Comparison of tef to other grasses. A) Syntenic dotplot between tef scaffolds (x-axis) and sorghum chromosomes (y-axis) produced by CoGe. Scaffolds of tef have been ordered and oriented based on synteny to sorghum (minimum of 3 syntenic genes, see: http://goo.gl/ECKmA9) and joined to create a pseudo-assembly. Each dots represents a syntenic gene pair between tef and sorghum. For each sorghum position, two tef scaffolds, one from the A genome and one from the B genome, are expected. The sinusoidal shape is a result of very few tef scaffolds aligning to the gene-poor centromeric regions of sorghum. B) Tef pseudo-chromosomes were then sorted into tef A and tef B pseudo-chromosomes. A dot plot of the 1A and 1B pseudo-chromosomes shows the correspondence between the A and B pseudo-chromosomes. C) The distributions of pairwise synonymous substitutions per synonymous site estimated between tef and other genomes. The corresponding dates can be found in Additional file 5: Table S13. D) Histogram of synonymous rate values (Ks) for all syntenic gene-pairs within the tef and within the maize genomes. The dates estimated from modes of the peaks using a molecular clock rate of 6.5 × 10-9 substitutions per synonymous site per year can be found in Additional file 5: Table S13.