Table 3 Classification of transposable elements in P. tinctoria genome.
Class | Order | Super family | RepeatMasker TEs Length (bp) (% in genome) | RepeatProteinMask TEs Length (bp) (% in genome) | De novo Length (bp) (% in genome) | Combined TEs Length (bp) (% in genome) |
|---|---|---|---|---|---|---|
Class I | Non-LTR | LINE | 28,496,857 (1.69) | 32,713,763 (1.94) | 120,009,541 (7.12) | 140,799,803 (8.36) |
SINE | 368,461 (0.02) | 0 (0) | 0 (0) | 368,461 (0.02) | ||
LTR | Copia | 87,944,582 (5.22) | 110,409,663 (6.55) | 278,920,979 (16.56) | 477,275,224 (28.33) | |
Gypsy | 54,684,796 (3.25) | 96,132,429 (5.7) | 332,188,380 (19.72) | 483,005,605 (28.67) | ||
Class II | DNA | 31,422,276 (1.87) | 1,252,105 (0.07) | 62,701,020 (3.72) | 88,388,999 (5.25) | |
Other | 21,043 (0) | 0 (0) | 0 (0) | 21,043 (0) | ||
Unknown | 292,845(0.02) | 0 (0) | 78,954,360 (4.69) | 79,237,325 (4.7) | ||
Total TE | 201,438,375 (11.96) | 200,276,820 (11.89) | 1,262,156,073 (74.92) | 1,302,444,751 (77.31) | ||
