Mapping Gene Models Back to a Reference Genome of Closely Related Species

Question

[gtasource]

I have about ~50,000 gene models from an unannotated species, that I am looking to map back to a reference genome of a closely related one. The issue I keep running into when I am BLASTing the gene models to the reference genome is that multiple gene models are going to the same gene. I want to use some type of mapper (bowtie, gmap, ect), but that can potentially address this redundancy issue. Perhaps, if 3 gene models map to the same gene, only return the closest related match. Or, is there a way to see if these gene models are overlapping at all? Just trying to figure out the best course of action.

Cheers!

Answer 1

[Vitis]

Could you check whether the multiple gene models mapping to the same gene are just different transcript (alternatively transcribed) forms from the same gene? I image because you're mapping to a closely related species, you probably don't have a reference for your transcripts/gene models, and you probably got them from de novo assemblies of transcriptomes. I'd suggest to do a more rigorous clean-up of your assembled transcriptomes, with a process similar as EST clustering. Then I'd suggest to use gmap or BLAT to anchor them to the closely related species. This could also be tricky, as a lot of parameters are dependent on how closely they are related phylogenetically.