Repository logo
 

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Published version
Peer-reviewed

Loading...
Thumbnail Image

Type

Article

Change log

Authors

Thybert, David 
Roller, Maša 
Navarro, Fábio CP 
Fiddes, Ian 
Streeter, Ian 

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 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.

Description

Keywords

Animals, Binding Sites, CCCTC-Binding Factor, Chromosomes, Evolution, Molecular, Genome, Karyotyping, Long Interspersed Nucleotide Elements, Mice, Muridae, Phylogeny, Retroelements, Species Specificity

Journal Title

Genome Res

Conference Name

Journal ISSN

1088-9051
1549-5469

Volume Title

28

Publisher

Cold Spring Harbor Laboratory
Sponsorship
Cancer Research UK (C14303/A17197)
European Research Council (615584)
Cancer Research UK (20412)
Wellcome Trust (202878/Z/16/Z)