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dc.contributor.authorThybert, David
dc.contributor.authorRoller, Maša
dc.contributor.authorNavarro, Fábio CP
dc.contributor.authorFiddes, Ian
dc.contributor.authorStreeter, Ian
dc.contributor.authorFeig, Christine
dc.contributor.authorMartin-Galvez, David
dc.contributor.authorKolmogorov, Mikhail
dc.contributor.authorJanoušek, Václav
dc.contributor.authorAkanni, Wasiu
dc.contributor.authorAken, Bronwen
dc.contributor.authorAldridge, Sarah
dc.contributor.authorChakrapani, Varshith
dc.contributor.authorChow, William
dc.contributor.authorClarke, Laura
dc.contributor.authorCummins, Carla
dc.contributor.authorDoran, Anthony
dc.contributor.authorDunn, Matthew
dc.contributor.authorGoodstadt, Leo
dc.contributor.authorHowe, Kerstin
dc.contributor.authorHowell, Matthew
dc.contributor.authorJosselin, Ambre-Aurore
dc.contributor.authorKarn, Robert C
dc.contributor.authorLaukaitis, Christina M
dc.contributor.authorJingtao, Lilue
dc.contributor.authorMartin, Fergal
dc.contributor.authorMuffato, Matthieu
dc.contributor.authorNachtweide, Stefanie
dc.contributor.authorQuail, Michael A
dc.contributor.authorSisu, Cristina
dc.contributor.authorStanke, Mario
dc.contributor.authorStefflova, Klara
dc.contributor.authorVan Oosterhout, Cock
dc.contributor.authorVeyrunes, Frederic
dc.contributor.authorWard, Ben
dc.contributor.authorYang, Fengtang
dc.contributor.authorYazdanifar, Golbahar
dc.contributor.authorZadissa, Amonida
dc.contributor.authorAdams, David J
dc.contributor.authorBrazma, Alvis
dc.contributor.authorGerstein, Mark
dc.contributor.authorPaten, Benedict
dc.contributor.authorPham, Son
dc.contributor.authorKeane, Thomas M
dc.contributor.authorOdom, Duncan
dc.contributor.authorFlicek, Paul
dc.date.accessioned2018-09-08T06:33:59Z
dc.date.available2018-09-08T06:33:59Z
dc.date.issued2018-04
dc.identifier.issn1088-9051
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/279898
dc.description.abstractUnderstanding 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.
dc.format.mediumPrint-Electronic
dc.languageeng
dc.publisherCold Spring Harbor Laboratory
dc.rightsAttribution 4.0 International (CC BY 4.0)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectChromosomes
dc.subjectAnimals
dc.subjectMuridae
dc.subjectMice
dc.subjectRetroelements
dc.subjectKaryotyping
dc.subjectEvolution, Molecular
dc.subjectPhylogeny
dc.subjectSpecies Specificity
dc.subjectBinding Sites
dc.subjectLong Interspersed Nucleotide Elements
dc.subjectGenome
dc.subjectCCCTC-Binding Factor
dc.titleRepeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.
dc.typeArticle
prism.endingPage459
prism.issueIdentifier4
prism.publicationDate2018
prism.publicationNameGenome Res
prism.startingPage448
prism.volume28
dc.identifier.doi10.17863/CAM.27266
dcterms.dateAccepted2018-03-05
rioxxterms.versionofrecord10.1101/gr.234096.117
rioxxterms.licenseref.urihttp://www.rioxx.net/licenses/all-rights-reserved
rioxxterms.licenseref.startdate2018-04
dc.contributor.orcidFeig, Christine [0000-0003-1385-7049]
dc.contributor.orcidOdom, Duncan [0000-0001-6201-5599]
dc.identifier.eissn1549-5469
rioxxterms.typeJournal Article/Review
pubs.funder-project-idCancer Research UK (C14303/A17197)
pubs.funder-project-idEuropean Research Council (615584)
pubs.funder-project-idCancer Research UK (20412)
pubs.funder-project-idWellcome Trust (202878/Z/16/Z)
cam.issuedOnline2018-03-21


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Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's licence is described as Attribution 4.0 International (CC BY 4.0)