This is a great suggestion. Thank you for this.
I've added one additional step, which is to merge the FeatureData[Taxonomy] associated with my OTUs with the FeatureData[Taxonomy] associated with the reference database:
qiime feature-table merge-taxa --i-data rep_seqs_mitofish_blast_taxonomy.qza 12S-tax-derep-uniq.qza --o-merged-data rep_seqs_mitofish_blast_taxonomy_12S-tax-derep-uniq.qza
I couldn't find a way to filter the FeatureData[Taxonomy] artifact of the reference database (12S-tax-derep-uniq.qza) prior to merging. I did find this post on the topic.
However, in the end it doesn't seem to matter because I am importing the tree, feature-table, and taxonomy into a phyloseq object in R to draw a tree with the plot_tree function. And according to phyloseq documentation: "OTUs and samples are included in the combined object only if they are present in all components. For instance, extra “leaves” on the tree will be trimmed off when that tree is added to a phyloseq object."
If you have any suggestions on how to circumvent this problem, I'd love to know. The end goal is to draw a phylogenetic tree of my OTUs that contains some reference sequences (with taxonomic labels or accession numbers for reference sequences).