Bacterium named "Apis mellifera" with no SILVA information

[hyanwong]

This is presumably some sort of honeybee symbiont, but when I click on the SILVA link on the taxonomy info sidebar, it says "No sequences with an accession number matching "HP459622" were found in our databases."

================================================ Metadata	Do not edit below this line
Author	Yan Wong
Upvotes	0
URL	https://tree.opentreeoflife.org/opentree/argus/opentree13.4@ott5900566/Apis-mellifera
Target node label	Apis mellifera
Synthetic tree id	opentree13.4
Synthetic tree node id	ott5900566
Source tree id(s)
Open Tree Taxonomy id
Supporting reference	N/A

[jar398]

SILVA probably redoes its whole process with each version. That means that some sequences will be reclassified (because NCBI reclassified them), some will fail their QC process (which is probably improved with each version), and so on. So this behavior could be because Open Tree is based on a non-current version of SILVA.

One fix might be to move OTT to the latest SILVA. Another would be to suppress this taxon in a patch, or move it to wherever it belongs.

[hyanwong]

Another SILVA misplaced name is Oncorhynchus mykiss (rainbow trout, https://tree.opentreeoflife.org/opentree/argus/ottol@165368), which is also present with a different OTT in the bacteria (https://tree.opentreeoflife.org/opentree/argus/ottol@5256670) - weirdly, this tip doesn't appear in search hits though.

[hyanwong]

And another one:https://tree.opentreeoflife.org/opentree/argus/ottol@5901391, which is not a bacterial bumblebee!

[mtholder]

this and many more examples will be fixed by https://github.com/OpenTreeOfLife/edOTTs/commit/34d1090debc636663a82f609c1131ba34e871551