Hello,
First of all, thanks for maintaning PR2, a great resource!
I'm posting here because @Latimeria94 and I noticed some incongruences in the PR2 (v5.1.1) taxonomy of the genera of Vermamoeba and Hartmannella compared to the NCBI taxonomy and Adl et al. (2019, https://doi.org/10.1111/jeu.12691).
In both of those resources, the taxonomic ranks to which these genera belong to are:
- Vermamoeba: Amoebozoa; Tubulinea; Echinamoebida; Vermamoebidae (NCBI link)
- Hartmannella: Amoebozoa; Tubulinea; Elardia; Euamoebida; Hartmannellidae (NCBI link)
In PR2 both genera are under "Amoebozoa; Tubulinea, Tubulinea_X; Elardia; Euamoebida; Vermamoebidae".
This PR2 clade includes both the species Vermamoeba vermiformis, as well as _Hartmannella vermiformis.
This PR2 clade contains other species in the Hartmanella genus which have not been subject to such a reclassification, as well as Vermamoeba spp. and Hartmanella spp.
V. vermiformis_ was initially called H. vermiformis based on phenotypical characteristics, but it was later reclassified under a new genus (in a distinct clade, as reflected by NCBI) based on 18S phylogeny (https://doi.org/10.1007/s00248-018-1199-8).
We compared the PR2 sequences belonging to H. vermiformis and V. vermiformis and Vermamoeba spp. and Hartmanella spp. we noticed that they are highly similar. The similarity of the sequences within a species (excluding self-hits) is the same as the one between genera. The unclassified species show a small drop in similarity across genera, but they are still pretty similar.
V. vermiformis vs H. vermiformis
Vermamoeba spp. vs Hartmannella spp.
I noticed that the sequences from my experiment are classified as Hartmannella, but upon Manual inspection they seem very similar to the ones belonging to V. vermiformis. For H. vermiformis I think I can easily rename them, but I have doubts on what to do with the Harmannella spp. found in my dataset.
Do you have some suggestions for my taxonomic assignment?
Thanks
Hello,
First of all, thanks for maintaning PR2, a great resource!
I'm posting here because @Latimeria94 and I noticed some incongruences in the PR2 (v5.1.1) taxonomy of the genera of Vermamoeba and Hartmannella compared to the NCBI taxonomy and Adl et al. (2019, https://doi.org/10.1111/jeu.12691).
In both of those resources, the taxonomic ranks to which these genera belong to are:
In PR2 both genera are under "Amoebozoa; Tubulinea, Tubulinea_X; Elardia; Euamoebida; Vermamoebidae".
This PR2 clade includes both the species Vermamoeba vermiformis, as well as _Hartmannella vermiformis.
This PR2 clade contains other species in the Hartmanella genus which have not been subject to such a reclassification, as well as Vermamoeba spp. and Hartmanella spp.
V. vermiformis_ was initially called H. vermiformis based on phenotypical characteristics, but it was later reclassified under a new genus (in a distinct clade, as reflected by NCBI) based on 18S phylogeny (https://doi.org/10.1007/s00248-018-1199-8).
We compared the PR2 sequences belonging to H. vermiformis and V. vermiformis and Vermamoeba spp. and Hartmanella spp. we noticed that they are highly similar. The similarity of the sequences within a species (excluding self-hits) is the same as the one between genera. The unclassified species show a small drop in similarity across genera, but they are still pretty similar.
V. vermiformis vs H. vermiformis
Vermamoeba spp. vs Hartmannella spp.
I noticed that the sequences from my experiment are classified as Hartmannella, but upon Manual inspection they seem very similar to the ones belonging to V. vermiformis. For H. vermiformis I think I can easily rename them, but I have doubts on what to do with the Harmannella spp. found in my dataset.
Do you have some suggestions for my taxonomic assignment?
Thanks