Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly

Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species f...

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Autores: Shipilina, Daria, Näsvall, Karin, Höök, Lars, Vila, Roger, Talavera, Gerard, Backström, Niclas
Formato: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Recursos:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/280016
Acesso em linha:http://hdl.handle.net/10261/280016
Access Level:acceso abierto
Palavra-chave:Genomics
Recombination
Linkage map
Gene family
Painted lady
Lepidoptera
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spelling Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterflyShipilina, DariaNäsvall, KarinHöök, LarsVila, RogerTalavera, GerardBackström, NiclasGenomicsRecombinationLinkage mapGene familyPainted ladyLepidopteraCharacterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.Financial support for this project was provided by FORMAS (Research grant 2019-00670 to N.B.) and The Swedish Collegium for Advanced Science (Natural Sciences Programme, Knut and Alice Wallenberg Foundation, Postdoc funding for D.S.). R.V. was supported by the grant PID2019-107078GB-I00 funded by MCIN/AEI/10.13039/501100011033. G.T. was supported by the grant PID2020-117739GA-I00 funded by MCIN/AEI/10.13039/501100011033 and by “La Caixa” Foundation (ID 100010434) through the grant LCF/BQ/PR19/11700004.1. Introduction 2. Results 2.1. Linkage map and genome annotation 2.2. Synteny 2.3. Gene family evolution 2.4. Patterns of recombination rate variation 2.4.1. Global and chromosome specific recombination rates 2.4.2. Intra-chromosomal variation in recombination rate and associations with genomic elements 3. Discussion 3.1. The genome of the painted lady butterfly 3.2. Sex chromosomes 3.3. Gene family analysis 3.4. Patterns of recombination rate variation 4. Conclusions 5. Methods 5.1. Linkage map 5.1.1. Sampling and DNA-extraction 5.1.2. Building the linkage map 5.2. Genome annotation and whole genome statistics 5.2.1. Genome assembly statistics 5.2.2. Gene and repeat annotation 5.3. Manual curation 5.4. Gene family evolution 5.5. Gene ontology enrichment 5.6. Recombination rate analysis 5.6.1. Chromosome level analysis 5.6.2. Window-based analysis Data access CRediT authorship contribution statement Declaration of Competing Interest Acknowledgements Appendix A. Supplementary data Data availability ReferencesElsevier BVSwedish Collegium for Advanced StudyMinisterio de Ciencia e Innovación (España)La CaixaConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2022202220222022info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/280016reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-107078GB-I00info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-117739GA-I00http://dx.doi.org/10.1016/j.ygeno.2022.110481Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/2800162026-05-22T06:33:51Z
dc.title.none.fl_str_mv Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
title Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
spellingShingle Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
Shipilina, Daria
Genomics
Recombination
Linkage map
Gene family
Painted lady
Lepidoptera
title_short Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
title_full Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
title_fullStr Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
title_full_unstemmed Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
title_sort Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
dc.creator.none.fl_str_mv Shipilina, Daria
Näsvall, Karin
Höök, Lars
Vila, Roger
Talavera, Gerard
Backström, Niclas
author Shipilina, Daria
author_facet Shipilina, Daria
Näsvall, Karin
Höök, Lars
Vila, Roger
Talavera, Gerard
Backström, Niclas
author_role author
author2 Näsvall, Karin
Höök, Lars
Vila, Roger
Talavera, Gerard
Backström, Niclas
author2_role author
author
author
author
author
dc.contributor.none.fl_str_mv Swedish Collegium for Advanced Study
Ministerio de Ciencia e Innovación (España)
La Caixa
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Genomics
Recombination
Linkage map
Gene family
Painted lady
Lepidoptera
topic Genomics
Recombination
Linkage map
Gene family
Painted lady
Lepidoptera
description Characterization of gene family expansions and crossing over is crucial for understanding how organisms adapt to the environment. Here, we develop a high-density linkage map and detailed genome annotation of the painted lady butterfly (Vanessa cardui) - a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior and almost cosmopolitan distribution. Our results reveal a complex interplay between regional recombination rate variation, gene duplications and transposable element activity shaping the genome structure of the painted lady. We identify several lineage specific gene family expansions. Their functions are mainly associated with protein and fat metabolism, detoxification, and defense against infection - critical processes for the painted lady's unique life-history. Furthermore, the detailed recombination maps allow us to characterize the regional recombination landscape, data that reveal a strong effect of chromosome size on the recombination rate, a limited impact of GC-biased gene conversion and a positive association between recombination and short interspersed elements.
publishDate 2022
dc.date.none.fl_str_mv 2022
2022
2022
2022
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/280016
url http://hdl.handle.net/10261/280016
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2019-107078GB-I00
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-117739GA-I00
http://dx.doi.org/10.1016/j.ygeno.2022.110481
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier BV
publisher.none.fl_str_mv Elsevier BV
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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