Chr1a conservation and recombination among different chromosomes in the genetic cross. A) Plot of the annotated coding sequences (CDS) on ChrIa (blue top strand, red, bottom strand) based on TOXODBv8 (top line). Beneath this are the similarity plots for the independent assemblies of the ME49 and VAND genomes constructed using Mauve (see methods). White bars reflect gaps in the assembly, typically denoted by “N”s in the reference sequence. B) Comparison of the relationship between physical size and recombination frequency in centimorgans (cM) for prior genetic crosses between clonal lineages (I &III, II&III) (blue symbols, r2 = 0.61)) and between VAND&ME49 (red symbols, r2 = 0.12). Comparison of the two curve fits revealed that the genetic distances of chromosomes (Y axis) of the prior genetic crosses (I&III, II&II) were significantly higher than that of the present VAND&ME49 cross (P ≤ 0.0005). C) Comparison of the relationship between physical size and recombination frequency in centimorgans (cM) for the VAND and ME49 genetic cross based on single conventional recombinations (red symbols) and double crossovers (black symbols). Chromosome numbers are indicated on the plot.