Figure 2: TE comparison analyses in B. oleracea and B. rapa.

(a) TE copy number and total length in each assembly and B. oleracea–B. rapa syntenic blocks. (b) The number of intact LTR (Copia-like and Gypsy-like) birthed at different times (million years ago, MYA) in the syntenic regions of B. oleracea and B. rapa. (c) The comparison of TE distribution and composition in B. oleracea–B. rapa syntenic blocks along B. oleracea chromosomes. We divided B. oleracea–B. rapa syntenic region into non-overlapping sliding 200 kb windows to compare TE contents. For each window, the ratio log₁₀(B. oleracea/B. rapa) was calculated for total syntenic block length (blue line), LTR length (purple line), gene length (yellow point), exons length (red point) and intron length (green point). If B. oleracea > B. rapa in absolute length of TE composition in a compared window, the dot or line is above the line y=0. The corresponding B. rapa chromosome segments along B. oleracea C08 were indicated by coloured bars. All other B. oleracea chromosomes are showed in Supplementary Fig. 31. (d) Phylogeny of the Copia-like elements as an example of LTR-RTs of the syntenic regions in B. rapa and B. oleracea. The neighbor-joining (NJ) trees were generated based on the conserved RT domain nucleotide sequences using the Kimura two-parameter method⁶⁸ in MEGA4 (ref. 69).