Mouse T2T and reference genomes update

Dear mouse colleagues,

I’m writing to provide a brief update on the new mouse reference genomes and also to ask for you opinion.

My group has been working through the pandemic on creating the next version of the inbred strain reference genomes using the latest long read sequencing technologies. We are nearing completion of 17 strain high quality genomes - comparable to GRCm39 in terms of sequence content, gene content, gaps, and strain specific haplotype representation. These annotated genomes should be fully released later this year.

Now for the question to the community: Some of you may have heard of the first telomere-to-telomere complete human genome that was produced last year for CHM13, and is rapidly being followed by many more population specific T2T references. The current mouse reference (GRCm39) is far from being a T2T genome, having hundreds of remaining gaps and many whole incomplete loci (e.g. PAR). I’ve started plans to create the first mouse T2T complete genome, and I want to ask your opinion on which strain(s) would be of most value to the community. My current thoughts would be B6J and CAST/EiJ, but can imagine there might be other opinions (e.g. B6J and DBA/2J).

Hope to see many of you at the next IMGC meeting, even if only virtually!