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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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