Completed genomes from Variovorax provide insight into genome diversification through horizontal gene transfer

Approximately 10% of all bacterial genomes sequenced thus far contain a secondary replicon. This property of bacterial populations vastly increases genomic diversity within phylogenetically narrow groups. Members of the genus Variovorax have extensive heterogeneity in genome architecture, including sequenced isolates containing plasmids, megaplasmids, and chromids. Many of the Variovorax genomes in the NCBI database were generated using only short-read data and were assembled to the permanent draft stage. We acquired a set of these isolates and used the MinION long-read sequencing device to generate additional data to allow hybrid assemblies of these genomes. Here we present the finished assemblies of 15 Variovorax isolates from diverse ecosystems that were previously only available as permanent drafts. When added to the previously published Variovorax assemblies for EPS, CSUSB, and VAI-C and those published by other groups, we found significant diversity in genome architecture. We found that there are plasmids, megaplasmids, and chromids that are distinguishable using Guanine-Cytosine (G+C content) content as a signal. We identified a plasmid integration event in NFACC27 and identify potential evolutionary relationships in the second replicons based on ParB homology as well as ANI. The evidence suggests that Variovorax is like its sister taxon Burkholderia, highly capable of acquiring and maintaining stable secondary replicons. The plasticity of these architectures and the mechanisms for maintenance remain a topic for future research.