Rhizobium leguminosarum 13

The F-clade – Rhizobium laguerreae and its relatives

Here is the clade that is the sister group to gsB and its relatives, which were considered in an earlier post (Rhizobium leguminosarum 11).

 

When we first defined genospecies A to E (Kumar et al. 2015 http://dx.doi.org/10.1098/rsob.140133), we noted three genomes already in GenBank that were related to gsB but not close enough to be included in it (Table S3 in Kumar et al.). Strains TOM and UPM1131 were closely related, but 248 was far enough from these to be another genospecies, distinct from them and from gsB. In the recent paper by Boivin et al. (2020, https://doi.org/10.1111/nph.16392), we named these new groups gsF-1 and gsF-2, respectively and included some more strains. One of those in gsF-2 was FB206, the type strain of R. laguerreae, so at least part of gsF-2 is R. laguerreae. The question is, how far does this genospecies extend, and how many other genospecies are there in this “F cluster”? We can see from the phylogeny that the cluster now includes many genomes, but is indeed split into two clades, F-1 at the top and F-2 at the bottom. I have labelled some of the subclades within these so that I can refer to them.

 

Here is an ANI plot (just for F-clade strains) using strain BIHB 1148 as the standard. I chose this strain because it is reasonably central in the F-1 clade and it has a fully assembled genome.

 

There are 14 strains with ANI above 96% (above 97%, in fact), and they are exactly clade N. There is a large drop in ANI beyond that, so clade N looks like a good genospecies.

Next, I took JHI2449 as a representative of clade O. I chose this strain because it is on a short branch, so should have fewer unique substitutions. All members of clade O have ANI of 96.30 or above, while the next closest is Vaf-108 at 95.96, followed by members of clade N. Vaf-10 is way down the list at rank 37, so we can’t amalgamate clades O and P, and should consider clade O as a potential genospecies. The two Vaf strains have ANI of 96.24, so we can also treat clade P as a genospecies.

 

In the F-2 part of the tree, I took strain 248 to represent clade Q. There are two assemblies of 248 in the phylogeny, and you can see that they are close but not exactly identical (I have not explored the reason for the difference). The later one is fully assembled, so that is the one I used. All strains in clade Q have ANI of 96.09 or above, then there is a noticeable gap before strain CL8 at 95.60, so Q seems coherent enough to be a genospecies.

Clade R looks a tight group in the phylogeny, and includes FB206, the type strain of R. laguerreae, so we must use that as the reference.

 

All clade R strains have ANI of 98.16 or above, and there is then a massive gap before SPF2A11 (96.72), HP3 (96.71) and CCBAU10279 (96.54). There is then another gap before WSM1689 (95.90). This is slightly awkward because we have already assigned SPF2A11 and HP3 to gsQ. In fact, they have ANI > 96 to the reference strains of both clade Q and clade R, though their ANIs with FB206 (just quoted) are actually rather higher than with strain 248 (96.09 and 96.13, respectively). On the other hand, the phylogeny places them firmly with Q, so we will leave them there for now. One could consider CCBAU10279 to be an outlying member of gsR, but I prefer to keep it separate because the R clade is very tight and its members presumably share a lot of similarities that CCBAU10279 will not have. WSM1689 does not have an ANI above 96 with any other genome, though its closest relatives are in clade R, so is also not placed in a genospecies for now. 

 

WSM1689 is also unusual in being sv. trifolii. I think it may be the only strain in the F-clade that is not sv. viciae, though I have not checked them all.

 

Since it is clear that the F-clade includes several genospecies, I have not used “F” as the name of any of them, as this might lead to confusion. We have now split it into putative genospecies N, O, P, Q and R (= R. laguerreae), plus two unplaced strains. Here are the strain lists.

 

gsN

R._leguminosarum_BIHB_1148_GCF_002240185.1.fna

R._leguminosarum_CCBAU83268_GCF_012276475.1.fna

R._leguminosarum_TOM_GCF_000372205.1.fna

R._leguminosarum_L143_GCF_012276245.1.fna

R._leguminosarum_FRF1D12_GCF_004330655.1.fna

R._leguminosarum_RSP1F10_GCF_004330075.1.fna

R._leguminosarum_FWPou38_GCF_013391705.1.fna

R._leguminosarum_FWPou32_GCF_013391665.1.fna

R._leguminosarum_FWPou15_GCF_013391685.1.fna

R._leguminosarum_RSF1B9_GCF_004330175.1.fna

R._leguminosarum_RSP1F2_GCF_004330005.1.fna

R._sp._PEPV16_PEPV16_GCF_008919455.1.fna

R._leguminosarum_L141_GCF_012276275.1.fna

R._leguminosarum_RSP1A1_GCF_004330105.1.fna

 

gsO

R._laguerreae_JHI2449_GCF_010668165.1.fna

R._leguminosarum_L361_GCF_012276075.1.fna

R._leguminosarum_L563_GCF_012276025.1.fna

R._leguminosarum_L231_GCF_012276175.1.fna

R._leguminosarum_L364_GCF_012276085.1.fna

R._leguminosarum_L244_GCF_012276155.1.fna

R._leguminosarum_UPM1131_GCF_000427945.1.fna

R._leguminosarum_L411_GCF_012275615.1.fna

 

gsP

R._leguminosarum_Vaf10_GCF_001679785.1.fna

R._leguminosarum_Vaf-108_GCF_001890425.1.fna

 

gsQ

R._leguminosarum_248_GCF_010365265.1.fna

R._leguminosarum_L241_GCF_012276195.1.fna

R._leguminosarum_L353_GCF_012276115.1.fna

R._leguminosarum_L144_GCF_012276225.1.fna

R._leguminosarum_GLR17_GCF_012276335.1.fna

R._leguminosarum_GLR2_GCF_012276355.1.fna

R._laguerreae_HP3_GCF_012276365.1.fna

R._laguerreae_SPF2A11_GCF_004329805.1.fna

 

gsR = R. laguerreae

R._laguerreae_FB206_GCF_002008165.1.fna

R._laguerreae_SP4_GCF_012275785.1.fna

R._laguerreae_OL29_GCF_012275995.1.fna

R._laguerreae_FB403_GCF_004346285.1.fna

R._laguerreae_SL16_GCF_012275885.1.fna

R._laguerreae_SPF4F7_GCF_004329795.1.fna

R._laguerreae_SPF2F4_GCF_004329785.1.fna

R._laguerreae_SP15_GCF_012275855.1.fna

R._laguerreae_HUTR05_GCF_013004195.1.fna

R._laguerreae_OS25_GCF_012276015.1.fna

R._laguerreae_CL8_GCF_012276455.1.fna

R._laguerreae_SS21_GCF_012275795.1.fna

 

unique

R._laguerreae_CCBAU10279_GCF_012276585.1.fna

R._leguminosarum_WSM1689_GCF_000517605.1.fna