Differential expression between two different species tomato and pepper

Question

[Amior]

Hey fellow researchers!

I'm currently diving into a comparative gene expression analysis between two species: tomatoes and peppers. I've realized that to make meaningful comparisons, I need to create a common annotation file that bridges the gap between these two species. Has anyone here tackled a similar challenge before? Do you have any insights on how I can go about creating this common annotation file effectively?

Any tips, tools, or strategies that you've found helpful?

Thanks a bunch in advance for your help!