Rapid increase in genome size as a consequence of transposable element hyperactivity in wood-white (leptidea) butterflies

Talla, Venkat, Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992, Kalsoom, Faheema, Dinca, Vlad, Vila, Roger, Friberg, Magne, Wiklund, Christer and Backström, Niclas (2017) Rapid increase in genome size as a consequence of transposable element hyperactivity in wood-white (leptidea) butterflies. Genome Biology and Evolution, 9 (10). pp. 2491-2505. ISSN 1759-6653

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Abstract

Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genomesize variation and associationwith transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the commonwood-white (Leptidea sinapis) and population re-sequencing data fromboth L. sinapis and the closely related L. reali and L. juvernica togetherwith 12 previously available lepidopteran genome assemblies.Aphylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643Mb) and genome size is correlatedwith abundance of TEs, both inLepidoptera in general andwithin Leptideawhere L. juvernica fromKazakhstanhas considerably larger genomesize than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.

Item Type: Article
Additional Information: Funding Information: This study was supported by a Junior Research Grant from the Swedish Research Council [VR 2013-4508 to N.B.], MINECO and AEI/FEDER, UE project grants [CCGL2013-48277-P; CGL2016-76322-P to R.V.], and a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme [project no. 625997 to V.D.]. We acknowledge additional funding for library preparation and sequencing from Kungliga Fysiografiska Sallskapet i Lund (Nilsson-Ehle Donations) and the Science for Life Laboratory (SciLife Sweden) Biodiversity Program. The SNP&SEQ Technology Platform and Uppsala Genome Center performed the library preparations and the sequencing supported by Science for Life Laboratory (SciLife, Stockholm); a national infrastructure funded by the Swedish Research Council (VR-RFI) and the Knut and Alice Wallenberg Foundation. The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX; Lampa et al. 2013) under Project # b2014034. We thank Remi-Andre Olsen for help with the Allpaths-LG assembly, Roy N. Platt II and David A. Ray for providing the TE library for H. erato, Aurélie Kapusta for providing the Perl script to merge TE libraries, Clément Goubert for help with optimizing dnaPipeTE and for commenting on an earlier version of the manuscript, and Brian Nelson and Catherine Bertrand for advice and help with sampling L. juvern-ica in Ireland. We thank the associate editor and four anonymous reviewers for constructive and insightful suggestions and comments that helped improve and clarify the manuscript. Publisher Copyright: © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Uncontrolled Keywords: butterfly,genome expansion,lepidoptera,leptidea,population,transposable elements,ecology, evolution, behavior and systematics,genetics ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 16 Sep 2022 14:33
Last Modified: 24 Sep 2022 07:15
URI: https://ueaeprints.uea.ac.uk/id/eprint/88406
DOI: 10.1093/gbe/evx163

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