Extended Data Fig. 6: Tandem repeat content and composition in the genome assemblies.

a, The assemblies of EP1 and F7 captured the highest amounts of tandem repeats and knob sequences. The in spite of high fish intensities much lower contents in the B73 and PH207 assemblies reflect the assembly difficulties of these highly repetitive genome regions. b, Relationship between the six lines derived from knob location similarities. The input matrix for clustering contained three relative intensities of fish knob locations per chromosome. The knob patterns of the two Dents B73 and PH207 are very similar, as well as the patterns of DK105 and PE0075. c, Multiple sequence alignment of selected knob monomers from EP1 together with known knob monomers. The knob sequences in the EP1 assembly consist of 180 and 202 bp monomers with a surplus of the 180 bp monomer by a factor of 6.8. Both monomers are highly similar to previously reported knob monomers from maize with the following Genbank IDs marked as 1, 2, 3 in the figure, 1: AF030934.1, 2: M32521.1 and M32525.1, 3: DQ352544.1_a and DQ352544.1_b. Consensus sequences of the monomers where used to identify all major and minor knob locations in the assemblies. d, Gene expression (maximal expression of 7 different conditions per Gene, log10) in relation to the nearest upstream knob signature (left) and tandem repeat (right). Both axes are logarithmic.