Table 1 Annotation of TE superfamilies in flax WGS assembly determined using a filtered consolidated library produced with de-novo repeats from PILER, RepeatScout, LTR_finder and LTR_STRUC, and a library of TE from the viridiplantae division from Repbase
Class | Order | Superfamily | No. of matches | Elements percentage (%) | Sequence occupied (bp) | Sequence percentage of TEs (%) | Sequence percentage of genome (%) |
|---|---|---|---|---|---|---|---|
Retrotransposons | LTR | Copia | 89951 | 38.31 | 29594882 | 40.08 | 9.30 |
| Â | Â | Gypsy | 72626 | 30.93 | 25123127 | 34.02 | 7.89 |
| Â | Â | unclassified | 2797 | 1.19 | 902298 | 1.22 | 0.28 |
| Â | DIRS | DIRS | 2 | 0.00 | 102 | 0.00 | 0.00 |
| Â | PLE | Penelope | 548 | 0.23 | 30214 | 0.04 | 0.01 |
| Â | LINE | RTE | 11 | 0.00 | 618 | 0.00 | 0.00 |
| Â | Â | L1 | 27632 | 11.77 | 6684243 | 9.05 | 2.10 |
| Â | SINE | unclassified | 1 | 0.00 | 49 | 0.00 | 0.00 |
DNA transposons | TIR | Tc1-Mariner | 191 | 0.08 | 38231 | 0.05 | 0.01 |
| Â | Â | hAT | 7935 | 3.38 | 1986522 | 2.69 | 0.62 |
| Â | Â | Mutator | 21124 | 9.00 | 6320424 | 8.56 | 1.99 |
| Â | Â | P | 2 | 0.00 | 96 | 0.00 | 0.00 |
| Â | Â | Harbinger | 1384 | 0.59 | 344876 | 0.47 | 0.11 |
| Â | Â | En-Spm/CACTA | 8330 | 3.55 | 2372592 | 3.21 | 0.75 |
| Â | Helitron | Helitron | 2154 | 0.92 | 434859 | 0.59 | 0.14 |
| Â | unclassified | unclassified | 95 | 0.04 | 8981 | 0.01 | 0.00 |
TOTALS | Â | Â | 234783 | 100.00 | 73842114 | 100.00 | 23.06 |