If I have a hybrid yeast strain sequenced, is it okay to use saccer3 as reference sequence for mapping?

Question

[ptlrushabh]

what should I use as reference sequence if I have a hybrid strain of yeast cells?

[grant.hovhannisyan]

Do you know the parentals?

[ptlrushabh]

W303 x SK1 75% SK1 25% w303

Answer 1

[Carambakaracho]

That depends on what your hybrid is. I used to annotate the S. cerevisiae part with the better curated SGD reference S288c R64-2-1 (saccer3 is based on R64-1-1). I'd recommend to annotate the other part with whatever reference suits better, typically you can distinguish both relatively easy.

[ptlrushabh]

W303 x SK1 75% SK1 25% w303

[Carambakaracho]

Ah, well I thought you mean a hybrid as in S. pastorianus (hybrid between S. cerevisiae and S. eubayanus)

With W303 and SK1, from a bioinformatic point of view (at least from the annotation angle) you still have a pure yeast. Except that there are assemblies for those out there. Did you look into the W303 and SK1 genome annotations on SGD or at the NCBI?

Note not everybody on this forum has a yeast background and can decipher strain or assembly names like S288c, Saccer3, W303, or SK1. I recommend you put more effort into your questions in the future