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The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch

1
Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden
2
Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
3
Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, and Faculdade de Ciências Naturais (ICEN), Universidade Federal do Pará, Belém 66075-110, Brazil
*
Authors to whom correspondence should be addressed.
Genes 2019, 10(4), 301; https://doi.org/10.3390/genes10040301
Received: 6 March 2019 / Revised: 5 April 2019 / Accepted: 5 April 2019 / Published: 13 April 2019
(This article belongs to the Special Issue Repetitive DNA Sequences)
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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. View Full-Text
Keywords: transposable elements; transposons; LTR retrotransposons; ERV; genome; genome annotation; karyotype; estrildidae; zebra finch; Uraeginthus cyanocephalus transposable elements; transposons; LTR retrotransposons; ERV; genome; genome annotation; karyotype; estrildidae; zebra finch; Uraeginthus cyanocephalus
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Boman, J.; Frankl-Vilches, C.; da Silva dos Santos, M.; de Oliveira, E.H.C.; Gahr, M.; Suh, A. The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch. Genes 2019, 10, 301.

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