SILVA: why is chloroplast defined as bacteria?



Hi everyone,

I’m using SILVA for my analysis and I’m getting chloroplast reads which is to be expected from my sample.
But what I don’t get is why it falls under bacteria? I can see how cyanobacteria (phylum) falls under bacteria (domain). But I don’t get how chloroplast (class) falls under cyanobacteria? Is this an error in SILVA’s classification?

Bacteria; Cyanobacteria; Chloroplast;

I would think it should be:
Eukaryota; Plantae; Chloroplast;


(Nicholas Bokulich) #2

Great question! See here:


Ah, I see thanks! Does that mean 16S sequences from one plant cell can map to both eukaryota and bacteria simultaneously? Phylogenetically, is a plant a eukaryota, a prokaryote or both? That might be more of a philosophical question.

(Nicholas Bokulich) #4

Correct. Mitochondria will also map to bacteria:

Philosophical indeed. Phylogenetically it would be considered a plant. But philosophically I suppose we might say both.