Multi-species RNA-seq comparsion

Question

[weather]

Hi. I currently have five different species exposed to the same conditions (toxin) and would like to do a species comparison for molecular response.

Just wondering if there are any ways to do a multi-species RNA-seq comparison, especially for the functional (pathway) analysis.

Answer 1

[Matthias Zepper]

I have never done a similar thing, but I would start with quantifying gene expression for each species separately against a reference transcriptome for that species. This assumes that there is a well annotated reference available for each of your five species. Then call the differentially expressed genes versus the untreated controls for the same species.

Once you have individually determined the transcriptional response to toxin exposure for each species, you can use reference databases of orthology relationships or respective tools to establish the interspecies similarities and differences. That would be the unbiased approach.

If you have some prior knowledge about the toxin in question, e.g. about its metabolism, targets and damage patterns, you can screen specifically for the implicated enyzmes and signalling proteins (e.g. those implicated in relevant metabolic pathways, apoptosis, DNA damage repair).