Table 5.
Percentage Distribution of Repeat Classes in the Olive Genome
| Sequence type | Order | Superfamily | Number of Contigs | Number of Matched Reads | Percentage | |
|---|---|---|---|---|---|---|
| Retrotransposons | Unclassified | 42 | 34,017 | 0.025 | ||
| (Class I) | LTR | Copia | 54,110 | 24,725,640 | 17.821 | |
| Gypsy | 47,920 | 28,884,342 | 20.819 | |||
| Retrovirus | 101 | 74,960 | 0.054 | |||
| Endogenous retrovirus | 4 | 6,314 | 0.005 | |||
| Solo-LTR | 52 | 18,355 | 0.013 | |||
| Unknown | 189 | 174,016 | 0.125 | |||
| LINE | L1 | 2384 | 1,739,119 | 1.253 | ||
| RTE | 453 | 123,845 | 0.089 | |||
| Unknown | 38 | 20,591 | 0.015 | |||
| Short-interspersed elements | tRNA | 268 | 64,093 | 0.046 | ||
| Total | 40.265 | |||||
| DNA transposons | Unclassified | 67 | 32,668 | 0.024 | ||
| (Class II, subclass I) | TIR | Tc1-Mariner | 217 | 74,711 | 0.054 | |
| hAT | 7,187 | 2,784,674 | 2.007 | |||
| Mutator | 5,790 | 3,335,678 | 2.404 | |||
| PiggyBac | 1 | 34 | 0.000 | |||
| PIF-Harbinger | 754 | 250,771 | 0.181 | |||
| CACTA | 1,212 | 496,957 | 0.358 | |||
| Crypton | Crypton | 7 | 2,054 | 0.001 | ||
| (ClassII, subclass II) | Helitron | Helitron | 1,297 | 672,682 | 0.485 | |
| Total | 5.514 | |||||
| Tandem repeats | 11,260 | 43,233,770 | 31.161 | |||
| rDNA | 356 | 1,932,081 | 1.393 | |||
| Unknown | 308 | 179,225 | 0.129 | |||
| No hits found | 74,292 | 14,584,090 | 10.512 | |||
| Total reads excluding organellar ones | 138,741,954 | |||||