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G3 (Bethesda). 2019 Jun 5;9(6):1795-1805. doi: 10.1534/g3.119.400071.

The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain.

Author information

1
The Jackson Laboratory for Mammalian Genetics, Bar Harbor ME.
2
UC Santa Cruz Genomics Institute, Santa Cruz, California, Department of Biomolecular Engineering, University of California, Santa Cruz, California.
3
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894.
4
Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
5
NanoString Technologies, Inc, and.
6
The Jackson Laboratory for Genomic Medicine, Farmington, CT.
7
The Jackson Laboratory for Genomic Medicine, Farmington, CT laura.reinholdt@jax.org anuj.srivastava@jax.org.
8
The Jackson Laboratory for Mammalian Genetics, Bar Harbor ME laura.reinholdt@jax.org anuj.srivastava@jax.org.

Abstract

Isogenic laboratory mouse strains enhance reproducibility because individual animals are genetically identical. For the most widely used isogenic strain, C57BL/6, there exists a wealth of genetic, phenotypic, and genomic data, including a high-quality reference genome (GRCm38.p6). Now 20 years after the first release of the mouse reference genome, C57BL/6J mice are at least 26 inbreeding generations removed from GRCm38 and the strain is now maintained with periodic reintroduction of cryorecovered mice derived from a single breeder pair, aptly named Adam and Eve. To provide an update to the mouse reference genome that more accurately represents the genome of today's C57BL/6J mice, we took advantage of long read, short read, and optical mapping technologies to generate a de novo assembly of the C57BL/6J Eve genome (B6Eve). Using these data, we have addressed recurring variants observed in previous mouse genomic studies. We have also identified structural variations, closed gaps in the mouse reference assembly, and revealed previously unannotated coding sequences. This B6Eve assembly explains discrepant observations that have been associated with GRCm38-based analyses, and will inform a reference genome that is more representative of the C57BL/6J mice that are in use today.

KEYWORDS:

C57BL/6J; Mus musculus domesticus; de novo genome assembly; laboratory mouse; long read sequencing; reference genomes; reproducibility

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