I am using the PR2 database to assign taxonomy to my samples, and as I understand it, the “Division” rank is equivalent to the “Phylum” rank used by other databases. However, I see that the assignments at the “Subdivision” level correspond more closely to what other databases call a Phylum. This is giving me incorrect classifications.
Hi @Laura_R,
Taxonomic ranks and naming conventions can vary quite a bit. Not only between the groups of organisms under study, but between the organizations and societies that curate the taxonomy for those organisms / databases. These taxonomic labels are often used interchangeably, at least coerced into using similar nomenclatural rules for ease of use. This often occurs within larger databases to help keep things comparable within themselves. Also, there may be a lack of expertise for certain groups of organisms, which can result in a mismatch of taxonomy and ranks... This all generates a lot of confusion, but this is what happens when there are different societies that preside of the the naming of various groups of taxa. 
That being said, taxonomy curation is necessary, but is quite difficult and often under appreciated.
My general understanding is:
- Phylum == Division
- Phylum is often use for animals, bacteria, archaea. Sometimes protists and fungi .
- Division (Phylum) is often used for plants, sometimes protists and fungi.
- SubPhylum == SubDivision.
I think the reason that you sometimes see one naming system over another for protists, has to do with the fact that there are animal-like, plant-like, and fungal-like protists. Ultimately it is up to the curators on which nomenclatural rules they choose for their database.
Anyway, I view the labels like this:
- domain : domain
- supergroup : supergroup
- division : phylum
- subdivision : subphylum
- class : class
- order : order
- family : family
- genus : genus
- species : species
Note: "supergroup " was added to help unite microbial and macroscopic eukaryotes.
The taxonomic classifications you are observing for your sequences are derived from the PR2 database itself (here is their description, along with some caveats). As I alluded to earlier, when a database is constructed, the curators often have to make decisions about the consistency of taxonomic labels used for each specific rank they'd like to include. So, your classifications are "correct" relative to the reference database you are using. Generally speaking, I often trust specialist taxonomy databases over general ones. So, I might lean towards the PR2 taxonomy for protists over another generalized database.
If you'd like to know more about the myriad details that go into taxonomic curation, and the various organizations that maintain these disparate rules of nomenclature, I'd highly recommend reading NCBI Taxonomy: a comprehensive update on curation, resources and tools.. Also, eukaryotic taxonomy is messy and always evolving. Check out: Evaluating Support for the Current Classification of Eukaryotic Diversity.
I hope this helps. 
2 Likes