RT Journal
A1 Thybert, David
A1 Roller, Maša
A1 Navarro, Fábio C.P.
A1 Fiddes, Ian
A1 Streeter, Ian
A1 Feig, Christine
A1 Martin-Galvez, David
A1 Kolmogorov, Mikhail
A1 Janoušek, Václav
A1 Akanni, Wasiu
A1 Aken, Bronwen
A1 Aldridge, Sarah
A1 Chakrapani, Varshith
A1 Chow, William
A1 Clarke, Laura
A1 Cummins, Carla
A1 Doran, Anthony
A1 Dunn, Matthew
A1 Goodstadt, Leo
A1 Howe, Kerstin
A1 Howell, Matthew
A1 Josselin, Ambre-Aurore
A1 Karn, Robert C.
A1 Laukaitis, Christina M.
A1 Jingtao, Lilue
A1 Martin, Fergal
A1 Muffato, Matthieu
A1 Nachtweide, Stefanie
A1 Quail, Michael A.
A1 Sisu, Cristina
A1 Stanke, Mario
A1 Stefflova, Klara
A1 Van Oosterhout, Cock
A1 Veyrunes, Frederic
A1 Ward, Ben
A1 Yang, Fengtang
A1 Yazdanifar, Golbahar
A1 Zadissa, Amonida
A1 Adams, David J.
A1 Brazma, Alvis
A1 Gerstein, Mark
A1 Paten, Benedict
A1 Pham, Son
A1 Keane, Thomas M.
A1 Odom, Duncan T.
A1 Flicek, Paul
T1 Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
JF Genome Research 
JO Genome Research 
YR 2018 
FD April 01 
VO 28 
IS 4 
SP 448 
OP 459 
DO 10.1101/gr.234096.117 
UL http://genome.cshlp.org/content/28/4/448.abstract 
AB 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.