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

被引：147

作者：

Lilue, Jingtao ^{[1
,2
]}

Doran, Anthony G. ^{[1
,2
]}

Fiddes, Ian T. ^{[3
]}

Abrudan, Monica ^{[2
]}

Armstrong, Joel ^{[3
]}

Bennett, Ruth ^{[1
]}

Chow, William ^{[2
]}

Collins, Joanna ^{[2
]}

Collins, Stephan ^{[4
,5
]}

Czechanski, Anne ^{[6
]}

Danecek, Petr ^{[2
]}

Diekhans, Mark ^{[3
]}

Dolle, Dirk-Dominik ^{[2
]}

Dunn, Matt ^{[2
]}

Durbin, Richard ^{[2
,7
]}

Earl, Dent ^{[3
]}

Ferguson-Smith, Anne ^{[7
]}

Flicek, Paul ^{[1
,2
]}

Flint, Jonathan ^{[8
]}

Frankish, Adam ^{[1
,2
]}

Fu, Beiyuan ^{[2
]}

Gerstein, Mark ^{[9
]}

Gilbert, James ^{[2
]}

Goodstadt, Leo ^{[10
]}

Harrow, Jennifer ^{[2
]}

Howe, Kerstin ^{[2
]}

Ibarra-Soria, Ximena ^{[2
]}

Kolmogorov, Mikhail ^{[11
]}

Lelliott, Chris J. ^{[2
]}

Logan, Darren W. ^{[2
]}

Loveland, Jane ^{[1
,2
]}

Mathews, Clayton E. ^{[12
]}

Mott, Richard ^{[13
]}

Muir, Paul ^{[9
]}

Nachtweide, Stefanie ^{[14
]}

Navarro, Fabio C. P. ^{[9
]}

Odom, Duncan T. ^{[15
,16
]}

Park, Naomi ^{[2
]}

Pelan, Sarah ^{[2
]}

Pham, Son K. ^{[17
]}

Quail, Mike ^{[2
]}

Reinholdt, Laura ^{[6
]}

Romoth, Lars ^{[14
]}

Shirley, Lesley ^{[2
]}

Sisu, Cristina ^{[9
,18
]}

Sjoberg-Herrera, Marcela ^{[19
]}

Stanke, Mario ^{[14
]}

Steward, Charles ^{[2
]}

Thomas, Mark ^{[2
]}

Threadgold, Glen ^{[2
]}

机构：

[1] European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge, England

[2] Wellcome Sanger Inst, Wellcome Genome Campus, Hinxton, England

[3] Univ Calif Santa Cruz, Ctr Biomol Sci & Engn, Santa Cruz, CA 95064 USA

[4] Univ Strasbourg, Ctr Natl Rech Sci UMR7104, Inst Natl Sante & Rech Med U964, Inst Genet & Biol Mol & Cellulaire, Illkirch Graffenstaden, France

[5] Univ Bourgogne Franche Comte, Ctr Sci Gout & Alimentat, Dijon, France

[6] Jackson Lab, 600 Main St, Bar Harbor, ME 04609 USA

[7] Univ Cambridge, Dept Genet, Cambridge, England

[8] Univ Calif Los Angeles, Brain Res Inst, Los Angeles, CA 90024 USA

[9] Yale Univ, Yale Computat Biol & Bioinformat, New Haven, CT USA

[10] OxFORD Asset Management, OxAM House, Oxford, England

[11] Univ Calif San Diego, Dept Comp Sci & Engn, La Jolla, CA 92093 USA

[12] Univ Florida, Dept Pathol Immunol & Lab Med, Gainesville, FL USA

[13] UCL, Genet Inst, London, England

[14] Univ Greifswald, Inst Math & Comp Sci, Greifswald, Germany

[15] Univ Cambridge, Canc Res UK Cambridge Inst, Robinson Way, Cambridge, England

[16] German Canc Res Ctr, Div Signaling & Funct Genom, Heidelberg, Germany

[17] BioTuring Inc, San Diego, CA USA

[18] Brunel Univ London, Dept Biosci, Uxbridge, Middx, England

[19] Pontificia Univ Catolica Chile, Fac Ciencias Biol, Dept Biol Celular & Mol, Santiago, Chile

[20] Earlham Inst, Norwich Res Pk, Norwich, Norfolk, England

[21] Univ Nottingham, Sch Life Sci, Nottingham, England

来源：

NATURE GENETICS | 2018年 / 50卷 / 11期

基金：

欧洲研究理事会; 英国生物技术与生命科学研究理事会; 英国惠康基金; 英国医学研究理事会;

关键词：

COLLABORATIVE CROSS; GENETIC-ANALYSIS; NK CELLS; MICE; EXPRESSION; SUSCEPTIBILITY; IDENTIFICATION; INFLAMMASOMES; ANNOTATION; RESISTANCE;

D O I：

10.1038/s41588-018-0223-8

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：1574 / +

页数：12

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