Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Autor: Leo Goodstadt, Mark Gerstein, Mark G. Thomas, Jingtao Lilue, Glen Threadgold, Fengtang Yang, Sarah Pelan, Jane E. Loveland, Kim Wong, Fabio C. P. Navarro, Jennifer Harrow, Ruth Bennett, Richard Durbin, Dent Earl, Monica Abrudan, Mario Stanke, David J. Adams, Adam Frankish, Son Pham, Anne Czechanski, Charles A. Steward, Jonathan Flint, Beiyuan Fu, Ian T. Fiddes, William Chow, Duncan T. Odom, Marcela K. Sjoberg-Herrera, Naomi Park, Paul Flicek, Anne C. Ferguson-Smith, James G. R. Gilbert, Lelliott C, Mikhail Kolmogorov, Mark Diekhans, Laura G. Reinholdt, Stefanie Nachtweide, Cristina Sisu, Thomas M. Keane, James Torrance, Richard Mott, Benedict Paten, Petr Danecek, Dirk-Dominik Dolle, Paul R. Muir, Ximena Ibarra-Soria, Stephan C. Collins, Binnaz Yalcin, Darren W. Logan, Lars Romoth, Matthew Dunn, Lesley Shirley, Kerstin Howe, David Thybert, Michael A. Quail, Clayton E. Mathews, Jonathan Wood, Anthony G. Doran, Joanna Collins, Joel Armstrong
Přispěvatelé: European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of California [Santa Cruz] (UCSC), University of California, The Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute [Cambridge], Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Université Bourgogne Franche-Comté [COMUE] (UBFC), The Jackson Laboratory [Bar Harbor] (JAX), University of Cambridge [UK] (CAM), University of California [Los Angeles] (UCLA), Yale University [New Haven], OxAM House, University of California [San Diego] (UC San Diego), University of Florida [Gainesville] (UF), University College of London [London] (UCL), University of Greifswald, BioTuring Inc., Brunel University London [Uxbridge], Pontificia Universidad Católica de Chile (UC), University of Nottingham, UK (UON), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Centre National de la Recherche Scientifique (CNRS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Lilue, Jingtao [0000-0002-1958-0231], Diekhans, Mark [0000-0002-0430-0989], Flicek, Paul [0000-0002-3897-7955], Gerstein, Mark [0000-0002-9746-3719], Kolmogorov, Mikhail [0000-0002-5489-9045], Lelliott, Chris J [0000-0001-8087-4530], Logan, Darren W [0000-0003-1545-5510], Mott, Richard [0000-0002-1022-9330], Navarro, Fabio CP [0000-0002-5640-9070], Odom, Duncan T [0000-0001-6201-5599], Sjoberg-Herrera, Marcela [0000-0001-7173-048X], Thybert, David [0000-0001-7806-7318], Wong, Kim [0000-0002-0984-1477], Yalcin, Binnaz [0000-0002-1924-6807], Yang, Fengtang [0000-0002-3573-2354], Keane, Thomas M [0000-0001-7532-6898], Apollo - University of Cambridge Repository, University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), Julien, Sabine
Jazyk: angličtina
Rok vydání: 2018
Předmět:
0301 basic medicine
Transposable element
[SDV.IMM] Life Sciences [q-bio]/Immunology
Retrotransposon
Mice
Inbred Strains
[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics
Biology
de novo assembly
Genome
Polymorphism
Single Nucleotide
Article
03 medical and health sciences
Mice
0302 clinical medicine
Species Specificity
Mice
Inbred NOD
Animals
Laboratory
Genetics
Animals
Gene
mouse
Phylogeny
Mice
Inbred BALB C
Mice
Inbred C3H
Strain (biology)
Haplotype
Laboratory mouse
allele
Chromosome Mapping
Molecular Sequence Annotation
Mice
Inbred C57BL
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
030104 developmental biology
Haplotypes
Genetic Loci
Mice
Inbred DBA
Mice
Inbred CBA
[SDV.IMM]Life Sciences [q-bio]/Immunology
subspecies
030217 neurology & neurosurgery
Reference genome
Zdroj: Nature Genetics
Nature Genetics, Nature Publishing Group, 2018, 50 (11), pp.1574-1583. ⟨10.1038/s41588-018-0223-8⟩
Nature Genetics, 2018, 50 (11), pp.1574-1583. ⟨10.1038/s41588-018-0223-8⟩
Nature genetics
ISSN: 1061-4036
1546-1718
DOI: 10.1038/s41588-018-0223-8⟩
Popis: 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. Medical Research Council and the Wellcome Trust
Databáze: OpenAIRE
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