Dear PR2 maintainers,
@Latimeria94 and I found another potential discrepancy in PR2 (v5.1.1) regarding taxonomy and phylogeny of Cyanidiales.
In short, while analyzing our data we noticed a high prevalence of Cyanidiales, which, given our knowledge of our environment of interest, surprised us. We then compared our suspect Cyanidiales ASVs with the data in NCBI and found high similarity with Angulamoeba sequences.
We then compared our ASVs with 18S sequences from both Cyanidiales and Angulamoeba and noticed how except for one 18S sequence (HM161754.1.1870) all our ASVs do not cluster with the rest of the Cyanidiales families (confirming our initial gut feeling).
The taxonomic assignment was likely caused by the similarity of our ASVs with sequence HM161754.1.1870. However, our tree shows how this sequence is in a different clade from the other Cyanidiales genera (Cyanidium,Cyanidiococcus), as well as with another strain technically from the same genus (Cyanidioschyzon merolae strain 10D).
The source of HM161754.1.1870 is a paper in which this sequence is only compared briefly to other sequences without any further analyses (10.1128/AEM.05371-11).
We thus think that this is a misannotated sequence and wanted to bring this to your attention.
Thanks again for maintaining PR2 and making it such a great resource for the community!
Best,
Dear PR2 maintainers,
@Latimeria94 and I found another potential discrepancy in PR2 (v5.1.1) regarding taxonomy and phylogeny of Cyanidiales.
In short, while analyzing our data we noticed a high prevalence of Cyanidiales, which, given our knowledge of our environment of interest, surprised us. We then compared our suspect Cyanidiales ASVs with the data in NCBI and found high similarity with Angulamoeba sequences.
We then compared our ASVs with 18S sequences from both Cyanidiales and Angulamoeba and noticed how except for one 18S sequence (HM161754.1.1870) all our ASVs do not cluster with the rest of the Cyanidiales families (confirming our initial gut feeling).
The taxonomic assignment was likely caused by the similarity of our ASVs with sequence HM161754.1.1870. However, our tree shows how this sequence is in a different clade from the other Cyanidiales genera (Cyanidium,Cyanidiococcus), as well as with another strain technically from the same genus (Cyanidioschyzon merolae strain 10D).
The source of HM161754.1.1870 is a paper in which this sequence is only compared briefly to other sequences without any further analyses (10.1128/AEM.05371-11).
We thus think that this is a misannotated sequence and wanted to bring this to your attention.
Thanks again for maintaining PR2 and making it such a great resource for the community!
Best,