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

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.

journal_name

Nat Genet

journal_title

Nature genetics

authors

Lilue J,Doran AG,Fiddes IT,Abrudan M,Armstrong J,Bennett R,Chow W,Collins J,Collins S,Czechanski A,Danecek P,Diekhans M,Dolle DD,Dunn M,Durbin R,Earl D,Ferguson-Smith A,Flicek P,Flint J,Frankish A,Fu B,Gerstein

doi

10.1038/s41588-018-0223-8

subject

Has Abstract

pub_date

2018-11-01 00:00:00

pages

1574-1583

issue

11

eissn

1061-4036

issn

1546-1718

pii

10.1038/s41588-018-0223-8

journal_volume

50

pub_type

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