Population genomics of Sinorhizobium medicae
Last week, the November issue of The ISME Journal arrived in my pigeon hole. I mean a real paper copy of the journal. In this electronic age, I rarely see a paper issue of a journal, but I receive ISMEJ because I am on the editorial board. The distinction between publication on paper and publication online can be significant: the articles in this issue had already been published online six months ago.
This issue was of special interest to us because we have a paper in it (reference below). What is more, the editors selected ours as one of the special papers that are listed on the front cover and can be viewed free of charge by all readers, not just those with a subscription. You really have no excuse not to read and cite this one! We like to celebrate our publications, so Friday afternoon was time to open a bottle. Our rule is that the cost of the bottle should reflect the Impact Factor of the journal, so it was a good bottle this time.
Most of the authors have now left York, since it took us a long time to finish the paper. In fact, the original proposal for this NERC-funded project was to use comparative genomic hybridisation on microarrays to compare the accessory gene content of a large number of rhizobial strains. The two postdocs, Xavier Bailly and Elisa Giuntini, both had relevant expertise, so they set to work to isolate a set of strains that would be a suitable population sample. By the time the isolates were ready, though, the technical revolution of Next-Generation Sequencing was upon us. Xavier worked out that if we spent the microarray funds on randomly sequencing part of the genome of each isolate using the 454 sequencing platform, we would get more data and much better data. No doubt Xavier also worked out that this would mean far less lab work for Elisa and himself! This new paper reports the result of our first tentative step into high-thoughput sequencing. We had 39 isolates of Sinorhizobium medicae, but for the first run we randomly picked 12 of them. Even though the sequence coverage was really low, we still got much more informative data than we could have had from microarrays, so the trial was a success. The isolates were not very diverse, though, so we decided that it was not really interesting to sequence the rest of them. Instead, we turned to another rhizobium species, Rhizobium leguminosarum, that was isolated from the same patch of ground. This time we sequenced many more isolates and got much fuller data. The strains were much more diverse and interesting – but it will be a little while yet before we publish that story.
An undergraduate project student, Connor Sexton, made a significant contribution to the S. medicae project under Elisa’s guidance. He confirmed some of the 454 data and extended the study to the whole set of strains. The S. medicae strains showed differences in whether they had certain accessory genes that came and went together, as though they were carried together on a plasmid. The strains were also unusual in that they all had a set of genes that look very much as though they encode the enzymes for synthesis of rhizobitoxine. Rhizobitoxine is an interesting compound that has the potential to increase a strain’s competitiveness for nodulation by inhibiting the plant’s production of ethylene, which is a hormone that decreases nodule formation. Until now, the only rhizobia known to produce rhizobitoxine were some strains of Bradyrhizobium, so it is tantalising to think that Sinorhizobium may also use this strategy. We don’t have proof yet, but we’re working on it.
Xavier did a lot of the detailed calculations that went into the paper, but three other authors, Ryan, Peter and Nitin, were dedicated bioinformaticians and also contributed to the final product. If you are going to generate high-thoughput data, it is very important to have a good team of bioinformaticians!
Bailly X, Giuntini E, Sexton MC, Lower RPJ, Harrison PW, Kumar N, Young JPW (2011) Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates. ISME Journal 5, 1722-1734.