Coordinate Correspondences Between Mouse Reference Genome And Sanger Mouse Genomes

Question

[Sakti]

Hello fellow BioStars!

I've ben working for a time now using the CastEi and 129S5 sequences generated by the Mouse Genomes Project from the Sanger.

Something I've always wished for is to have a correspondence between the coordinates of the reference genome (C57Bl6) and these genomes, as it is useful for making quick table comparisons and computing other info. However, I do't seem to think on a way to perform this task, or if it has already been done.

Any ideas?? I'd appreciate very much all your comments.

Cheers!

[David Quigley]

I'm confused. Sanger generated reads, which were mapped onto the C57BL/6 genome using MAQ. You can try to assemble your own complete CastEi genome, but I don't think it's a good idea since the indels aren't as reliable and it would be hard to map genome coordinates between assemblies. What's wrong with using the C57BL/6 coordinates as a standard reference? That's what I'm doing in a similar project at the moment.

[Sakti]

Thanks both for your replies. My issue is that, for example, if I call with seqIO to obtain a region from one chromosome in C57Bl6, and if I use the same command for CastEi genomes, it gives me different sequences. I think I whould then just use the BAM files for this operations.

[David Quigley]

You would get different sequences in CaseEi and C57 for a given region because the castaneous genome isn't the same as C57.

[Jorge Amigo]

I'm not in mouse as David seems to be, but what I understood when I read about the mouse genomes project was that they sequenced different mouse strains as if they were sequencing different mouse populations, but since all strains are from the same organism Mus Musculus they were all mapped to the same reference NCBIM37, hence the genome coordinates should be directly comparable. I'm not writing this as an answer since, as I said, I'm not an expert on mouse, but I really hope this point that David first arose would help you to realize all the potential information you already have in your hands.

Answer 1

[deanna.church]

I assume you are referring to the sequence described here: http://www.sanger.ac.uk/resources/mouse/genomes/ If that is the case, there are no assembly coordinates for the non-C56BL/6J genomes because this project has not produced assemblies for the strains they sequenced. You are correct that because of structural variation, the length of a chromosome in CastEI genomes will not be the the same as the length of a C57BL/6J chromosome (you can see the latest update for this assembly here: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/index.shtml

The only assembly coordinates (that is chromosome coordinates) currently available for mouse are those of the reference assembly (GRCm38, although the Sanger project used MGSCv37 for their alignments). The primary assembly for the reference is based on C57BL/6J. There are a few finished sequences available for other strains- but these only represent small regions of the genome. The only other mouse assembly available that attempted to produce chromosome level assemblies was the assembly produced by Celera Genomics (http://www.ncbi.nlm.nih.gov/genome/assembly/2608/) but this was a mixed strain assembly that was predominantly C57BL/6J.

You cannot get assembly coordinates for any other mouse strains currently.

Answer 2

[Sakti]

Thanks guys, yes, I was checking that. It would be nice though to have a table where to check for a certain region in C57Bl6 then what would be the homologous region in another mouse genome, but it'd be quite problematic to deal with duplications and other repeats. Thanks David Quigley, Jorge Amigo, and Deanna Church :) I keep learning more and more!!

[David Quigley]

Hope this was helpful. The format of this website is if you are just commenting on an answer, use the "comment" link rather than adding a new answer to the bottom of the list. Thanks.

[deanna.church]

I agree that it would be nice to have a table that lists the homologous regions between strains, but this will not be possible until we have complete assemblies for other strains.