Figure 2.

Annotation of repetitive sequences in MD2 v2 and other pineapple genomes (MD2 v1, F153 v7, and CB5). (a) Intact transposable elements (TEs) assembled in each pineapple genome; (b) Raw LTR Assembly Index (LAI) score for each pineapple genome. The LAI score is calculated as the ratio of intact elements to total elements in the assembly; therefore, a higher LAI score indicates a higher quality assembly with a larger proportion of intact elements assembled; (c) Insertion time for Ty3/Gypsy LTR and Ty1/Copia LTR elements in pineapple genomes. Lower insertion time indicates more recent origin. Density was calculated using the function geom_density from ggplot2 using the insertion time of all intact elements in million years.