Last year, I had the pleasure to host (now Dr.) Nadia Andreani from the University of Padua in Italy for a six-month visit in 2015. She did lab work on blue, food-spoiling Pseudomonas but we also did a population genomics meta-analysis, together with BioSciences/ESI Research Associate Dr. Elze Hesse. We tried to figure out what determines ‘genomic fluidity‘, or the degree to which different strains differ in gene content, using data on many species. From the Abstract:
Many prokaryote species are known to have fluid genomes, with different strains varying markedly in accessory gene content through the combined action of gene loss, gene gain via lateral transfer, as well as gene duplication. However, the evolutionary forces determining genome fluidity are not yet well understood. We here for the first time systematically analyse the degree to which this distinctive genomic feature differs between bacterial species. We find that genome fluidity is positively correlated with synonymous nucleotide diversity of the core genome, a measure of effective population size Ne. No effects of genome size, phylogeny or homologous recombination rate on genome fluidity were found. Our findings are consistent with a scenario where accessory gene content turnover is for a large part dictated by neutral evolution.
The paper is Open Access:
Nadia Andrea Andreani, Elze Hesse and Michiel Vos. Prokaryote genome fluidity is dependent on effective population size. The ISME Journal advance online publication 31 March 2017; doi: 10.1038/ismej.2017.36
P.S. If you are interested in more on the background of genomic fluidity, please check out an Opinion paper from 2015 on the topic mentioned in this post.