Document Type

Article

Publication Date

6-2019

Keywords

JGM, JMG

JAX Source

G3 (Bethesda) 2019 Jun; 9:1795-1805

Volume

9

Issue

6

First Page

1795

Last Page

1805

ISSN

2160-1836

PMID

30996023

DOI

https://doi.org/10.1534/g3.119.400071

Grant

OD02135, CA034196

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.

Comments

We are grateful to the services provided by The Jackson Laboratory Genome Technologies and Computational Sciences Core.

This open access article is licensed under a Creative Commons Attribution 4.0 International License.

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