Please use this identifier to cite or link to this item: http://bura.brunel.ac.uk/handle/2438/16068
Title: Repeat associated mechanisms of genome evolution and function revealed by theMus caroliandMus paharigenomes.
Authors: Roller, M
Navarro, FCP
Fiddes, I
Streeter, I
Feig, C
Martin-Galvez, D
Kolmogorov, M
Janoušek, V
Akanni, W
Aken, B
Aldridge, S
Chakrapani, V
Chow, W
Clarke, L
Cummins, C
Doran, A
Dunn, M
Goodstadt, L
Howe, K
Howell, M
Josselin, A-A
Karn, RC
Laukaitis, CM
Jingtao, L
Martin, F
Muffato, M
Nachtweide, S
Quail, MA
Sisu, C
Stanke, M
Stefflova, K
Van Oosterhout, C
Veyrunes, F
Ward, B
Yang, F
Yazdanifar, G
Zadissa, A
Adams, DJ
Brazma, A
Gerstein, M
Paten, B
Pham, S
Keane, TM
Odom, DT
Flicek, P
Issue Date: 2018
Citation: Genome Res, 2018
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 theMus caroliandMus paharigenomes. Together with theMus musculusandRattus norvegicusgenomes, 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 ofMus musculusandMus carolibetween 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 inMus 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.
URI: http://bura.brunel.ac.uk/handle/2438/16068
DOI: http://dx.doi.org/10.1101/gr.234096.117
ISSN: https://www.ncbi.nlm.nih.gov/pubmed/29563166
gr.234096.117
https://www.ncbi.nlm.nih.gov/pubmed/29563166
gr.234096.117
1549-5469
Appears in Collections:Dept of Life Sciences Research Papers

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