Fig. 2: Strain-specific DNA barcoding as an approach to track strain-level population dynamics of phytopathogens.

a General scheme of the random chromosomal barcoding approach and the experimental design. First, we edited a 25-nucleotide random sequence (the ‘barcode’) and the adjacent marker of selection between the Tn7 arms on the integration plasmid. The helper plasmid and Tn7 plasmid were then integrated at a defined, neutral position in the chromosome of the R. solanacearum cells by inducing the transposase machinery. The fate of each barcoded strain can then be tracked by sequencing; b proportion of the barcoded individuals after in vitro growth for 24 h initially mixed at equal concentrations with an increasing number of total barcoded strains per inoculum. The x-axis represents the starting number, i.e., 10 (n = 10), 30 (n = 30), 50 (n = 50), 90 (n = 90), of mixed-barcoded strains. The boxes represent the 25th−75th percentile, lines and dots represent medians and individuals. c Survival curve of tomato plants inoculated with the pathogen wild-type strain and the barcoded strain pool of R. solanacearum. P values > 0.05 indicate no fitness variation of barcoded strains on pathogen virulence based on the log-rank test of survival curves. Source data are provided as a Source data file.