Fig. 5: Graphical representation of large homoeologous exchanges in C. arabica.

Blue and green vertical ideograms represent native canephora and eugenioides homoeologous copies, respectively, and the chromosome(s) resulting from homoeologous exchange found in C. arabica germplasm (> 200 Kb). Each event of homoeologous exchange is identified by a number as in Supplementary Data 6 and n indicates the number of accessions in which the event was detected. The black arrowheads indicate the approximate location of the exchange. Ideograms are not drawn to scale. The exact lengths are reported in Supplementary Table 2 and Supplementary Data 5-6. In the sequence identity plot, dots represents sequence alignments with >70% of identity between non-overlapping 2 Kb windows. The color of each dot represents the % of sequence identity. Bar plots illustrate structural variation between homoeologous chromosomes, showing the fraction of nucleotides shared between (white and gray) or private to (pink and magenta) the homoeologs. These categories are further sorted into the fraction of nucleotides in annotated transposable elements (gray and magenta) and in non-repetitive DNA (white). The pink stack includes low-copy DNA as well as other DNA tracts that are not annotated as transposable elements outside of collinear regions. The axis indicating the chromosomal coordinates in million base pairs (Mbp) of each homoeolog refers to both the bar plot and the sequence identity plot. Source data are provided as a Source Data file and in Supplementary Data 6.