Table 1.
TRACKPOSON results for 32 transposable elements families in 3000 rice genomesa
| TE family | Families | Total TE insertions number | Total TE insertions number in traditional rice | Mean insertion in japonica varieties | Mean insertion in indica varieties | Distance from gene (kb) | Activity |
|---|---|---|---|---|---|---|---|
| Poprice | Copia | 2324 | 1678 | 98.3 ± 12.1b | 91.6 ± 14.0b | 22.5 ± 31.4b | Recent |
| Tos17 | Copia | 181 | 121 | 7.6 ± 3.6 | 7.9 ± 2.9 | 21.1 ± 35.8 | Recent |
| Houba | Copia | 5976 | 5112 | 523.8 ± 65.1 | 388.8 ± 57.0 | 22.6 ± 32.0 | Recent |
| Fam89_osr7 | Copia | 587 | 425 | 47.4 ± 8.7 | 32.0 ± 7.0 | 23.4 ± 33.3 | Recent |
| Fam35-fam36 | Copia | 1756 | 1678 | 669.0 ± 63.7 | 637.2 ± 77.0 | 22.9 ± 32.2 | Old |
| Fam67_echidne | Copia | 438 | 371 | 105.8 ± 20.5 | 102.2 ± 24.4 | 23.4 ± 33.4 | Recent |
| Rn304 | Copia | 52 | 30 | 2.2 ± 1.5 | 1.9 ± 1.2 | 24.8 ± 36.9 | Continuous |
| Scaff6 | Copia | 29 | 23 | 1.7 ± 0.5 | 1.9 ± 0.9 | 27.9 ± 41.0 | — |
| Lullaby | Copia | 153 | 92 | 5.6 ± 2.1 | 3.1 ± 1.8 | 26.8 ± 37.4 | Recent |
| Fam51_osr4 | Copia | 1788 | 1328 | 104.6 ± 11.0 | 100.0 ± 12.2 | 22.6 ± 31.6 | Recent |
| Fam90 | Copia | 285 | 166 | 17.9 ± 2.9 | 16.6 ± 4.1 | 24.4 ± 32.5 | Recent |
| Fam93_ors14 | Copia | 2194 | 1521 | 22.9 ± 13.5 | 56.4 ± 12.9 | 22.0 ± 31.8 | Recent |
| Fam98_rn81 | Copia | 153 | 123 | 20.6 ± 5.1 | 10.8 ± 4.0 | 26.4 ± 35.1 | Recent |
| Hopi | Gypsy | 5152 | 5027 | 695.7 ± 179.5 | 701.3 ± 215.0 | 23.5 ± 33.7 | Continuous |
| Dagul | Gypsy | 2924 | 2742 | 571.8 ± 67.9 | 527.8 ± 75.6 | 22.6 ± 31.9 | Recent |
| Fam17_Rn215_125 | Gypsy | 7096 | 7006 | 575.9 ± 175.5 | 930.1 ± 319 | 23.8 ± 34.6 | Continuous |
| Fam80_rire7 | Gypsy | 382 | 338 | 66.5 ± 12.8 | 69.9 ± 14.2 | 23.4 ± 32.8 | Continuous |
| Dasheng | Gypsy | 5723 | 4806 | 586.4 ± 60.5 | 486.7 ± 61.1 | 22.8 ± 32.3 | Recent |
| Rire2 | Gypsy | 3061 | 2785 | 304.6 ± 53.0 | 295.9 ± 70.3 | 22.8 ± 32.2 | Recent |
| Fam81-fam82 | Gypsy | 2758 | 2558 | 474.2 ± 74.3 | 463.3 ± 94.3 | 23.6 ± 34.5 | Continuous |
| Fam31_osr37 | Gypsy | 3368 | 2797 | 393.1 ± 53.4 | 430.7 ± 57.0 | 23.4 ± 33.2 | Recent |
| Fam49_osr29 | Gypsy | 968 | 904 | 304.4 ± 36.0 | 284.0 ± 44.6 | 23.5 ± 33.6 | Old |
| Fam124_rn208 | Gypsy | 112 | 68 | 11.02 ± 1.9 | 10.47 ± 1.8 | 26.3 ± 35.8 | Continuous |
| Fam108 | Gypsy | 594 | 570 | 201.5 ± 31.3 | 188.1 ± 36.6 | 26.2 ± 37.6 | Continuous |
| Fam106 | Gypsy | 213 | 148 | 15.8 ± 3.7 | 9.3 ± 3.7 | 23.7 ± 32.7 | Recent |
| Fam86 | Gypsy | 506 | 450 | 202.1 ± 16.7 | 192.0 ± 20.8 | 23.9 ± 33.5 | Continuous |
| Fam79_rn206 | Gypsy | 601 | 461 | 125.8 ± 10.8 | 120.9 ± 13.3 | 23.5 ± 32.4 | Recent |
| Rn60 | Gypsy | 16 | 15 | 1.3 ± 1.4 | 1.2 ± 0.9 | 25.6 ± 38.7 | — |
| Scaff3 | Gypsy | 56 | 28 | 1.4 ± 1.1 | 1.9 ± 1.3 | 32.8 ± 48.1 | Recent |
| Scaff5 | Gypsy | 19 | 1 | 1 ± 0 | 0.7 ± 0.5 | 27.0 ± 42.6 | — |
| Rire3 | Gypsy | 3719 | 3576 | 458 ± 147.0 | 408.2 ± 152.3 | 23.9 ± 34.9 | Continuous |
| Karma | LINE | 78 | 59 | 3.7 ± 1.4 | 4.2 ± 2.2 | 25.2 ± 36.7 | Recent |
| 32 families | 53,262 | 47,007 |
aThe transpositional history of each TE families was based on the histogram in Fig. 2
bNumbers after “±” denote standard deviation