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

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

Authors :
Kerstin Howe
Thomas M. Keane
Paul Flicek
David Thybert
Bronwen Aken
David Martín-Gálvez
Golbahar Yazdanifar
Christine Feig
Cristina Sisu
Duncan T. Odom
Son Pham
Stefanie Nachtweide
Laura Clarke
Ian Streeter
Carla Cummins
Varshith Chakrapani
Lilue Jingtao
Cock van Oosterhout
Ian T. Fiddes
Alvis Brazma
David J. Adams
William Chow
Frédéric Veyrunes
Maša Roller
Mikhail Kolmogorov
Christina M. Laukaitis
Ambre Aurore Josselin
Matthew Howell
Fergal J. Martin
Klara Stefflova
Benedict Paten
Mario Stanke
Matthieu Muffato
Mark Gerstein
Leo Goodstadt
Fengtang Yang
Michael A. Quail
Anthony G. Doran
Václav Janoušek
Ben J. Ward
Sarah Aldridge
Amonida Zadissa
Fabio C. P. Navarro
Robert C. Karn
Matthew Dunn
Wasiu Akanni
Feig, Christine [0000-0003-1385-7049]
Odom, Duncan [0000-0001-6201-5599]
Apollo - University of Cambridge Repository
European Bioinformatics Institute [Hinxton] (EMBL-EBI)
EMBL Heidelberg
University of East Anglia [Norwich] (UEA)
Institut des Sciences de l'Evolution de Montpellier (UMR ISEM)
Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)
Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Source :
Genome Research, Genome Research, Cold Spring Harbor Laboratory Press, 2018, 28 (4), pp.448-459. ⟨10.1101/gr.234096.117⟩, Genome Research, 2018, 28 (4), pp.448-459. ⟨10.1101/gr.234096.117⟩
Publication Year :
2018
Publisher :
Cold Spring Harbor Laboratory, 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 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.

Details

ISSN :
10889051 and 15495469
Database :
OpenAIRE
Journal :
Genome Research, Genome Research, Cold Spring Harbor Laboratory Press, 2018, 28 (4), pp.448-459. ⟨10.1101/gr.234096.117⟩, Genome Research, 2018, 28 (4), pp.448-459. ⟨10.1101/gr.234096.117⟩
Accession number :
edsair.doi.dedup.....609fd04d943fa94511f96a605cf6355f
Full Text :
https://doi.org/10.1101/gr.234096.117⟩