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

D. Thybert, M. Roller, FCP. Navarro, I. Fiddes, I. Streeter, C. Feig, D. Martin-Galvez, M. Kolmogorov, V. Janoušek, W. Akanni, B. Aken, S. Aldridge, V. Chakrapani, W. Chow, L. Clarke, C. Cummins, A. Doran, M. Dunn, L. Goodstadt, K. Howe, M....

. 2018 ; 28 (4) : 448-459. [pub] 20180321

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc19000858
E-zdroje Online Plný text

NLK Free Medical Journals od 1991 do Před 6 měsíci
Freely Accessible Science Journals od 1991-08-01 do Před 1 rokem
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Europe PubMed Central od 1997 do Před 6 měsíci
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Open Access Digital Library od 1991-08-01

Odkazy

PubMed 29563166
DOI 10.1101/gr.234096.117
Knihovny.cz E-zdroje

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.

Bioturing Inc San Diego California 92121 USA

Department of Biomolecular Engineering University of California Santa Cruz California 95064 USA

Department of Computer Science and Engineering University of California San Diego La Jolla California 92092 USA

Department of Medicine College of Medicine University of Arizona Tuscon Arizona 85724 USA

Department of Zoology Faculty of Science Charles University Prague 128 44 Prague Czech Republic

Earlham Institute Norwich Research Park Norwich NR4 7UH United Kingdom

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Earlham Institute Norwich Research Park Norwich NR4 7UH United Kingdom

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom Wellcome Sanger Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SA United Kingdom

Institut des Sciences de l'Evolution de Montpellier Université Montpellier CNRS 34095 Montpellier France

Institute of Mathematics and Computer Science University of Greifswald Greifswald 17487 Germany

School of Environmental Sciences University of East Anglia Norwich Research Park Norwich NR4 7TJ United Kingdom

University of Cambridge Cancer Research UK Cambridge Institute Robinson Way Cambridge CB2 0RE United Kingdom

University of Cambridge Cancer Research UK Cambridge Institute Robinson Way Cambridge CB2 0RE United Kingdom Wellcome Sanger Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SA United Kingdom

Wellcome Sanger Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SA United Kingdom

Wellcome Trust Centre for Human Genetics Oxford OX3 7BN United Kingdom

Yale University Medical School Computational Biology and Bioinformatics Program New Haven Connecticut 06520 USA

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