Tom,
No answer here, but I'm in a similar boat and was waiting to see if anyone had an answer to your question. I've got a mustard that is 85-90% similar in nucleotide sequences of coding regions to Arabidopsis thaliana. I think I'll need to assemble de novo, then tBlastx my contigs to the Arabidopsis unigenes. Has anyone tried this for transcriptomes of non-model (but close to model) systems?
Justen
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