Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992, Smeds, Linnéa and Ellegren, Hans (2018) Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes. Molecular Ecology, 27 (1). pp. 99-111. ISSN 0962-1083

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Abstract

Transposable elements (TEs) are genomic parasites capable of inserting virtually anywhere in the host genome, with manifold consequences for gene expression, DNA methylation and genomic stability. Notably, they can contribute to phenotypic variation and hence be associated with, for example, local adaptation and speciation. However, some organisms such as birds have been widely noted for the low densities of TEs in their genomes and this has been attributed to a potential dearth in transposition during their evolution. Here, we show that avian evolution witnessed diverse and abundant transposition on very recent timescales. First, we made an in-depth repeat annotation of the collared flycatcher genome, including identification of 23 new, retrovirus-like LTR retrotransposon families. Then, using whole-genome resequencing data from 200 Ficedula flycatchers, we detected 11,888 polymorphic TE insertions (TE presence/absence variations, TEVs) that segregated within and among species. The density of TEVs was one every 1.5–2.5 Mb per individual, with heterozygosities of 0.12–0.16. The majority of TEVs belonged to some 10 different LTR families, most of which are specific to the flycatcher lineage. TEVs were validated by tracing the segregation of hundreds of TEVs across a three-generation pedigree of collared flycatchers and also by their utility as markers recapitulating the phylogenetic relationships among flycatcher species. Our results suggest frequent germline invasions of songbird genomes by novel retroviruses as a rich source of structural variation, which may have had underappreciated phenotypic consequences for the diversification of this species-rich group of birds.

Item Type: Article
Additional Information: Funding Information: We thank Homa Papoli Yazdi, Alexander Nater, Fritjof Lammers, Takeshi Kawakami, Toby Fountain, Ludovic Dutoit, Rory Craig and Reto Burri for helpful discussions. We thank two anonymous reviewers for their valuable comments on an earlier version of this manuscript. This work was supported by grants from the Knut and Alice Wallenberg Foundation, and the Swedish Research Council. Computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX). Publisher Copyright: © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd
Uncontrolled Keywords: bird,insertion polymorphism,pedigree,retrotransposon,retrovirus,structural variation,transposon,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 13:37
Last Modified: 01 Oct 2022 07:54
URI: https://ueaeprints.uea.ac.uk/id/eprint/88403
DOI: 10.1111/mec.14439

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