Question: Aligning scaffolds to reference genome of a related species
gravatar for thjnant
4.4 years ago by
thjnant90 wrote:


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.

assembly • 2.5k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 4.4 years ago by thjnant90
gravatar for Istvan Albert
4.4 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k wrote:

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. 

ADD COMMENTlink written 4.4 years ago by Istvan Albert ♦♦ 79k
gravatar for Lucas Mitsuo Taniguti
4.2 years ago by
Brazil/Piracicaba/University of São Paulo
Lucas Mitsuo Taniguti0 wrote:

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.

ADD COMMENTlink written 4.2 years ago by Lucas Mitsuo Taniguti0
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