First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence
Fig 5
HERB_1937_Xci post-mortem DNA damage patterns.
Post-mortem DNA damage patterns were measured on historical HERB_1937_Xci (full, dotted or dashed blue lines for chromosome, pXAC33 and pXAC64 respectively) and compared with three modern Xci strains isolated from SWIO in 2012, 2013 and 2015 respectively (red lines, see results and S1 Table for full description). (A) Fragment length distribution (nucleotides; relative frequency in arbitrary units). (B) Deamination percentages of the first 25 nucleotides from the 5’ (C to T substitutions) and 3’ (G to A substitutions) ends, respectively. Dots: five most extreme nucleotides of the reads, showing a significant increase (towards the extremity) between each nucleotide along the five first or last positions of all HERB_1937_Xci reads. Along the five extreme nucleotides, reads matching to HERB_1937_Xci harboured significantly higher values than modern controls, and reads matching to the HERB_1937_Xci chromosome harboured significantly lower deamination rates than sequences matching to either plasmid (see results for statistics).