De novo assembly of the ancestral Eve for the laboratory mouse reference strain, C57BL/6J. Eve Genome

The Mouse Reference Genome represents the most widely used inbred, laboratory mouse strain, C57BL/6J, from The Jackson Laboratory. While this is one of the best-characterized published genomes, some limitations contribute to increased false positive rates in variant discovery. First, there are 187 and 211 regions reported assembly issues (Genome Reference Consortium Mouse Build 38, patch 5), and the genome does not represent a single individual. Also, the C57BL/6J mice available from the current source colonies at The Jackson Laboratory source are up to 26 inbreeding generations removed from the mouse reference genome. Moreover, the strain is now maintained through the periodic reintroduction of mice from cryopreserved embryo stock, a husbandry practice that is designed to maximize genetic homogeneity by effectively limiting the number of inbreeding generations over time. The embryo stock is derived from a single breeder pair, appropriately named C57BL/6J Adam and Eve. Therefore, to better represent C57BL/6J mice that are currently in use by the research community and to address poorly represented regions in the existing reference genome, we have generated a parallel assembly by performing the whole genome de novo assembly of C57BL/6J Eve with ~60X PacBio single molecule sequencing and optical map data generated from Bionano Genomics platform. Hybrid assembly of genome yielded 12,690 contigs/scaffolds with the N50 size of 1. 29 MB and went under comprehensive annotation using comparative annotation toolkit from UCSC. Using this data, we resolved recurring variants observed in previous mouse studies, identified 60 structural variations of eve genome to GRCm38 and closed 23 gaps in the assembly. With the help of PacBio brain transcriptome (Iso-Seq data) of mouse and assembled B6Eve genome, we were able to identify a deletion of ~640bp deletion in GRCm38 vs B6Eve that removes an exon of the gene Mia3 (Figure3), as well as filling two gaps in GRCm38 that contain exons in the genes Traf5 and Slc26a6 . This B6Eve assembly will provide a handy resource to scientific community working with C57BL6/J mouse in genomics research as well as genetic engineering/mouse model development.