Sequencing technologies have evolved dramatically since the first two bacterial genomes were published. Currently, due to second generation sequencing, millions of bacterial genomic sequences exist, although a significantly smaller amount represent completely assembled genomes. Third generation sequencing allows the analysis of single molecules, with read-lengths that cover highly complex repetitive regions previously inaccessible by short-read sequencing. However, long-read sequencing is known for producing errors which make long-read-only genome assemblies unreliable or complex if high accuracy is important for further applications. Here, Oxford Nanopore Technology's MinION, the first handheld nanopore sequencing device, is evaluated in comparison with competing sequencing platforms. The MinION's applications, potential and limitations are reviewed, focusing on its utility for bacterial genome de novo or hybrid assembly.

Background Paenarthrobacter nicotinovorans ATCC 49919 uses the pyridine-pathway to degrade nicotine and could provide a renewable source of precursors from nicotine-containing waste as well as a model for studying the molecular evolution of catabolic pathways and their spread by horizontal gene transfer via soil bacterial plasmids.Results In the present study, the strain was sequenced using the Illumina NovaSeq 6000 and Oxford Nanopore Technology (ONT) MinION platforms. Following hybrid assembly with Unicycler, the complete genome sequence of the strain was obtained and used as reference for whole-genome-based phylogeny analyses. A total of 64 related genomes were analysed; five Arthrobacter strains showed both digital DNA-DNA hybridization and average nucleotide identity values over the species threshold when compared to P. nicotinovorans ATCC 49919. Five plasmids and two contigs belonging to Arthrobacter and Paenarthrobacter strains were shown to be virtually identical with the pAO1 plasmid of Paenarthrobacter nicotinovorans ATCC 49919. Moreover, a highly syntenic nic-genes cluster was identified on five plasmids, one contig and three chromosomes. The nic-genes cluster contains two major locally collinear blocks that appear to form a putative catabolic transposon. Although the origins of the nic-genes cluster and the putative transposon still elude us, we hypothesise here that the ATCC 49919 strain most probably evolved from Paenarthrobacter sp. YJN-D or a very closely related strain by acquiring the pAO1 megaplasmid and the nicotine degradation pathway.Conclusions The data presented here offers another snapshot into the evolution of plasmids harboured by Arthrobacter and Paenarthrobacter species and their role in the spread of metabolic traits by horizontal gene transfer among related soil bacteria.