Extended Data Fig. 4: Distribution of various types of Transposable Elements across the F. esculentum genome.
For LTR retrotransposons, only full-length LTR retrotransposons whose nucleotide divergence could be calculated with an alignment length of ≥100 nucleotides are shown and the colour represents the nucleotide divergence between the flanking LTRs. The divergence corresponds to those shown in Extended Data Fig. 3 and Supplementary Fig. 11. Those with divergence > 0.1 are shown as 0.1. Athila_11 and Athila_18 are the two largest Gypsy-type subfamilies. CRM_44 and CRM_88 are Gypsy-type subfamilies of the CRM clade not associated with centromeric regions in F. esculentum and F. homotropicum, whereas the remaining CRM subfamilies (that is, other) are associated with centromeric regions in F. esculentum and F. homotropicum (FeCEN). The numbers 11, 18, 44, and 88 correspond to the ClusterIDs of Supplementary Table 17 (see also Supplementary Fig. 12). Number of elements plotted are as follows - Copia: n = 2,750, Athila_18: n = 2,712, Athila_11: n = 2,603, Athila_other: n = 4,515, Tekay: n = 1,174, CRM_44: n = 201, CRM_88: n = 321, CRM_other: n = 632, LINE/SINE: n = 6,818, Helitron: n = 1,098.
