I would like to alert you to an anomaly that I have come across in the GTDB taxon s__Rhizobium sophorae. In the current public release 05-RS95 (17th July 2020), the representative is GCA_002008155.1. This purported to be the sequence of CCBAU 03386, the type strain of R. sophorae, but it did not match the 16S of this species and appeared to belong to a strain of R. sophoriradicis. This sequence has now been suppressed by NCBI, and an alternative sequence of R. sophorae CCBAU 03386 is available as GCF_013087515.1. This seems to be the genuine article and should be the type of s__Rhizobium sophorae. Meanwhile, the genome of the type strain of R. sophoriradicis is available as GCF_003939025.1 and could be the basis for a taxon s__Rhizobium sophoriradicis. At the moment, this species is erroneously considered to be a synonym of s__Rhizobium sophorae.
Hi Peter. Thank you for bringing this to our attention. In line with the updates at NCBI, I can confirm that in the next GTDB release, which should be available in the next month or two, the GTDB representative of R. sophorae will be GCF_013087515.1 and R. sophoriradicis will be GCF_003939025.1.
Thanks for the confirmation. I enjoyed your contribution to the UnCode Workshop last week. GTDB is currently my favourite resource for a consistent phylogeny-based taxonomy. I particularly like that it includes all available genomes, not just type strains, as this makes it clear where new names are needed.