Fig. 9

Identification of structurally intact TE loci potentially having transcripts for autonomous mobilisation. a-c The alignment properties of the ONT reads mapping to a structurally intact Gypsy-V1 locus whose INT domain was > 90% covered by ONT reads. For each read, the read length was plotted against the number of bases overlapping with the autonomous locus and coloured by mapping specificity (multi−/unique-mapping; a) and alignment start site (b) and end site (c) relative to the TE locus. All reads plotted in (a) were presented at the same coordinates in (b) and (c). The black arrows indicate an ONT read covering most of the structurally intact TE locus. Note that this ONT read is multi-mapping to other structurally intact Gypsy-V1 loci, but only the locus indicated here is TE expression candidate (i.e. supported by short-read data). d-f The alignment properties of the ONT reads mapping to three structurally intact hAT-7 loci whose ORF was > 90% covered by ONT reads. (d)-(f) were plot following the approach used for (a)-(c). g-h Genome browser images of the structurally intact Gypsy-V1 locus (Gypsy-V1_chr15_3486647–3,489,471) and the representative hAT-7 locus (hAT-7_chr14_21994787–21,998,695), whose INT and ORF (teal blue strips) was fully covered by individual ONT reads, respectively. The two black stars label full coverage of the INT or ORF, while the single black star marks > 90% coverage of the ORF. INT, internal domain; ORF, open reading frame; F, forward reads