I am trying to do a differential expression analysis to identify potential targets of interest in Bdelloidae species. I am working with RNA-Seq data of Philodina sp. however there is not much available sequence information for this genus. However Adineta (a different order) has a published information on ensembl. My plan, at this moment, is to compare the expression levels of my data to that of published Adineta.
I have mapped my data (Philodina) to the Adineta reference available on ensembl using salmon. However the mapping rate of my samples to the Adineta reference were consistently >10%. Additionally, I also mapped similarly divergent published RNA Bdelloidae data (from Rotaria, a third order) and had similar mapping rates to that of my samples.
Is this to be expect with the mapping of diverged species? Although the mapping rates of my samples are very low, can my salmon output still be used?