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 |
| |
|
Gypsy |
72626 |
30.93 |
25123127 |
34.02 |
7.89 |
| |
|
unclassified |
2797 |
1.19 |
902298 |
1.22 |
0.28 |
| |
DIRS |
DIRS |
2 |
0.00 |
102 |
0.00 |
0.00 |
| |
PLE |
Penelope |
548 |
0.23 |
30214 |
0.04 |
0.01 |
| |
LINE |
RTE |
11 |
0.00 |
618 |
0.00 |
0.00 |
| |
|
L1 |
27632 |
11.77 |
6684243 |
9.05 |
2.10 |
| |
SINE |
unclassified |
1 |
0.00 |
49 |
0.00 |
0.00 |
|
DNA transposons |
TIR |
Tc1-Mariner |
191 |
0.08 |
38231 |
0.05 |
0.01 |
| |
|
hAT |
7935 |
3.38 |
1986522 |
2.69 |
0.62 |
| |
|
Mutator |
21124 |
9.00 |
6320424 |
8.56 |
1.99 |
| |
|
P |
2 |
0.00 |
96 |
0.00 |
0.00 |
| |
|
Harbinger |
1384 |
0.59 |
344876 |
0.47 |
0.11 |
| |
|
En-Spm/CACTA |
8330 |
3.55 |
2372592 |
3.21 |
0.75 |
| |
Helitron |
Helitron |
2154 |
0.92 |
434859 |
0.59 |
0.14 |
| |
unclassified |
unclassified |
95 |
0.04 |
8981 |
0.01 |
0.00 |
| TOTALS | 234783 | 100.00 | 73842114 | 100.00 | 23.06 |