Population genomics of Rhizobium leguminosarum
I am following up my last post with some slightly more technical comments about our new paper. Firstly, here is the full reference, and a link that I hope will work better:
Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. 2015 Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol. 5: 140133.
For those interested in Rhizobium, the first point is that, although we only looked in one square metre, we found five genetic clusters within our R. leguminosarum population that were sufficiently distinct in sequence that each could be described as a new species. Furthermore, these genospecies, and a small number of others, can also be identified in locations around the world. All of these fall within R. leguminosarum as presently defined, and are definitely more similar to each other than to related species such as R. pisi, R. fabae, R. phaseoli or R. etli. On the other hand, the recently described R. laguerreae seems much closer, though it is not possible to match it with any one of these genospecies on the basis of the very limited sequence information that is currently available for it. At the moment, our five genospecies have no distinguishing phenotypic features, so traditional taxonomists are unlikely to let us describe them as formal species. I wouldn’t want to, anyway – it would just create unnecessary complications for people who wanted to use R. leguminosarum to do some real science.
Another interesting point is that a large part of the extrachromosomal genome seems to have little mobility between the genospecies. This is not just true of the two chromids (chromosome-like plasmids) that are homologous to pRL12 and pRL11, but also of the genes that occur on the smaller pRL10 and pRL9. Incidentally, a search for the repABC genes reveals that all 72 isolates have replicons equivalent to pRL12 and pRL11, and nearly all have one like pRL10. The other replicons of strain 3841 are relatively rare in our population, though all of them are found. Much more frequent is the replicon of the pR132503 plasmid of strain WSM 1325. This information on plasmids is not in the paper – it comes from an extensive analysis in the PhD thesis of Nayoung Kim, who has now returned to a bioinformatics job in Korea.
A study of 72 genome sequences is bound to reveal a lot of things, and there are plenty more points I would like to draw to your attention, but I will save them for future posts.