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  The blackcap (Sylvia atricapilla) genome reveals a species-specific accumulation of LTR retrotransposons

Bours, A., Pruisscher, P., Bascón-Cardozo, K., Odenthal-Hesse, L., & Liedvogel, M. (2023). The blackcap (Sylvia atricapilla) genome reveals a species-specific accumulation of LTR retrotransposons. Scientific Reports, 13: 16471. doi:10.1038/s41598-023-43090-1.

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https://zenodo.org/deposit/7813728# (Research data)
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 Creators:
Bours, Andrea1, 2, Author           
Pruisscher, Peter2, Author           
Bascón-Cardozo, Karen1, 2, Author           
Odenthal-Hesse, Linda3, Author           
Liedvogel, Miriam2, Author           
Affiliations:
1IMPRS for Evolutionary Biology, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_1445639              
2Max Planck Research Group Behavioural Genomics (Liedvogel), Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2129640              
3Research Group Meiotic Recombination and Genome Instability, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, ou_2355693              

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 Abstract: Transposable elements (TEs) are mobile genetic elements that can move around the genome, and as such are a source of genomic variability. Based on their characteristics we can annotate TEs within the host genome and classify them into specific TE types and families. The increasing number of available high-quality genome references in recent years provides an excellent resource that will enhance the understanding of the role of recently active TEs on genetic variation and phenotypic evolution. Here we showcase the use of a high-quality TE annotation to understand the distinct effect of recent and ancient TE insertions on the evolution of genomic variation, within our study species the Eurasian blackcap (Sylvia atricapilla). We investigate how these distinct TE categories are distributed along the genome and evaluate how their coverage across the genome is correlated with four genomic features: recombination rate, gene coverage, CpG island coverage and GC content. We found within the recent TE insertions an accumulation of LTRs previously not seen in birds. While the coverage of recent TE insertions was negatively correlated with both GC content and recombination rate, the correlation with recombination rate disappeared and turned positive for GC content when considering ancient TE insertions.

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Language(s): eng - English
 Dates: 2022-10-142023-09-192023-09-302023
 Publication Status: Issued
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 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41598-023-43090-1
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Project name : MPRG Grant
Grant ID : MFFALIMN0001
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Title: Scientific Reports
  Abbreviation : Sci. Rep.
Source Genre: Journal
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Publ. Info: London, UK : Nature Publishing Group
Pages: - Volume / Issue: 13 Sequence Number: 16471 Start / End Page: - Identifier: ISSN: 2045-2322
CoNE: https://pure.mpg.de/cone/journals/resource/2045-2322