Figure 3

Diagram of gene content and structural organisation of the REN1 interval in PN40024 (chr13:16690324..18130936, horizontal panel at the bottom), and relationships with its paralogous loci on the same chromosome (other horizontal panels). The distribution of dispersed NBS genes and NBS gene clusters along chr13 are shown as solid and open circles in the diagram on the right, with distances along the chromosomes given in Mbp. Blocks containing NBS genes at the REN1 locus and at its paralogous loci (chr13:11.8..12.2 Mb and chr13:21.5..21.9 Mb) are shown as red boxes along the vertical diagram of chr 13, and are magnified in the horizontal panels in the middle of the figure. Conserved regions between chr13:11.8..12.2 Mb and REN1, as assessed by dotplot comparison [see Additional file 5], and identity of conserved nucleotide sequences (>70% identity in a sliding window of 100 bp) are indicated by horizontal coloured bars. NBS and CAD gene-rich islands within the REN1 locus were identified by dotplot self-comparison [see Additional file 5] and are indicated at the bottom of the figure by horizontal cyan bars (1 to 5). Connections between gene-rich islands are defined based on the percentage of conserved non-coding sequence. NBS gene relationships within REN1 in segmentally duplicated fragments and in single-gene duplications are defined based on the percentage of conserved sequence in blocks of 10 kb around each gene (Figure 4). The fraction of transposable elements (TEs) in a sliding window of 5 kb along the REN1 locus is given below the locus bar. Full length (red) and partial (orange) CC-NBS-LRR genes are indicated by boxes with their orientation and named from NBSa to NBSk; complete and partial genes of other categories [see Additional file 3] are shown as green and cyan ticks; microsatellite markers are shown by black ticks. Gene models are not drawn to scale. Evolutionary dynamics that have shaped these chromosomal regions from three NBS-LRR founders (in yellow) to the present-day structure of the REN1 locus and its paralogous loci are described in the text.