Reconcile reference transcriptome with reference genome from different labs with different naming schemes

Question

[thomas.welch]

I am not quite sure what kind of category or tags this question should fall under, so I hope people won't mind me leaving them quite vague.

I am currently trying to find a way of using a pipeline for the detection of R-genes (https://github.com/AndolfoG/HRP#1) on the Oak genome. However, unfortunately this pipeline works in a way that requires both a reference genome and reference proteome sequence encoded by the same gene set. A reference proteome is not currently available for Oak.

Now I could generate my own reference proteome using TransDecoder (https://github.com/TransDecoder/TransDecoder/wiki) from a reference transcriptome. But this reference transcriptome was created by another lab and is thus annotated differently. So proteins and genes would have different names.

Is there a way I could reconcile the reference genome and a reference proteome generated from a reference transcriptome created by another lab. Or do they both have to be under the same annotation/ naming scheme from the start? which would make this impossible.

[GenoMax]

Can you provide the scientific name of exact Oak species you are referring?

[thomas.welch]

Quercus robur. The reference genome I have always used is the one created by Plomion et al. (https://www.oakgenome.fr/?page_id=587). And the highly comprehensive reference transcriptome I could generate the proteome from is the OakContigDF159.1 hybrid assembly (https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.12317)

Answer 1

[GenoMax]

NCBI has a genome version that should be all in sync: https://www.ncbi.nlm.nih.gov/genome/?term=Quercus+robur

You can find the genome, transcriptome and protein sequences all in one spot. Perhaps you could use this version?

[thomas.welch]

Thank you very much for your help. I'll give this a try.