Table 2 Predicted retrotransposons length and genome coverage statistics.
N. sylvestris | N. tomentosiformis | N. tabacum | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
length | % of TE | % of genome | length | % of TE | % of genome | length | % of TE | % of genome | ||||
Class I | LINE | 9,675,761 | 1.6% | 0.4% | 9,615,294 | 1.7% | 0.6% | 19,745,491 | 1.7% | 0.5% | ||
LTR | Ty1/copia | Ale | 13,558,929 | 2.2% | 0.6% | 11,670,567 | 2.1% | 0.7% | 24,896,186 | 2.1% | 0.6% | |
LTR | Ty1/copia | Alesia | 299,556 | 0.0% | 0.0% | 102,813 | 0.0% | 0.0% | 380,375 | 0.0% | 0.0% | |
LTR | Ty1/copia | Angela | 3,989,230 | 0.6% | 0.2% | 1,986,947 | 0.4% | 0.1% | 5,826,451 | 0.5% | 0.1% | |
LTR | Ty1/copia | Bianca | 14,202,928 | 2.3% | 0.6% | 12,796,742 | 2.3% | 0.7% | 26,200,095 | 2.2% | 0.7% | |
LTR | Ty1/copia | Ikeros | 2,115,094 | 0.3% | 0.1% | 1,471,616 | 0.3% | 0.1% | 3,637,043 | 0.3% | 0.1% | |
LTR | Ty1/copia | Ivana | 1,366,613 | 0.2% | 0.1% | 1,775,454 | 0.3% | 0.1% | 3,081,268 | 0.3% | 0.1% | |
LTR | Ty1/copia | SIRE | 24,828,773 | 4.0% | 1.1% | 14,684,980 | 2.6% | 0.8% | 38,903,674 | 3.3% | 1.0% | |
LTR | Ty1/copia | TAR | 9,154,238 | 1.5% | 0.4% | 12,202,057 | 2.2% | 0.7% | 20,574,287 | 1.8% | 0.5% | |
LTR | Ty1/copia | Tork | 14,900,248 | 2.4% | 0.6% | 7,980,408 | 1.4% | 0.5% | 21,895,949 | 1.9% | 0.5% | |
LTR | Ty3/gypsy | chromovirus|CRM | 2,617,599 | 0.4% | 0.1% | 2,797,010 | 0.5% | 0.2% | 5,522,890 | 0.5% | 0.1% | |
LTR | Ty3/gypsy | chromovirus|Chlamyvir | 0 | 0.0% | 0.0% | 0 | 0.0% | 0.0% | 5,786 | 0.0% | 0.0% | |
LTR | Ty3/gypsy | chromovirus|Galadriel | 5,700,997 | 0.9% | 0.2% | 5,500,007 | 1.0% | 0.3% | 11,145,772 | 1.0% | 0.3% | |
LTR | Ty3/gypsy | chromovirus|Reina | 2,340,197 | 0.4% | 0.1% | 2,730,019 | 0.5% | 0.2% | 4,966,891 | 0.4% | 0.1% | |
LTR | Ty3/gypsy | chromovirus|Tcn1 | 0 | 0.0% | 0.0% | 0 | 0.0% | 0.0% | 3,227 | 0.0% | 0.0% | |
LTR | Ty3/gypsy | chromovirus|Tekay | 248,756,499 | 40.3% | 10.7% | 310,558,487 | 55.4% | 17.8% | 559,106,371 | 47.7% | 14.0% | |
LTR | Ty3/gypsy | chromovirus|chromo-outgroup | 0 | 0.0% | 0.0% | 5,356 | 0.0% | 0.0% | 15,594 | 0.0% | 0.0% | |
LTR | Ty3/gypsy | non-chromovirus|OTA|Athila | 59,196,881 | 9.6% | 2.5% | 50,111,064 | 8.9% | 2.9% | 108,359,430 | 9.3% | 2.7% | |
LTR | Ty3/gypsy | non-chromovirus|OTA|Tat|Ogre | 116,167,517 | 18.8% | 5.0% | 21,672,795 | 3.9% | 1.2% | 135,653,424 | 11.6% | 3.4% | |
LTR | Ty3/gypsy | non-chromovirus|OTA|Tat|Retand | 75,130,400 | 12.2% | 3.2% | 81,189,167 | 14.5% | 4.7% | 155,002,488 | 13.2% | 3.9% | |
pararetrovirus | 6,158,720 | 1.0% | 0.3% | 3,683,969 | 0.7% | 0.2% | 9,724,069 | 0.8% | 0.2% | |||
Class II | Subclass 1 | TIR | EnSpm/CACTA | 758,007 | 0.1% | 0.0% | 1,412,566 | 0.3% | 0.1% | 2,030,473 | 0.2% | 0.1% |
Subclass 1 | TIR | MuDR/Mutator | 2,475,225 | 0.4% | 0.1% | 1,382,863 | 0.2% | 0.1% | 4,014,994 | 0.3% | 0.1% | |
Subclass 1 | TIR | PIF/Harbinger | 114,448 | 0.0% | 0.0% | 128,968 | 0.0% | 0.0% | 294,983 | 0.0% | 0.0% | |
Subclass 1 | TIR | Tc1/Mariner | 26,044 | 0.0% | 0.0% | 100,923 | 0.0% | 0.0% | 83,809 | 0.0% | 0.0% | |
Subclass 1 | TIR | hAT | 3,476,633 | 0.6% | 0.1% | 3,931,259 | 0.7% | 0.2% | 7,522,070 | 0.6% | 0.2% | |
Subclass 2 | Helitron | Helitron | 860,377 | 0.1% | 0.0% | 1,440,401 | 0.3% | 0.1% | 23,79,749 | 0.2% | 0.1% | |
Total | 617,870,914 | 100.0% | 26.6% | 560,931,732 | 100.0% | 32.2% | 1,170,972,839 | 100.0% | 29.3% | |||
