ArticleNature genetics2018
Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.
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Article in Nature genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 170 papers.
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170citing papers in PubMed
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170 citing papers in PubMed.
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- Diverse reference genomes detect variants in the US winter wheat.The plant genome · 2026Article
- High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape.Cell genomics · 2026Article
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- A mouse organoid platform for modeling cerebral cortex development and cis-regulatory evolution in vitro.Developmental cell · 2025Article
- Acquisition of ampliconic sequences marks a selfish mouse t-haplotype.Nature communications · 2025Article
- MoG+3.0: expanded structural variant visualization and integration of genomic data from five newly analyzed mouse strains.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Sex- and strain-differential plasma proteomic signatures in C57BL/6 and BALB/c mice.Scientific reports · 2025Article
- Molecular mechanisms and regulation of inflammasome activation and signaling: sensing of pathogens and damage molecular patterns.Cellular & molecular immunology · 2025Review
- Complete genome assemblies of two mouse subspecies reveal structural diversity of telomeres and centromeres.Nature genetics · 2025Article
110 more citing papers are in PubMed but not listed here.
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Authors and funding
59 authors.
Jingtao LilueEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0002-1958-0231
Anthony G DoranEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Ian T FiddesCenter for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
Monica AbrudanWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Joel ArmstrongCenter for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
Ruth BennettEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
William ChowWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Joanna CollinsWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Stephan CollinsInstitut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, Illkirch, France.
Anne CzechanskiThe Jackson Laboratory, Bar Harbor, ME, USA.
Petr DanecekWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Mark DiekhansCenter for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.ORCID http://orcid.org/0000-0002-0430-0989
Dirk-Dominik DolleWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Matt DunnWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Richard DurbinWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Dent EarlCenter for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
Anne Ferguson-SmithDepartment of Genetics, University of Cambridge, Cambridge, UK.
Paul FlicekEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0002-3897-7955
Jonathan FlintBrain Research Institute, University of California, Los Angeles, CA, USA.
Adam FrankishEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Beiyuan FuWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Mark GersteinYale Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-9746-3719
James GilbertWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Leo GoodstadtOxFORD Asset Management, OxAM House, Oxford, UK.
Jennifer HarrowWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Kerstin HoweWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Ximena Ibarra-SoriaWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Mikhail KolmogorovDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-5489-9045
Chris J LelliottWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.ORCID http://orcid.org/0000-0001-8087-4530
Darren W LoganWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.ORCID http://orcid.org/0000-0003-1545-5510
Jane LovelandEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Clayton E MathewsDepartment of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA.
Richard MottGenetics Institute, University College London, London, UK.ORCID http://orcid.org/0000-0002-1022-9330
Paul MuirYale Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
Stefanie NachtweideInstitute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany.
Fabio C P NavarroYale Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0002-5640-9070
Duncan T OdomCancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, UK.ORCID http://orcid.org/0000-0001-6201-5599
Naomi ParkWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Sarah PelanWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Son K PhamBioTuring Inc., San Diego, CA, USA.
Mike QuailWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Laura ReinholdtThe Jackson Laboratory, Bar Harbor, ME, USA.
Lars RomothInstitute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany.
Lesley ShirleyWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Cristina SisuYale Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
Marcela Sjoberg-HerreraDepartamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.ORCID http://orcid.org/0000-0001-7173-048X
Mario StankeInstitute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany.
Charles StewardWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Mark ThomasWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Glen ThreadgoldWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
David ThybertEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0001-7806-7318
James TorranceWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Kim WongWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.ORCID http://orcid.org/0000-0002-0984-1477
Jonathan WoodWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Binnaz YalcinInstitut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, Illkirch, France.ORCID http://orcid.org/0000-0002-1924-6807
Fengtang YangWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.ORCID http://orcid.org/0000-0002-3573-2354
David J AdamsWellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Benedict PatenCenter for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
Thomas M KeaneEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. tk2@ebi.ac.uk.ORCID http://orcid.org/0000-0001-7532-6898
Funding
The Mutant Mouse Resource and Research Center at The Jackson LaboratoryU42OD010921 · OD · JACKSON LABORATORY · PI LAURA G REINHOLDT · 2012 to 2026
$21.4MGENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MUse for ResourceP40OD011102 · OD · JACKSON LABORATORY · PI Stephen A Murray · 2012 to 2026
$15.0MTraining SubprojectU54HG007990 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI HAUSSLER, DAVID H, PATTERSON, DAVID · 2014 to 2018
$14.8Mmt-Nd2 and Resistance to Autoimmune DiabetesR01DK074656 · NIDDK · UNIVERSITY OF FLORIDA · PI MATHEWS, CLAYTON E · 2006 to 2015
$2.8MCancer Research UK 20412Medical Research Council MR/L007428/1Medical Research Council MR/R017565/1NHGRI NIH HHS U41 HG007234NHGRI NIH HHS U54 HG007990NIDDK NIH HHS R01 DK074656NIH HHS U42 OD010921Wellcome Trust 202878/Z/16/ZWellcome Trust 207492/Z/17/Z
Abstract
We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.
Indexed as
Chromosome MappingGenetic LociGenomeHaplotypesAnimalsAnimals, LaboratoryMiceMice, Inbred BALB CMice, Inbred C3HMice, Inbred C57BLMice, Inbred CBAMice, Inbred DBAMice, Inbred NODMice, Inbred StrainsMolecular Sequence AnnotationPhylogeny
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