Fig. 5

Identification of factors related to the long-term maintenance of old TEs using the comparison between A. halleri halleri and A. lyrata. a superfamily composition, b TE length, c frequency of orthologous and non-orthologous TEs within genic sequences. The red line indicates the proportion of genic sequences in the A. halleri halleri assembly, d frequency of orthologous and non-orthologous TEs within different categories of genic sequences, e: distance to the nearest gene for TEs outside of genes, f frequency of TEs with active siRNA production, as defined by the presence of at least 5 reads and siRNA reads covering at least 10% of the total length of the TE sequence g frequency of TEs related to the percentage of methylated cytosines, h normalized gene expression for genes containing a TE or genes without a TE. Statistical significance is indicated using the following code: “***” for p < 0.001, “**” for p between 0.001 and 0.01, “*” for p between 0.01 and 0.05, “.” for p between 0.05 and 0.1 and “NS” for p > 0.1