Thursday, May 23, 2019

Readying the release of GRCm39

GRCm38, the current mouse reference assembly, whose chromosomes represent the C57BL/6J strain, supports a broad range of research activities. Despite being one of the highest quality mammalian genome assemblies ever produced, it still has more than 600 gaps and includes sub-optimal representations for some genes. To address these issues and provide the murine research community with an improved substrate for their work, the GRC has been applying new technologies, such as optical/genome mapping, and using new sequence resources to curate an update to the reference genome assembly. The public release of the updated assembly, GRCm39, is planned for the end of 2019/early 2020.

Since the 2012 release of GRCm38, the last coordinate-changing update to the mouse reference, the GRC has provided 6 publicly accessible minor assembly updates, the last of which (GRCm38.p6) was released in September, 2017. These non-coordinate changing assembly versions, known as patch releases, cumulatively include 65 fix patches (chromosome path changes) and 9 novel patches (alternate representations of chromosome sequences, derived from other strains). In GRCm39, these fix patches will be incorporated into the chromosomes, and the novel patches will persist as alternate loci.

In preparation for the release of GRCm39, the GRC also analyzed a non-public updated version of the reference assembly. In the production of this updated assembly, 322 reported genome issues were resolved, 70% of which addressed gaps and problems with the sequence of underlying genomic clone components. The review evaluated the value and impact of the released patches and subsequent unreleased genome updates and assessed the need for additional work prior to the GRCm39 release.

Analyses of this assembly, known informally as "GRCm38B", reveal the removal of about 200 Kb over-expanded sequence found in GRCm38, and the addition of 254 new components, of which 95 are contigs assembled from WGS reads (PRJNA51977). Due to the curation effort, GRCm38B has fewer gaps, and increased contig and scaffold N50s in comparison to GRCm38 (Table 1).

Furthermore, an analysis of mouse RefSeq transcripts aligned to GRCm38B demonstrates the improved representation for at least 50 genes (Table 2).

One such example of improved gene representation in GRCm38B is shown in Figure 1. In GRCm38, an assembly gap at chromosome 4 nt 99,842,111, between components BX324127.8 and CU326395.5, results in a partial representation of Efcab7 (EF-hand calcium binding domain 7). In GRCm38B, sequences from MF597759.1 (a GRC-assembled contig of Illumina reads) closes this gap and provides the exons missing from Efcab7 transcript NM_145549.1.
Figure 1 Top: Incomplete representation of Efcab7 gene in GRCm38 due to an assembly gap. Middle: The gap is closed in GRCm38B with MF597759.1. It also provides complete representation of Efcab7. Bottom: Efcab7-mRNA partial representation in GRCm38 and complete representation in GRCm38B.

Based on GRCm38B analyses, 5 GRCm39 chromosomes will be comprised of a single scaffold (Chr. 11, 12, 15, 16, 18), 11 will be built from 2 scaffolds and the remaining 5 from more than 2 scaffolds.

In the months leading up to the GRCm39 release, the GRC will continue to curate additional genome issues. Sequences from the recently published C57BL/6J long-read based assembly ASM377452v2 are providing new resources for the update or closure of assembly gaps and correction of sequencing errors. Additionally, we are investigating individual bases at which the GRCm38 sequence differs from all 17 strain-specific genome assemblies (Mouse Genome Project) with the aim of correcting confirmed erroneous bases.

Upon the release of GRCm39, the GRC's curation of the mouse genome reference assembly will be limited to the resolution of community reported problems.

You can browse the status of GRC curation activities at our website, and we encourage you to contact the GRC for additional information on the curation of assembly regions of interest. Updates to the timeline for the GRCm39 release will be provided on the Mouse Genome Overview webpage. You can also subscribe to grc-announce email list to receive email notification for all GRC assembly updates .

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