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

View ORCID ProfileDaria Shipilina, View ORCID ProfileKarin Näsvall, View ORCID ProfileLars Höök, View ORCID ProfileRoger Vila, View ORCID ProfileGerard Talavera, View ORCID ProfileNiclas Backström
doi: https://doi.org/10.1101/2022.04.14.488360
Daria Shipilina
1Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
2Swedish Collegium for Advanced Study, Thunbergsvägen 2, 75236, Uppsala, Sweden
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  • For correspondence: daria.shipilina@ebc.uu.se
Karin Näsvall
1Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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Lars Höök
1Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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Roger Vila
3The Butterfly Diversity and Evolution Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
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Gerard Talavera
4Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s/n, 08038, Barcelona, Spain
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Niclas Backström
1Evolutionary Biology Program, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
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Abstract

Gene family expansions and crossing over are two main mechanisms for the generation of novel genetic variants that can be picked up by natural selection. Here, we developed a high-density, pedigree-based linkage map of the painted lady butterfly (Vanessa cardui) – a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior. We also performed detailed annotations of genes and interspersed repetitive elements for a previously developed genome assembly, characterized species-specific gene family expansions and the relationship between recombination rate variation and genomic features. Identified expanded gene families consisted of clusters of tandem duplications with functions associated with protein and fat metabolism, detoxification, and defense against infection - key functions for the painted lady’s unique lifestyle. The detailed assessment of recombination rate variation demonstrated a negative association between recombination rate and chromosome size. Moreover, the recombination landscape along the holocentric chromosomes was bimodal. The regional recombination rate was positively associated with the proportion of short interspersed elements (SINEs), but not the other repeat classes, potentially a consequence of SINEs hijacking the recombination machinery for proliferation. The detailed genetic map developed here will contribute to the understanding of the mechanisms and evolutionary consequences of recombination rate variation in Lepidoptera in general. We conclude that the structure of the painted lady genome has been shaped by a complex interplay between recombination, gene duplications and TE-activity and that specific gene family expansions have been key for the evolution of long-distance migration and the ability to utilize a wide range of host plants.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 14, 2022.
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Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
Daria Shipilina, Karin Näsvall, Lars Höök, Roger Vila, Gerard Talavera, Niclas Backström
bioRxiv 2022.04.14.488360; doi: https://doi.org/10.1101/2022.04.14.488360
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Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
Daria Shipilina, Karin Näsvall, Lars Höök, Roger Vila, Gerard Talavera, Niclas Backström
bioRxiv 2022.04.14.488360; doi: https://doi.org/10.1101/2022.04.14.488360

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