Rhizobium leguminosarum 11

 

Genospecies B

 

We are still working our way through the previously described genospecies of the Rlc, and have reached gsB. Here is the part of the phylogeny that includes this genospecies.

 

 

In the centre is a tight clade on a long branch with a large number of strains that are definitely gsB. At the top are two strains, WSM1455 and WSM1481, that are the sister group of this clade, and it is not immediately clear whether we should include them within gsB or keep them separate. Let’s call them clade J. At the bottom is a clade of six strains whose relationship to gsB is not very close, or very certain, so probably need to be considered a new genospecies, but we’ll call them clade K for now. We need ANI values to help us with these decisions. Here are ANI values using strain 3841 as reference.

 

The core of gsB is very tight – all above 98% ANI. The pair of strains in clade J, WSM1481 and WSM 1455, have ANI of 95.99 and 95.96, right on the 96% boundary, so there is no clear verdict on whether to include them in gsB or not. Strains in clade K have ANI between 95.05 and 95.61, which could be used to justify a separate genospecies.

 

Taking WSM1455 as the reference for clade J, WSM1481 has an ANI of 98.69, core gsB strains range from 95.78 to 96.06, clade K from 95.11 to 95.61. Again, we see that clade J is right at the boundary of gsB. My instinct is to exclude this clade from gsB, because the core gsB strains form such a tight cluster that they probably share many genospecies-specific characters that clade J strains do not have. For now, I will treat clade J as a new genospecies, gsJ.

 

For clade K, I took FA23 (first to be sequenced, sv. phaseoli) as the reference. The four JHI strains in clade K have ANI between 97.37 and 98.37, but for Vaf12 the value is just 95.68, lower than for some core gsB strains. This suggests that we should consider clade K as a new genospecies, gsK, but exclude Vaf12, which stands by itself.

 

Thus we have representatives of four potential genospecies in the phylogenetic clade that we are considering: gsB, gsJ, gsK and strain Vaf12. I am not going to give genospecies names if there is only a single representative. These strains already have a name, so little is gained by giving them an extra one.

 

The gsB strains are closely related, but they have been isolated in numerous different projects and places. The SM strains in gsB are all sv. trifolii from one site in western England. Strain 22B is also sv. trifolii, but from Russia. I think all the other strains are sv. viciae. The JHI strains (from the James Hutton Institute) are from the UK, especially Scotland, while the strains contributed by Stéphane Boivin and Marc Lepetit, with complicated names like RSP1E6, are from various countries in continental Europe. Then there are a couple of CCBAU strains from China. Finally, there are two strains that have supported important genetic studies for very many years.  VF39 is  from Germany, and 3841 is the strain from eastern England that has served as the R. leguminosarum reference genome since we published the sequence in 2006.

 

Here are lists of the strains we have been discussing, ranked by ANI similarity to 3841. Potential type strains are in bold.

 

gsB

R._leguminosarum_3841.fna

R._leguminosarum_JHI960.fna

R._leguminosarum_JHI963.fna

R._leguminosarum_SM30_gsB.fna

R._leguminosarum_SM35_gsB.fna

R._leguminosarum_SM37_gsB.fna

R._leguminosarum_SM40_gsB.fna

R._leguminosarum_SM24_gsB.fna

R._leguminosarum_SM31_gsB.fna

R._leguminosarum_SM10_gsB.fna

R._leguminosarum_SM38_gsB.fna

R._leguminosarum_SM39_gsB.fna

R._leguminosarum_SM20_gsB.fna

R._leguminosarum_SM5_gsB.fna

R._leguminosarum_SM6_gsB.fna

R._leguminosarum_SM21_gsB.fna

R._leguminosarum_SM15_gsB.fna

R._leguminosarum_SM27_gsB.fna

R._leguminosarum_SM14_gsB.fna

R._leguminosarum_SM16_gsB.fna

R._leguminosarum_SM18_gsB.fna

R._leguminosarum_SM22_gsB.fna

R._leguminosarum_SM25_gsB.fna

R._leguminosarum_SM19_gsB.fna

R._leguminosarum_JHI974.fna

R._leguminosarum_JHI973.fna

R._leguminosarum_SM13_gsB.fna

R._leguminosarum_SM34_gsB.fna

R._leguminosarum_SM3_gsB.fna

R._leguminosarum_SPF4F3.fna

R._leguminosarum_JHI1600.fna

R._leguminosarum_JHI1587.fna

R._leguminosarum_P1NP2H.fna

R._leguminosarum_RSF2G1.fna

R._leguminosarum_SM36_gsB.fna

R._leguminosarum_JHI535.fna

R._leguminosarum_JHI585.fna

R._leguminosarum_P1NP1J.fna

R._leguminosarum_SM11_gsB.fna

R._leguminosarum_JHI1415.fna

R._leguminosarum_SM7_gsB.fna

R._leguminosarum_SM4_gsB.fna

R._leguminosarum_JHI13.fna

R._leguminosarum_VF39.fna

R._leguminosarum_SM12_gsB.fna

R._leguminosarum_SM32_gsB.fna

R._leguminosarum_SM9_gsB.fna

R._leguminosarum_SM17_gsB.fna

R._leguminosarum_22B.fna

R._leguminosarum_RSP1E6.fna

R._leguminosarum_P1NP2K.fna

R._leguminosarum_CCBAU65264.fna

R._leguminosarum_CCBAU03058.fna

 

gsJ

R._leguminosarum_WSM1481.fna

R._leguminosarum_WSM1455.fna

 

gsK

R._leguminosarum_JHI10.fna

R._leguminosarum_FA23.fna

R._leguminosarum_JHI2450.fna

R._leguminosarum_JHI2451.fna

R._leguminosarum_JHI54.fna

 

unique

R._leguminosarum_Vaf12.fna