The genome of blue-capped cordon-bleu uncovers hidden diversity of ltr retrotransposons in zebra finch

Boman, Jesper, Frankl-Vilches, Carolina, da Silva dos Santos, Michelly, de Oliveira, Edivaldo H. C., Gahr, Manfred and Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992 (2019) The genome of blue-capped cordon-bleu uncovers hidden diversity of ltr retrotransposons in zebra finch. Genes, 10 (4). ISSN 2073-4425

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Abstract

Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms.

Item Type: Article
Additional Information: Funding Information: Funding: This research was funded by grants to A.S. from the Swedish Research Council Formas (2017-01597), the Swedish Research Council Vetenskapsrådet (2016-05139), and the SciLifeLab Swedish Biodiversity Program (2015-R14). A.S. acknowledges funding from the Knut and Alice Wallenberg Foundation via Hans Ellegren and 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. M.S.S. was supported by a Co-financed Short-Term Research Grant Brazil, 2018 (57417991), according to the joint agreement of the DAAD (German Academic Exchange Service) with CAPES (Coordenaçao de Aperfeiçoamento de Peesoal de Nível Superior, Brazil). Publisher Copyright: © 2019 by the authors. Licensee MDPI, Basel, Switzerland.
Uncontrolled Keywords: erv,estrildidae,genome,genome annotation,karyotype,ltr retrotransposons,transposable elements,transposons,uraeginthus cyanocephalus,zebra finch,genetics,genetics(clinical) ,/dk/atira/pure/subjectarea/asjc/1300/1311
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: 24 Sep 2022 07:15
URI: https://ueaeprints.uea.ac.uk/id/eprint/88395
DOI: 10.3390/genes10040301

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