Fig. 3
From: A high-continuity and annotated tomato reference genome
Repetitive sequence analysis. A The estimated insertion time of LTR retrotransposons, showing the statistics of Gypsy-type LTRs in red and Copia-type LTRs in blue. B Frequencies of transposable elements (TE) in the vicinity of genes. Gypsy and Copia had the highest frequencies in the intergenic region and the lowest frequencies near the gene regions. LINE, TcMar-Stowaway, PIF-Harbinger, and MULE-MuDR exhibited the opposite distribution pattern. C The top 12 TE subfamilies with the longest length, including 11 Gypsy and one Unknown-type subfamily. D The frequency distribution of the Unknown-type rnd-1_family-4 subfamily, showing that it was enriched towards the centromere of chromosome 1