I'm wondering if my unusual sequencing design seems ok to you.
I will sequence one male and one female (no biological replicates) in ~50 species of one animal taxa.
My only goal is to see general differential expression between the male condition and the female condition in this taxa, then compare the male/female difference between 2 groups of species (by example, 25 species with a strong sexual dimorphism vs 25 species without important sexual dimorphism).
I know that biological replicates are important, but here some species are difficult to obtain and I prefer to spend money on more species than more replicates of the same species. Here, the "biological replicates" would be the 50 males and the 50 females of different species. I know that it is unusual, but I believe that it can be an interesting approach to get a general pattern.
Does it seem a valid opinion to you?
Which strategy could be the best to achieve the analyses?
I though to do classical differential expression analyses without replicates on each species, then compare for each 1-1 ortholog genes the p-value of the 25 species (high sexual dimorphism) vs the p-values of the 25 other species (low sexual dimorphism).
Thanks for your feedback.