elsamdea:
When I extracted the taxonomy file of my samples, I found Eukaryote domain in it. This make no sensed, because as far as I know, the 16S rRNA gene codifies the 16S rRNA small subunit of prokaryotic ribosomal (Archaea and Bacteria domains). In Eukaryote is the 18S rRNA gene.
Hi @elsamdea ,
Silva has two reference databases, the Small Sub-unit (SSU; 16S & 18S) and the Large Sub-unit (LSU; 23S & 28S). The reasons are outlined in the following posts:
Remember the SILVA SSU contains not only Bacterial, Acrachaeal, and Eukaryal 16S rRNA gene sequences, but also contains the Eukaryal 18S rRNA gene sequences too (which are longer). That is, the 18S rRNA gene is a cystolic homologue of the 16S rRNA gene.
-Mike
Hi @Tiago_Bruno_Rezende , welcome to reduce alignment ambiguity . So, we honor the reality of the rRNA molecule when using this secondary structure information to inform our alignment. Also, it is easy enough to simple replace these when needed.
-Mike