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

Jingtao Lilue 1 Anthony Doran 1 Ian Fiddes 2 Monica Abrudan 3 Joel Armstrong 2 Ruth Bennett 1 William Chow 3 Joanna Collins 3 Stephan Collins 4, 5, 6 Anne Czechanski 7 Petr Danecek 3 Mark Diekhans 2 Dirk-Dominik Dolle 3 Matt Dunn 3 Richard Durbin 3 Dent Earl 2 Anne Ferguson-Smith 8 Paul Flicek 1 Jonathan Flint 9 Adam Frankish 1 Beiyuan Fu 3 Mark Gerstein 10 James Gilbert 3 Leo Goodstadt 11 Jennifer Harrow 3 Kerstin Howe 3 Ximena Ibarra-Soria 3 Mikhail Kolmogorov 12 Chris Lelliott 3 Darren Logan 3 Jane Loveland 1 Clayton Mathews 13 Richard Mott 14 Paul Muir 10 Stefanie Nachtweide 15 Fabio Navarro 10 Duncan Odom 8 Naomi Park 3 Sarah Pelan 3 Son Pham 16 Mike Quail 3 Laura Reinholdt 7 Lars Romoth 15 Lesley Shirley 3 Cristina Sisu 17 Marcela Sjoberg-Herrera 18 Mario Stanke 15 Charles Steward 3 Mark Thomas 3 Glen Threadgold 3 David Thybert 1 James Torrance 3 Kim Wong 3 Jonathan Wood 3 Binnaz Yalcin 4 Fengtang Yang 3 David Adams 3 Benedict Paten 2 Thomas Keane 19, 3, *
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.
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https://hal.inrae.fr/hal-03448286
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Jingtao Lilue, Anthony Doran, Ian Fiddes, Monica Abrudan, Joel Armstrong, et al.. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nature Genetics, Nature Publishing Group, 2018, 50 (11), pp.1574-1583. ⟨10.1038/s41588-018-0223-8⟩. ⟨hal-03448286⟩

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