There’s recently a type change on Agrobacterium tumefaciens, after Judicial Opinion 127. The new type strain is ATCC 4720, with a genome in GCA_011684035.1.
The current synonymization with A. fabacearum is somewhat expected as mentioned in the JO. The main issue here is that most members currently in s__Agrobacterium tumefaciens are probably going to be moved over to Agrobacterium radiobacter… if its type strain can have a passable assembly, that is. (GCF_963360635.1 seems fine)
I also raised the issue at NCBI, so maybe nothing will need to be manually done.
Hi,
Thank you for bringing this to our attention. We are actively working on the next release of GTDB. Unfortunately, GCA_011684035.1 will not be a GTDB representative genome in this next release since it wasn’t designated as type material at the time species dereplication was performed. GCA_011684035.1 is in a species cluster represented by genome GCA_009649785.1 (CNPSo 675), the type strain of Agrobacterium fabacearum. Given the similarity of CNPSo 675 and ATCC 4720 this clustering is in agreement with GTDB generally using a 95% ANI criterion for delineating species. I have flagged this with a nomenclature expert (Maria Chuvochina), but I believe A. tumerfaciens has naming priority and we can reflect this in the name of this species cluster even if the selected GTDB representative will necessarily be GCA_009649785.1 in the next GTDB release.
Thanks,
Donovan
I’m looking at the current (r226) pages for
ATCC 4720 had been marked as type strain of species as requested, but like you’ve said it’s still not the selected GTDB representative. That’s fine.
The main issue here is that B6 (= ATCC 23308) is still marked as a type strain of A. tumefaciens. It’s not after JO 127 has been applied. This incorrect mark causes the species cluster to be called “tumefaciens” instead of “radiobacter” (the cluster includes DSM 31047, the type strain for radiobacter). To fix it the mark on B6 needs to be removed. The result I’m hoping for is:
- s__Agrobacterium tumefaciens becomes s__Agrobacterium radiobacter
- s__Agrobacterium tumefaciens_J becomes s__Agrobacterium tumefaciens
A smaller issue is that currently ATCC 4720 and B6 are both marked as “type strain of genus”. JO 127 also makes the synonymization between tumefaciens and radiobacter to be invalid. This means that tumefaciens should not be considered the type species of Agrobacterium any more, and the true “type strain of genus” would be DSM 31047.
Hi Mingye,
I’m on leave until the end of the month, but will explore this issue in detail when I am back. It does seem like this situation continues to break our automated methods and escape the validation checks we are performing. Thank you for flagging this situation again.
Cheers,
Donovan
Hi Mingye,
I took a deeper look into this situation. The issue arises since the A. tumefaciens B6 strain was still consider to be type material at LPSN at the time we pulled this data for GTDB R226. I believe this situation should resolve itself in the next release, though I have flagged it for manual inspection.
Thanks again for flagging this situation.
Cheers,
Donovan