Table 1.
Genome proportion of annotated repeats in all three species in a comparative analysis.
| Repeat Annotation | Genomic Proportion % | ||
|---|---|---|---|
| A. cepa | A. ursinum | A. sativum | |
| mobile_element/Class_II/Subclass_1/TIR/EnSpm_CACTA | 0.12 | 0.64 | 0.07 |
| mobile_element/Class_I/LINE | 9.18 × 10−4 | 0.27 | 6.90 × 10−4 |
| mobile_element/Class_I/SINE | 4.59 × 10−4 | 0.17 | 0.09 |
| mobile_element/Class_I/LTR/Ty1_copia/SIRE | 3.12 | 1.11 | 0.58 |
| mobile_element/Class_I/LTR/Ty1_copia/TAR | 0.28 | 0.44 | 0.29 |
| mobile_element/Class_I/LTR/Ty1_copia/Tork | 0.00 | 0.05 | 0.00 |
| mobile_element/Class_I/LTR/Ty3_gypsy/chromovirus/CRM | 0.66 | 1.96 × 10−3 | 0.00 |
| mobile_element/Class_I/LTR/Ty3_gypsy/chromovirus/Tekay | 24.86 | 45.51 | 47.88 |
| mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila | 0.08 | 0.14 | 0.13 |
| mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV | 3.22 | 4.30 | 1.16 |
| rDNA/45S_rDNA | 0.38 | 0.26 | 0.33 |
| rDNA/5S_rDNA | 0.01 | 2.08 × 10−3 | 0.05 |
| satellite | 1.68 | 0.17 | 0.31 |
| mobile_element/Class_I/LTR/TRIM | 0.13 | 0.16 | 0.53 |
| unknown in analyzed clusters | 2.12 | 0.73 | 1.26 |
| total in analyzed clusters | 36.65 | 53.95 | 52.68 |
| small clusters that were not analyzed | 16.74 | 11.92 | 11.43 |
| non-clustered reads | 46.61 | 34.13 | 35.89 |
| total | 100.00 | 100.00 | 100.00 |