RT Journal Article
SR Electronic
T1 Repeat associated mechanisms of genome evolution and function revealed by the <em>Mus caroli</em> and <em>Mus pahari</em> genomes
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 158659
DO 10.1101/158659
A1 David Thybert
A1 Maša Roller
A1 Fábio C.P. Navarro
A1 Ian Fiddes
A1 Ian Streeter
A1 Christine Feig
A1 David Martin-Galvez
A1 Mikhail Kolmogorov
A1 Václav Janoušek
A1 Wasiu Akanni
A1 Bronwen Aken
A1 Sarah Aldridge
A1 Varshith Chakrapani
A1 William Chow
A1 Laura Clarke
A1 Carla Cummins
A1 Anthony Doran
A1 Matthew Dunn
A1 Leo Goodstadt
A1 Kerstin Howe
A1 Matthew Howell
A1 Ambre-Aurore Josselin
A1 Robert C. Karn
A1 Christina M. Laukaitis
A1 Lilue Jingtao
A1 Fergal Martin
A1 Matthieu Muffato
A1 Michael A. Quail
A1 Cristina Sisu
A1 Mario Stanke
A1 Klara Stefflova
A1 Cock Van Oosterhout
A1 Frederic Veyrunes
A1 Ben Ward
A1 Fengtang Yang
A1 Golbahar Yazdanifar
A1 Amonida Zadissa
A1 David Adams
A1 Alvis Brazma
A1 Mark Gerstein
A1 Benedict Paten
A1 Son Pham
A1 Thomas Keane
A1 Duncan T Odom
A1 Paul Flicek
YR 2017
UL http://biorxiv.org/content/early/2017/07/02/158659.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-gorillaorangutan). 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 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four- and seven-fold 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. For example, 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. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.