High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

Höök, Lars; Näsvall, Karin; Vila, Roger; Wiklund, Christer; Backström, Niclas; Swedish Research Council

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

© The Author(s) 2023. 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/.

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Bibliographic Details
Main Authors:	Höök, Lars, Näsvall, Karin, Vila, Roger, Wiklund, Christer, Backström, Niclas
Other Authors:	Swedish Research Council
Format:	artículo biblioteca
Language:	English
Published:	Springer 2023-01-20
Subjects:	Linkage map, Genome rearrangements, Karyotype evolution, Lepidoptera, Chromosome fissions/fusions,
Online Access:	http://hdl.handle.net/10261/348205
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institution	IBE ES
collection	DSpace
country	España
countrycode	ES
component	Bibliográfico
access	En linea
databasecode	dig-ibe-es
tag	biblioteca
region	Europa del Sur
libraryname	Biblioteca del IBE España
language	English
topic	Linkage map Genome rearrangements Karyotype evolution Lepidoptera Chromosome fissions/fusions Linkage map Genome rearrangements Karyotype evolution Lepidoptera Chromosome fissions/fusions
spellingShingle	Linkage map Genome rearrangements Karyotype evolution Lepidoptera Chromosome fissions/fusions Linkage map Genome rearrangements Karyotype evolution Lepidoptera Chromosome fissions/fusions Höök, Lars Näsvall, Karin Vila, Roger Wiklund, Christer Backström, Niclas High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)
description	© The Author(s) 2023. 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/.
author2	Swedish Research Council
author_facet	Swedish Research Council Höök, Lars Näsvall, Karin Vila, Roger Wiklund, Christer Backström, Niclas
format	artículo
topic_facet	Linkage map Genome rearrangements Karyotype evolution Lepidoptera Chromosome fissions/fusions
author	Höök, Lars Näsvall, Karin Vila, Roger Wiklund, Christer Backström, Niclas
author_sort	Höök, Lars
title	High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)
title_short	High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)
title_full	High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)
title_fullStr	High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)
title_full_unstemmed	High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)
title_sort	high-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (leptidea spp.)
publisher	Springer
publishDate	2023-01-20
url	http://hdl.handle.net/10261/348205
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spelling	dig-ibe-es-10261-3482052024-02-23T12:32:35Z High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.) Höök, Lars Näsvall, Karin Vila, Roger Wiklund, Christer Backström, Niclas Swedish Research Council Science for Life Laboratory Knut and Alice Wallenberg Foundation Uppsala Multidisciplinary Center for Advanced Computational Science Swedish National Infrastructure for Computing Ministerio de Ciencia, Innovación y Universidades (España) Agencia Estatal de Investigación (España) Uppsala University Vila, Roger [0000-0002-2447-4388] Linkage map Genome rearrangements Karyotype evolution Lepidoptera Chromosome fissions/fusions © The Author(s) 2023. 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/. Karyotypes are generally conserved between closely related species and large chromosome rearrangements typically have negative fitness consequences in heterozygotes, potentially driving speciation. In the order Lepidoptera, most investigated species have the ancestral karyotype and gene synteny is often conserved across deep divergence, although examples of extensive genome reshuffling have recently been demonstrated. The genus Leptidea has an unusual level of chromosome variation and rearranged sex chromosomes, but the extent of restructuring across the rest of the genome is so far unknown. To explore the genomes of the wood white (Leptidea) species complex, we generated eight genome assemblies using a combination of 10X linked reads and HiC data, and improved them using linkage maps for two populations of the common wood white (L. sinapis) with distinct karyotypes. Synteny analysis revealed an extensive amount of rearrangements, both compared to the ancestral karyotype and between the Leptidea species, where only one of the three Z chromosomes was conserved across all comparisons. Most restructuring was explained by fissions and fusions, while translocations appear relatively rare. We further detected several examples of segregating rearrangement polymorphisms supporting a highly dynamic genome evolution in this clade. Fusion breakpoints were enriched for LINEs and LTR elements, which suggests that ectopic recombination might be an important driver in the formation of new chromosomes. Our results show that chromosome count alone may conceal the extent of genome restructuring and we propose that the amount of genome evolution in Lepidoptera might still be underestimated due to lack of taxonomic sampling. This work was funded by the Swedish Research Council (VR research grant #019-04791 to N.B.). The authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We also acknowledge SciLifeLab in Uppsala for long-term bioinformatics support via the WABI initiative. R.V. was supported by project PID2019-107078GB-I00, funded by Ministerio de Ciencia e Innovación (MCIN)/Agencia Estatal de Investigación (AEI)/ 10.13039/501100011033. Open access funding provided by Uppsala University. Peer reviewed 2024-02-23T12:32:34Z 2024-02-23T12:32:34Z 2023-01-20 artículo Chromosome Research 31: 2 (2023) 0967-3849 http://hdl.handle.net/10261/348205 10.1007/s10577-023-09713-z 1573-6849 en #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-107078GB-I00/ES/GENOMICA DE LA ESPECIACION EN MARIPOSAS/ Publisher's version All raw sequence data have been deposited at the European Nucleotide Archive under accession PRJEB58697. All in-house developed scripts and pipelines are available in GitHub (https://github.com/EBC-butterfly-genomics-team/Leptidea_chromosome_research2022). The underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1007/s10577-023-09713-z https://doi.org/10.1007/s10577-023-09713-z Sí open application/pdf Springer

High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.)

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