Table 1 Summary of detected TEs
Species | Line | Accession | TEs by TEF | TEs by PCR | TEs from literature | Reference | New TEs found |
|---|---|---|---|---|---|---|---|
Rice | |||||||
| Â | ttm2 | SRR556173 | Tos17 | Tos17 | Tos17 | 3, 7, 8 | Â |
| Â | ttm5 | SRR556174 and SRR556175 | Tos17 | Tos17 | Tos17 | 3, 7, 8 | Â |
| Â | JRC01 | DRR240814 | CACTA, Mutator, Dasheng, Tos5, Osr4.3, Osr25.1, Osr25.6, Osr26.7, Osr27.13, Osr27.31, Osr27.45, Osr27.55, Osr34, Ty3/gypsy, Unclassified (29) | Osr4.3 | Â | 8, 17, 18 | CACTA, Mutator, Dasheng, Tos5, Osr4.3, Osr25.1, Osr25.6, Osr26.7, Osr27.13, Osr27.31, Osr27.45, Osr27.55, Osr34, Ty3/gypsy, Unclassified (29) |
| Â | JRC05 | DRR240817 | CACTA, Mutator, Dasheng, Tos5, Osr4.3, Osr25.1, Osr25.6, Osr26.7, Osr27.13, Osr27.31, Osr27.45, Osr27.55, Osr34, Ty3/gypsy, Unclassified (29) | Tos5 | Â | 8, 17, 18 | CACTA, Mutator, Dasheng, Tos5, Osr4.3, Osr25.1, Osr25.6, Osr26.7, Osr27.13, Osr27.31, Osr27.45, Osr27.55, Osr34, Ty3/gypsy, Unclassified (29) |
| Â | OsCmt3a-1 | SRR1610772 | Tos17, Dasheng, Osr4.3, Osr25.4, Ty3/gypsy (3) | nt | Tos17, Dasheng, Osr4.3 | 10 | Osr25.4, Ty3/gypsy |
| Â | OsCmt3a-2 | SRR1609962 | Tos17, Dasheng, Osr4.3, Osr25.4, Ty3/gypsy (2) | nt | Tos17, Dasheng, Osr4.3 | 10 | Osr25.4, Ty3/gypsy |
Arabidopsis | |||||||
| Â | ddm1(18H4) | DRR001193 | CACTA, Evade, AT2G13940, AT5G44925, Hi, MuDR-A, Ty1/copia (2), Ty3/gypsy (1), Unclassified (10) | nt | CACTA, Hi | 12, 14, 15 | Evade, AT2G13940, AT5G44925, MuDR-A, Ty1/copia (2), Ty3/gypsy (1), Unclassified (11) |
| Â | ddm1(18J1) | DRR001194 | CACTA, Evade, AT2G13940, AT5G44925, Hi, Ty1/copia (3), Ty3/gypsy (2), Unclassified (9) | nt | CACTA, Hi | 12, 14, 15 | Evade, AT2G13940, AT5G44925, Ty1/copia (3), Ty3/gypsy (2), Unclassified (10) |
| Â | hc4 | hc4 | ONSEN | nt | ONSEN | 9 | Â |
| Â | hc31 | hc31 | ONSEN | nt | ONSEN | 9 | Â |
Drosophila | |||||||
| Â | RIL46 | SRR82377 | P, FB, hobo, roo, 412, Diver, mgd1, hopper, Ty1/copia (4), Ty3/gypsy (2), Unclassified (4) | nt | Â | 7, 19, 20, 21 | P, FB, hobo, roo, 412, Diver, mgd1, hopper, Ty1/copia (4), Ty3/gypsy (2), Unclassified (4) |
| Â | RIL80 | SRR82382 | P, FB, hobo, roo, 412, Diver, mgd1, mgd3, Ty1/copia (5), Ty3/gypsy (2), Unclassified (4) | nt | Â | 7, 19, 20, 21 | P, FB, hobo, roo, 412, Diver, mgd1, mgd3, Ty1/copia (5), Ty3/gypsy (2), Unclassified (4) |
|  | 33–27 | SRR866314 | P, hobo, roo, Ty3/gypsy | nt | P, hobo, roo, 1360, Flea, Rt1, mdg | 19, 21, 24 | Ty3/gypsy |
|  | 33–45 | SRR866312 | P, hobo, hopper, roo, Ty3/gypsy | nt | P, hobo, roo, 1360, Flea, Rt1, mdg, G, hopper | 19, 21, 24 | Ty3/gypsy |