Genome plots of Arachis vs . model legumes, and graphs of, synteny with Arachis , retrotransposon, and resistance gene homolog distributions for the model legumes. In the plots, marker correspondences are solid red dots for top Blastp and tBlastn homologies of anchor markers, and hollow black dots for top Blastn homologies of all sequence characterized markers. Chromosome orders and numbering of SBs (with addition of SB11) the same as in , allowing direct comparisons. Corresponding Medicago chromosomes and Lotus LGs are joined with slanted lines in the middle of the figure. For interactive versions of the plots see Additional file 1. (a) Genome Plot of Arachis (cM) vs. Medicago (bp). (b) Density of tBlastn detected sequence similarities (E-values < 1E-20) for the TNL (red line) and CNL (green line) subclasses of resistance gene homologs plotted along the Medicago genome. Values averaged over 6 Mbp window size. High densities of resistance gene homologs and retrotransposons coincide. (c) Black line: density of Blastn detected sequence similarities (E-values < E-60) for retrotransposons plotted along the Medicago genome. Cyan-blue line: synteny score of Medicago with Arachis scaled by multiplying by 100. Values averaged over 6 Mbp window size. SBs occur in regions of low retrotransposon density. (d) Percentage genome coverage of retrotransposons plotted along the Lotus genome (values averaged over 10 cM window size). Cyan-blue line: synteny score of Lotus with Arachis multiplied by 7. (Values averaged over 10 cM window size). SBs tend to occur in regions of low retrotransposon coverage. (e) Density of resistance gene homolog encoding sequences, TNL (red) and CNL (green), plotted along the Lotus genome (averaged over 10 cM window size). Clusters of resistance gene homologs and retrotransposons coincide. (f) Genome Plot of Arachis (cM) vs. Lotus MG-20 (cM). Markers mapped to intervals are plotted as horizontal lines. fLj indicates that the Lotus chromosome has been inverted. The reference orientation of Lj5 has recently been inverted, thus Lj5 in this plot is equivalent to fLj5 in .