Table 1. Statistics of the LTR retrotransposons in the eight AA-genome Oryza species.
| Total | SAT | RUF | NIV | GLA | BAR | GLU | LON | MER | |
|---|---|---|---|---|---|---|---|---|---|
| Assembled lengtha | 373 | 394 | 307 | 312 | 308 | 305 | 298 | 311 | |
| Estimated lengthb | 389 | 473 | 395 | 370 | 376 | 366 | 344 | 388 | |
| Numbers of LTR retrotransposon families | |||||||||
| Total | 790 | 582 | 733 | 641 | 643 | 606 | 634 | 698 | 649 |
| Ty1-copia | 126 | 104 | 123 | 113 | 108 | 107 | 116 | 114 | 113 |
| Ty3-gypsy | 166 | 132 | 155 | 131 | 136 | 125 | 133 | 149 | 138 |
| Unclassified | 498 | 346 | 455 | 397 | 399 | 374 | 385 | 435 | 398 |
| Sequence lengths of retrotransposons in the genomesc | |||||||||
| Total | 124.02 | 97.32 | 76.88 | 78.13 | 74.97 | 74.73 | 62.83 | 80.67 | |
| Ty1-copia | 12.65 | 10.94 | 8.86 | 8.97 | 8.59 | 8.92 | 6.61 | 9.49 | |
| Ty3-gypsy | 66.63 | 39.01 | 30.02 | 30.82 | 28.75 | 29.14 | 20.87 | 33.43 | |
| Unclassified | 44.73 | 47.37 | 38.00 | 38.34 | 37.62 | 36.67 | 35.35 | 37.75 | |
SAT, O. sativa ssp. japonica. cv. Nipponbare (Release 7); RUF, O. rufipogon; NIV, O. nivara; GLA, O. glaberrima; BAR, O. barthii; GLU, O. glumaepatula; LON, O. longistaminata; MER, O. meridionalis; LTR, long terminal repeat.
a
Assembled length (Mb) stands for total contig length.
b
Estimated length (Mb) was assessed by reads at 17 k-mer.
c
Sequence lengths of LTR retrotransposons in genomes (Mb) were calculated based on the annotation using RepeatMasker.