Fig. 2

Repeat element composition, evolutionary dynamics and transcriptional profiles. Repeat elements were annotated by combining de novo identification and homology-based searches. A Pie chart shows the relative abundance of main TE families (42.7% total) as percentage of the genome; histogram shows the composition as percentage of the genome of major TE superfamilies as a function of the divergence (Kimura2Distance) from the reference consensus sequence of each TE. Given the correlation between divergence from the consensus and time of transposition, the lower the K2D (left) and the younger a TE is. As previously identified in Myotis and other bat species, we recovered recent expansion and activity of multiple DNA elements, in particular Helitrons and more recently hAT elements. B Histograms show expression levels of major TE families as a fraction (%) of normalized read counts from RNA sequencing data of IFNa-stimulated and unstimulated cells at 4 h and 24 h post treatment. C MAplots of apeglm [41] transformed data show differentially expressed TEs at 4 h (top) and 24 h (bottom) post IFN treatment. For the 4 h time point, only the top three TEs per family with the highest Log2 fold change were labelled. For both time points, only TEs that met a threshold of adjusted p-value < 0.05 and log2 fold change > 1.5 (accepted fdr = 0.05) were labelled. Counts of upregulated (blue dots) and downregulated (orange dots) TEs are based on adjusted p-value (< 0.05; accepted fdr = 0.05) only. Among induced TEs at 4 h (45 total based on our cutoffs) we recovered for the most part ERV retrotransposons (green outline), DNA hAT transposons (red outline) and L1 LINEs (light blue outline). At 24 h post treatment we only found 10 families that met the filtering criteria, for the majority ERV shared with the 4 h dataset