If you grind up a human being, they say, and extract DNA from the whole thing and nextgen-sequence it, you get 85% bacterial reads. As some of our colleagues know very well, if you sequence DNA from a diatome algae culture you get 85% bacterial reads. So when sequencing wholesale Epischura, guts and all, we were fully expecting to get a metagenome (rather, metatranscriptome). It’s a very interesting task of its own, the metagenomics (metagovnomics as some of my Russian colleagues call it), but it’s not what we wanted in this case. Fortunately, the partial transcriptome we obtained consists mostly of the right sequences. Vast majority of ORFs that could be identified to a phylum have been identified to Arthropods; of those that could be identified to an order – to Copepods, sensum latum (two leftmost bars on the bottom histogram).
As expected, more sequences have a closer hit in Drosophila or other insects than in Daphnia.