I have three transcriptome assemblies representing two different tissues from three different species within the same genus. Each transcriptome assembly consists of three biological replicates (two tissues from each individual, so six RNA-seq libraries per transcriptome assembly). I have Salmon generated TPM values across all three assemblies for each RNA-seq library.
One of these species has an ecological trait that the other two species have, but to a much lesser extent, and it's hypothesized that this ecological trait in sp.1 is attributed to a novel protein found only in this genus and is highly expressed within the aforementioned tissues (we already know it's highly expressed for sp. 1). When I look at the TPM value for this transcript in sp.1, it is among the top 10 most highly expressed transcripts (which we predicted), however, the TPM values for this transcript in the other two species is much lower (which we also predicted).
Is it okay to directly compare TPM values for the same transcript across three different transcriptome assemblies from three different species? Can I infer that this transcript is more highly expressed in sp.1 relative to the other two species? I cannot find any literature or posts in regard to this, if you can point me to any resources, PLEASE DO.