Rhizobium leguminosarum 14

The F-clade was the last large group that we need to consider, but there are a number of small clades left over that we need to look at before we have finished our dissection of the Rlc.

 

Genospecies I – Rhizobium indicum

 

Here is the sister group to the gsB+gsJ+gsK+F-clade grouping:

 

 

There are five strains here, but two of them have two genome versions that I have included just to check that they agree.

Strain JKLM12A2 has recently been designated the type strain of a new species, R. indicum (Rahi et al. 2020 https://doi.org/10.1016/j.syapm.2020.126127), with JKLM13E as another member of the species. It is clear that the three WYCCWR strains in this clade also belong to this species, because their minimum ANI with JKLM12A2 is  97.91%. The next highest ANI values in the Rlc are Vaf12 at 95.15 (unique strain) and JHI2450 at 95.14 (gsK), both related to gsB (see Rhizobium leguminosarum 11), so R. indicum is well separated from other genospecies.

 

Genospecies G – Rhizobium sophorae

 

This is the next group out - the sister clade to gsI and its sister:

 

CCBAU03386 is the type strain of R. sophorae (Jiao et al. 1015 https://doi.org/10.1099/ijs.0.068916-0), and the other two CCBAU strains definitely belong to this species (ANI at least 98.66). On the other hand the ANI values for WYCCWR11279 (95.55) and WYCCWR11290 (95.50) are considerably below the level of 96% or above that we have consistently seen as a natural breakpoint in genospecies with more representatives, so I think we should consider these two strains as a separate genospecies, gsS. That leaves Tri-43, which has no close affinity to anything else. Its highest ANI is 94.82 with WYCCWR11146, in R. indicum.

 

WYCCWR 10014

 

I have looked through the entire phylogeny of the Rlc, and I can only find one strain that we have not yet discussed. WYCCWR10014 is all by itself as the sister taxon to the whole clade that we have just been considering (gsB+gsJ+gsK+F-clade+gsI+gsG+gsS). Its highest ANI is with strains in gsB and gsK, but these do not exceed 94.47.

 

So here is the cast list for today’s production:

 

gsI = R. indicum

R._sp._JKLM12A2_JKLM12A2_GCF_005862305.2.fna

R._sp._WYCCWR_11152_WYCCWR_11152_GCF_013087615.1.fna

R._sp._WYCCWR_11128_WYCCWR_11128_GCF_013416305.1.fna

R._sp._JKLM13E_JKLM13E_GCF_005860925.2.fna

R._sp._WYCCWR_11146_WYCCWR_11146_GCA_013591995.1.fna

 

gsG = R. sophorae

R._sophorae_CCBAU_03386_GCF_013087515.1.fna

R._leguminosarum_CCBAU33195_GCF_012276535.1.fna

R._leguminosarum_CCBAU11080_GCF_012276545.1.fna

 

gsS

R._sp._WYCCWR_11279_WYCCWR_11279_GCF_013087625.1.fna

R._sp._WYCCWR_11290_WYCCWR_11290_GCF_013426945.1.fna

 

unique

R._leguminosarum_Tri-43_GCF_004123835.1.fna

R._sp._WYCCWR10014_WYCCWR10014_GCF_001657485.1.fna

 

Unless something has slipped through the net, I think that completes the first stage of the analysis – we have considered all the genomes that fall within the Rlc and classified them into groups that we are tentatively considering as possible genospecies. Next, I’ll try to present an overview of the findings.