Rhizobium leguminosarum 10

Genospecies A

Here is the part of the tree that includes genospecies A.

 

 The majority of the strains are SM strains isolated by Sara Moeskjær in our NCHAIN project, and we already know that these are gsA (Cavassim et al. 2020, https://doi.org/10.1099/mgen.0.000351). The question is how many of the other strains should be included in the genospecies. What about WSM78? What about that clade of five strains at the top? ANI can help us to answer these questions. Here is a plot of ANI for the Rlc, using CC275e as the reference.

 

There is a large gap in the ANI values between WSM78 (96.44) and SRDI943 (94.74), so WSM78 is definitely in gsA and the other five strains are definitely out. It is clear that they form a new genospecies – let’s call it genospecies H and make WSM1325 the reference strain, since this was one of the earliest Rlc strains to be sequenced and has a finished genome sequence. I haven’t calculated ANI within gsH, but it is obvious from the phylogeny that the strains are highly similar and the values are going to be high.

 

One interesting observation about gsA is that all the genome sequences available so far are of symbiovar trifolii. All the SM strains in gsA were from white clover in Denmark. CC275e was isolated in Australia from white clover, 9B in Russia (red clover), T88 in Colombia (red clover), and WSM78 in Australia (unspecified host, but it has a trifolii nodD sequence).

 

Here is a list of the strains in gsA:

R._leguminosarum_CC275e.fna

R._leguminosarum_SM138A_gsA.fna

R._leguminosarum_SM145C_gsA.fna

R._leguminosarum_SM140B_gsA.fna

R._leguminosarum_SM128A_gsA.fna

R._leguminosarum_SM128B_gsA.fna

R._leguminosarum_SM131_gsA.fna

R._leguminosarum_9B.fna

R._leguminosarum_SM146A_gsA.fna

R._leguminosarum_SM123_gsA.fna

R._leguminosarum_SM154A_gsA.fna

R._leguminosarum_SM154B_gsA.fna

R._leguminosarum_SM151B_gsA.fna

R._leguminosarum_SM151A_gsA.fna

R._leguminosarum_SM163B_gsA.fna

R._leguminosarum_SM138B_gsA.fna

R._leguminosarum_SM152A_gsA.fna

R._leguminosarum_SM154C_gsA.fna

R._leguminosarum_SM144B_gsA.fna

R._leguminosarum_SM137B_gsA.fna

R._leguminosarum_SM152B_gsA.fna

R._leguminosarum_SM152C_gsA.fna

R._leguminosarum_SM155B_gsA.fna

R._leguminosarum_SM130B_gsA.fna

R._leguminosarum_SM155A_gsA.fna

R._leguminosarum_SM144A_gsA.fna

R._leguminosarum_SM136A_gsA.fna

R._leguminosarum_SM163A_gsA.fna

R._leguminosarum_SM145A_gsA.fna

R._leguminosarum_SM155C_gsA.fna

R._leguminosarum_SM146B_gsA.fna

R._leguminosarum_SM140A_gsA.fna

R._leguminosarum_SM145B_gsA.fna

R._leguminosarum_SM130A_gsA.fna

R._leguminosarum_WSM78.fna

 

Here are the strains in gsH:

R._leguminosarum_SRDI943.fna

R._leguminosarum_WSM1325.fna

R._leguminosarum_CB2179.fna

R._leguminosarum_WSM1328.fna

R._leguminosarum_WSM409.fna