Rhizobium leguminosarum 18

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Last week, I asked my reader(s) for comments on what I had done so far, and ideas for further analysis. So far, I have received no response. Zero. It seems that nobody else is interested in defining the Rlc, and all my readers have deserted me. It may be a single-author publication, after all.

 

There are some small tasks that I will need help with, such as providing the country of origin and isolation host for every strain – something that the people who submitted the genomes are best placed to do. I have created a Google Sheet here that you can add the information to. If that doesn’t work, or demands that you create a Google account, just let me know and I will email you the file. Suggestions for more sophisticated analyses are also welcome.

 

Meanwhile, I have refined the list of genomes to incorporate the new ones and eliminate duplicates and erroneous genomes that do not correspond to the strain. That leaves 440 genomes altogether: 429 are Rlc and 11 in the R. anhuiense outgroup. I have repeated the analyses using this final set. I used the colours defined by Cavassim et al. 2020 (https://doi.org/10.1099/mgen.0.000351) for genospecies A to E, and chose colours for the 13 new genospecies. I worked out how to get the ANI plot in the same order as the phylogeny, and to add keys for the genospecies colours. Here are the results.

 

 

 

 

 

Fig: Phylogeny based on 120 core genes.

 

Fig: Pairwise ANI values for all genomes in the Rlc and R. anhuiense, showing genospecies assignment.

 

 

 

 

 

Fig: ANI values, as in previous figure, but showing values > 96% in black, 95-96% in grey.