise evolution of a butterfly supergene via duplication and inversion.
dc.contributor.author | Kim, K-W | |
dc.contributor.author | De-Kayne, R | |
dc.contributor.author | Gordon, IJ | |
dc.contributor.author | Omufwoko, KS | |
dc.contributor.author | Martins, DJ | |
dc.contributor.author | Ffrench-Constant, R | |
dc.contributor.author | Martin, SH | |
dc.date.accessioned | 2023-07-20T08:53:48Z | |
dc.date.issued | 2022-06-13 | |
dc.date.updated | 2023-07-19T15:24:15Z | |
dc.description.abstract | Supergenes maintain adaptive clusters of alleles in the face of genetic mixing. Although usually attributed to inversions, supergenes can be complex, and reconstructing the precise processes that led to recombination suppression and their timing is challenging. We investigated the origin of the BC supergene, which controls variation in warning coloration in the African monarch butterfly, Danaus chrysippus. By generating chromosome-scale assemblies for all three alleles, we identified multiple structural differences. Most strikingly, we find that a region of more than 1 million bp underwent several segmental duplications at least 7.5 Ma. The resulting duplicated fragments appear to have triggered four inversions in surrounding parts of the chromosome, resulting in stepwise growth of the region of suppressed recombination. Phylogenies for the inversions are incongruent with the species tree and suggest that structural polymorphisms have persisted for at least 4.1 Myr. In addition to the role of duplications in triggering inversions, our results suggest a previously undescribed mechanism of recombination suppression through independent losses of divergent duplicated tracts. Overall, our findings add support for a stepwise model of supergene evolution involving a variety of structural changes. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'. | en_GB |
dc.description.sponsorship | Royal Society | en_GB |
dc.description.sponsorship | Royal Society | en_GB |
dc.description.sponsorship | Swiss National Science Foundation (SNSF) | en_GB |
dc.description.sponsorship | National Geographic Society | en_GB |
dc.format.extent | 20210207- | |
dc.format.medium | Print-Electronic | |
dc.identifier.citation | Vol. 377, No. 1856, article 20210207 | en_GB |
dc.identifier.doi | https://doi.org/10.1098/rstb.2021.0207 | |
dc.identifier.grantnumber | URF\R1\180682 | en_GB |
dc.identifier.grantnumber | RGF\EA\181071 | en_GB |
dc.identifier.grantnumber | P2BEP3_195567 | en_GB |
dc.identifier.grantnumber | WW-138R-17 | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/133623 | |
dc.identifier | ORCID: 0000-0001-5385-9888 | 0000-0002-8704-2574 (Ffrench-Constant, Richard) | |
dc.identifier | ScopusID: 34975054200 (Ffrench-Constant, Richard) | |
dc.language.iso | en | en_GB |
dc.publisher | The Royal Society | en_GB |
dc.relation.url | https://www.ncbi.nlm.nih.gov/pubmed/35694743 | en_GB |
dc.relation.url | https://doi.org/10.5061/dryad.xwdbrv1g0 | en_GB |
dc.relation.url | https://github.com/RishiDeKayne/Danaus_supergene_structure | en_GB |
dc.relation.url | https://github.com/simonhmartin/Danaus_supergene_structure | en_GB |
dc.rights | © 2022 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited | en_GB |
dc.subject | Danaus chrysippus | en_GB |
dc.subject | chromosomal rearrangement | en_GB |
dc.subject | genome assembly | en_GB |
dc.subject | recombination suppression | en_GB |
dc.subject | repeats | en_GB |
dc.subject | structural variation | en_GB |
dc.title | Stepwise evolution of a butterfly supergene via duplication and inversion. | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2023-07-20T08:53:48Z | |
dc.identifier.issn | 0962-8436 | |
exeter.article-number | ARTN 20210207 | |
exeter.place-of-publication | England | |
dc.description | This is the final version. Available from the Royal Society via the DOI in this record. | en_GB |
dc.description | Data accessibility Sequencing reads and assemblies are available at the European Nucleotide Archive project (see the electronic supplementary material, table S1 for accession numbers [48]). Assemblies are available in the European Nucleotide Archive project accession PRJEB52180. Additional data files are available from the Dryad Digital Repository: https://doi.org/10.5061/dryad.xwdbrv1g0 [49], including genome assemblies and annotations, repeat library and windowed repeat content, whole-genome alignments, VCF and genotype files, window-based diversity and divergence measures and read depth, sequence alignments for genes and phylogenetic trees. Scripts for assembly polishing, the analysis of repeat content, genome annotation and phylogenetic tree construction are available at https://github.com/RishiDeKayne/Danaus_supergene_structure. Scripts for genome alignment and synteny block inference, ancestry painting and divergence analyses, and read depth and copy number analyses are available at https://github.com/simonhmartin/Danaus_supergene_structure. | en_GB |
dc.identifier.eissn | 1471-2970 | |
dc.identifier.journal | Philosophical Transactions of the Royal Society B: Biological Sciences | en_GB |
dc.relation.ispartof | Philos Trans R Soc Lond B Biol Sci, 377(1856) | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2022-03-28 | |
dc.rights.license | CC BY | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2022-06-13 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2023-07-20T08:49:14Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2023-07-20T08:53:52Z | |
refterms.panel | A | en_GB |
refterms.dateFirstOnline | 2022-06-13 |
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