Deconvoluting adaptive events using associative molecular barcoding of genomes and plasmids in E. coli
Plasmids are self-replicating genetic elements that are typically present in multiple copies within host cells. As a result the evolution of plasmids is governed by intracellular dynamics within individual host cells. However the majority of studies investigating adaptive dynamics within plasmid genomes are performed at the level of host populations--and not at the level of individual cells--where plasmid DNA is isolated from a large number of host cells and analyzed for the presence of sequence variants. Thus it remains difficult to trace plasmid lineages with the knowledge of which specific plasmid originates from which cell. We have developed a new method--siBar--for simultaneously barcoding chromosomes and plasmids in a lineage-specific way in Escherichia coli using random DNA barcodes. This technique relies on establishing associations between genomic and plasmid DNA via integration and subsequent excision of a barcoded plasmid construct. In this talk I present early results on the performance of this approach and its applications to fundamental questions of plasmid evolution.
Mei, H., Arbeithuber, B., Cremona, M. A., DeGiorgio, M., & Nekrutenko, A. (2019). A high-resolution view of adaptive event dynamics in a plasmid. Genome biology and evolution, 11(10), 3022-3034.