Aligning scaffolds to reference genome of a related species

Question

[thjnant]

Hello,

I have aligned an unannotated genome assembly which consists only of scaffolds to the reference genome of a closely related species using LASTZ.

The stange result that I have obtained is that I see that a given scaffold from my genome assemly gets mapped to several chromosomes of the reference, for example, scaffold71 gets mapped, to different positions, of chromosomes 1, 2, 3, 14, 15, Z (avian sex chromosome).

My reference is hard repeat masked, my genome assembly is not if that could be the problem.

What could be the reason of such results and how could one go about it to solve this issue?

Thank you very much in advance.

Answer 1

[Istvan Albert]

AFAIK only the target needs to be masked when one uses a query the information on repeats is not usually not present.

If you get alignments then it means that the sequence aligned to those locations, the mere presence of a duplicated sequence does not necessarily mean that it will be found by repeat masking, nor does aligning to two location mean that those locations are identical between them.

Finally there may be nothing to solve here, there is nothing inherently wrong having a scaffold aligning to multiple locations of your genome.

Answer 2

[Lucas Mitsuo Taniguti]

I agree with Istvan, probably it's ok your scaffold match with different chromosomes.

What is the size of some of your sequences with this kind of behavior? I recently worked with a fungal genome and observed that there was a region of ~6kb repeated in almost all chromosomes (in some of them just 3kb aligned), I don't know how it is in birds, maybe it can be a larger region.

I would suggest you to check the genes present in your 'problematic' scaffolds, some of than can provide clues, like the presence of proteins related to sub-telomeric regions (e.g. helicases) or to centromeric (centromeric histones).

I know it was 10 weeks ago, but hope it can help you.