Table 2.
Composition of repetitive sequence content.
| Type | Class | Order | Superfamily | Phatr3 | Coverage (bp) | Phatr2 | Coverage (bp) |
|---|---|---|---|---|---|---|---|
| Transposable Elements (TEs) | Class I | LTR retrotransposons | Copia | 1,434 | 2,083,619 | 1,869 | 1,735,622 |
| DIRS | 14 | 18,118 | — | — | |||
| Putative TRIM/LARD | 27 | 7,291 | — | — | |||
| Non-LTR retrotransposons | Putative SINE | 13 | 1,454 | — | — | ||
| Class II | Subclass I | MuDR | 152 | 100,450 | 197 | 87,637 | |
| PiggyBac | 65 | 79,036 | 116 | 73,479 | |||
| Other transposase | 9 | 12,068 | — | — | |||
| Putative non-autonomous | 261 | 182,589 | — | — | |||
| Subclass II | Crypton | 13 | 16,556 | — | — | ||
| Class III | MITE | 235 | 150,035 | — | — | ||
| Putative TEs | Confused TE | 52 | 98,167 | 35 | 20,289 | ||
| Others | Undetermined | Unclassified repeats | 873 | 421,894 | — | — | |
| Host genes | Putative host genes | 302 | 255,568 | — | — | ||
| SSR | SSR | 255 | 36,721 | 1,135 | 58,267 | ||
| Low-complexity repeats | — | — | 141 | 3,401 | |||
| Total | 3,705 | 3,373,161 | 3,493 | 1,834,123 |