Fig. 6

Bremia lactucae AFLAP results. a Markers unique to SF5 ordered in 19 linkage groups. Each horizontal bar indicates a genetic bin with > 1 marker. The sizes of the blue marks indicate the relative number of markers in each genetic bin. Genetic bins with large numbers of markers were observed at the end of some, but not all linkage groups. b Alignment of the genetic map on the 21 scaffolds larger than 1 Mb in the draft reference assembly (6). Multiple scaffolds spanned more than one linkage group, indicative of mis-assembly. Linkage groups included multiple scaffolds providing genetic support for reorienting and rejoining the scaffolds. c Scatter plot demonstrating collinearity between the revised genome assembly and the genetic map after fragmenting, reorienting, and re-scaffolding of the assembly. Coordinates of annotated genes that encode six categories of candidate effector proteins are plotted on tracks below the scatter plot. d Contact frequency obtained by aligning paired Hi-C reads to the genetically reoriented assembly. The strong dark diagonal indicates that the assembly is consistent with Hi-C data. Crosses off the diagonal indicate intra-chromosomal contacts, possibly involving centromeres