Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
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GenomeRes.-2018-Thybert-448-59.pdf
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Final Published Version
Author
Thybert, DavidRoller, Maša
Navarro, Fábio C.P.
Fiddes, Ian
Streeter, Ian
Feig, Christine
Martin-Galvez, David
Kolmogorov, Mikhail
Janoušek, Václav
Akanni, Wasiu
Aken, Bronwen
Aldridge, Sarah
Chakrapani, Varshith
Chow, William
Clarke, Laura
Cummins, Carla
Doran, Anthony
Dunn, Matthew
Goodstadt, Leo
Howe, Kerstin
Howell, Matthew
Josselin, Ambre-Aurore
Karn, Robert C.
Laukaitis, Christina M.
Jingtao, Lilue
Martin, Fergal
Muffato, Matthieu
Nachtweide, Stefanie
Quail, Michael A.
Sisu, Cristina
Stanke, Mario
Stefflova, Klara
Van Oosterhout, Cock
Veyrunes, Frederic
Ward, Ben
Yang, Fengtang
Yazdanifar, Golbahar
Zadissa, Amonida
Adams, David J.
Brazma, Alvis
Gerstein, Mark
Paten, Benedict
Pham, Son
Keane, Thomas M.
Odom, Duncan T.
Flicek, Paul
Affiliation
Univ Arizona, Coll Med, Dept MedIssue Date
2018-03-21
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Thybert, D., Roller, M., Navarro, F. C., Fiddes, I., Streeter, I., Feig, C., ... & Aken, B. (2018). Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome research, 28(4), 448-459.Journal
GENOME RESEARCHRights
© 2018 Thybert et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International).Collection Information
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.Abstract
Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.Note
6 month embargo; published online: 21 March 2018ISSN
1088-90511549-5469
PubMed ID
29563166Version
Final published versionSponsors
Wellcome Trust [WT108749/Z/15/Z, WT098051, WT202878/Z/16/Z, WT202878/B/16/Z]; National Human Genome Research Institute [U41HG007234]; Cancer Research UK [20412]; European Research Council [615584]; Biotechnology and Biological Sciences Research Council [BB/N02317X/a]; European Molecular Biology Laboratory; European Community's Seventh Framework Programme (FP7) [244356]; European Union's Seventh Framework Programme (FP7) [HEALTH-F4-2010-241504]Additional Links
http://genome.cshlp.org/lookup/doi/10.1101/gr.234096.117ae974a485f413a2113503eed53cd6c53
10.1101/gr.234096.117
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Except where otherwise noted, this item's license is described as © 2018 Thybert et al. This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International).
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