Dear EvolDir members, Thank you all for your responses to my request about general eukaryotic 454 primers. I received some very informative answers, and quite a few people have expressed their interest in the question. I attach the three papers suggested by Scott Fay and Simon Creer here. However, for my part, having checked the supposedly "general" primers on alignments of protozoa from the very diverse groups (Ciliates, cercozoans, bodonids, heterokonts), I would say that I am a bit skeptical about generality of the primers in some protozoan groups. But well, lets see - and certainly, there is sufficient variability in this region to enable a satisfactory taxonomic resolution from only 250 bp, let alone 500 bp. I guess I will simply have to give it a try and see how it plays out. Best regards, Christoffer I wrote: I am looking for a set of eukaryote specific 18S (SSU) primers amplifying a fragment about 3-400 bp long (i.e. suitable for 454 sequencing). So far those here (of Stoeck et al.) appear to be the best published ones (of about 250 bp) http://icomm.mbl.edu/microbis/project_pages/details/proposals/APP_propos al.pdf Simon Creer wrote: Hi Christoffer I have checked F04 and R22 for eukaryotes that have meiobenthic representatives - likewise, they span the most variable region for metazoa in 18S. Watch out though, there is a typo in the ME F04 in text primer. Figure is right and cross check with Nat Comms.... 250 bp is too short for Titanium sequencing. Cheers and best Si -- Scott A. Fay wrote: Hi Christoffer, I too have been agonizing a lot over universal Euk primers for 454. As you know, it's a new field. After looking at the sequences myself, I don't think there is a "magic bullet" to capture all of Euk diversity in one primer set. I plan on using the Amaral-Zeller (V9) ones. Can you please let me know what other responses you get? This is a topic that interests me. Warm regards, Scott Christoffer Bugge Harder