Fig. 2.

—LTR retrotransposon abundance, age, and activity in the Clementine reference genome. Only the nine main scaffolds of the Clementine reference are shown. All results are summarized in 1 Mb windows. (a) Distribution of LTR retrotransposons (LTR-TE) disaggregated into Copia, Gypsy, and total elements. Below, the per Mb genic content is shown. On the lowermost row, a per-window average of the transposon-associated deletions across 43 mandarin genomes is shown, the full data can be found in supplementary figure 2, Supplementary Material online. The intensity of each bin is proportional to the percentage of bases covered per window, with the maximum intensity normalized to the maximum value in each row. (b) LTR-based dating retrotransposons in Citrus clementina. The relative age was calculated as the Kimura-2-parameters genetic distance (K2p) (Hu et al. 2011) between LTR pairs. Each LTR retrotransposon was classified in an age interval (windows of 0.01 distance units) and genomic position. The coordinates of each bin are given by the genomic position of each element and its age, and the intensity is proportional to the number of transposons included in the bin. Elements with identical LTRs (K2p distance equals 0) are marked as black ticks under the x axis. (c) Total number of soloLTR (purple), nonsoloLTR (blue), and pairedLTRs (gray) across the C. clementina reference genome, shown as a stacked bar plot. Total LTR (totalLTRs) counts are given by the total height of each bar. (d) Genomic features of the C. clementina reference genome. On top, the centromeres predicted in this work based on the genic content (green), together to those of Aleza et al. (2015) (red) and (Wu et al. 2014) (blue). The last row shows the admixture map of the C. clementina haploid reference genome: genomic fragments coming from mandarin and pummelo are shown in orange and yellow, respectively, while fragments with unknown precedence are shown in gray. The data were obtained as explained in Wu et al. (2014).