TY  - JOUR
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
Y1  - 2018/04/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 448 
EP  - 459 
DO  - 10.1101/gr.234096.117 
VL  - 28 
IS  - 4 
UR  - http://genome.cshlp.org/content/28/4/448.abstract 
N2  - 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. 
ER  -