Fig. 5

Location bias of expressed TE loci. a Illustration of TE insertions in the different genomic region (genic or intergenic) or location (exon, intron, or flanks) relative to genes. b-e Hierarchical classification of all annotated V. vinifera TE loci (b) and all TE expression candidates of Vv_T = 0 (c), Vv_Mock (d), and Vv_Yeast (e), by location, integrity, and distinctiveness. TE loci were categorised in the order of region (centre), the transcriptional activity of co-localised genes (2nd layer), location (3rd layer), integrity (4th layer), and the presence/absence of unique-mapping reads (outer-most layer). f-h Hundred percent stacked bar charts showing the proportion of all annotated TE loci of V. vinifera and TE expression candidates (Vv_T = 0, Vv_Mock, and Vv_Yeast) distributed in genic/intergenic regions (f), in gene unit (including exon and intron)/flanks (g), and with expressed/non-expressed genes (h). i-k Hierarchical classification of all annotated A. thaliana TE loci (i) and all TE expression candidates of At_WT (j) and At_ddm1 (k), by location, integrity, and distinctiveness. l-n Hundred percent stacked bar charts showing the proportion of all annotated A. thaliana TE loci and TE expression candidates (At_WT and At_ddm1) distributed in genic/intergenic regions (l), in gene unit/flanks (m), and with expressed/non-expressed genes (n). Colour codes for different categories of location, integrity, and distinctiveness are as indicated at the right panel. Chi-square tests with p-value < 0.01 were as indicated. Expr., expressed; Non-expr., non-expressed; N-flank, N-terminal 2 kb-flanking region of gene; C-flank, C-terminal 2 kb-flanking region of gene; Exp., expected proportion; Obs., observed proportion