16S from eukariota plastid

I’m new Mothur user.

I will analyze reads from our Miseq experiment with Mothur. We are studying photosynthetic marine eukariota so amplicons will be 16S from plastid but and I’m not sure about the reference alignment to use.
Reference alignment for 16S is usually from bacteria sequences, however this gene structure is conserved but not identical between bacteria and eukaria (e.g. V6 is lost in eukariota).
What reference alignment can you suggest for my dataset?

thanks in advance

You will likely have to make your own database as the number of Chloroplast sequences in the silva.bacteria.fasta and RDP files is pretty small. I would look to those files for examples of what they should look like. For what it’s worth, “eukariota” should be spelled “eukarya” or “eukaryota” or “eukaryote”.