Fig. 1: Phylogenetic analysis and transposable element characteristics in B. oleracea.

a, Phylogenetic tree of 704 B. oleracea accessions. Different colors of branches indicate accessions from different morphotype groups. The images of the 27 representative accessions were placed next to their branches. The light blue, yellow and green backgrounds denote the following three main clusters: the wild/ancestral group, the arrested inflorescence lineage and the leafy head lineage. The red stars denote the 22 newly assembled genomes and the red rectangles denote five previously reported genomes. b, Phylogenetic tree of the 27 representative B. oleracea accessions, with the genome of B. rapa as the outgroup. c, The estimated insertion time (y axis) of all the full-length LTRs in the 27 B. oleracea genomes along the nine chromosomes (x axis) of B. oleracea. The lengths of nine chromosomes were normalized to 0–100, proportional to their physical lengths. Each dot represents one LTR insertion event. The heatmap denotes the density of the full-length LTRs. Purple bars below each chromosome denote centromeric regions detected by centromere-specific repetitive sequences. d, Distribution of insertion time of full-length Copia and Gypsy LTRs in the 27 individual genomes. Each line represents a genome in the left graph. The two circles show the Copia and Gypsy LTRs that can be clustered into groups with sequence similarity of ≥90%. e, The heatmap shows the TAD prediction on chromosome eight of T10 (as an example), in which the region colored in dark red denotes a TAD structure. The line charts below the heatmap show the density of Copia and Gypsy LTRs, respectively, highlighting the enrichment of Copia LTRs in the centromere region, which is surrounded by high density of Gypsy LTRs.