Table 2.
Genomic proportion of annotated repeats in all three species in separate clustering. Comparison of repeat elements according to their belonging to repeat class and lineage.
| Repeat Annotation | Genome proportion % | ||
|---|---|---|---|
| A. cepa | A. ursinum | A. sativum | |
| mobile_element/Class_II/Subclass_1/TIR/EnSpm_CACTA | 0.02 | 0.73 | 0.00 |
| mobile_element/Class_II/Subclass_1/TIR/MITE | 0.03 | 0.00 | 0.00 |
| mobile_element/Class_I/LINE | 0.00 | 0.36 | 0.03 |
| mobile_element/Class_I/SINE | 0.06 | 0.13 | 0.14 |
| mobile_element/Class_I/LTR/Ty1_copia/SIRE | 3.97 | 1.13 | 0.30 |
| mobile_element/Class_I/LTR/Ty1_copia/TAR | 0.27 | 0.51 | 0.35 |
| mobile_element/Class_I/LTR/Ty1_copia/Tork | 0.05 | 0.04 | 0.12 |
| mobile_element/Class_I/LTR/Ty3_gypsy/chromovirus/CRM | 0.73 | 0.00 | 0.00 |
| mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat | 0 | 8.71 × 10−3 | 0 |
| mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Ogre_Tat/TatV | 4.73 | 4.29 | 1.41 |
| mobile_element/Class_I/LTR/Ty3_gypsy/chromovirus/Tekay | 29.67 | 44.46 | 49.97 |
| mobile_element/Class_I/LTR/Ty3_gypsy/chromovirus | 0.00 | 2.85 | 0.00 |
| mobile_element/Class_I/LTR/Ty3_gypsy/non-chromovirus/OTA/Athila | 0.13 | 0.28 | 0.64 |
| mobile_element/Class_I/LTR/TRIM | 0.00 | 0.18 | 0.52 |
| mobile_element/Class_I | 0.00 | 5.64 × 10−3 | 0.00 |
| mobile_element/Class_I/LTR/Ty1_copia/Bianca | 0.02 | 0.01 | 0.05 |
| mobile_element/Class_I/LTR/Ty1_copia/Ikeros | 0.01 | 0.00 | 0.00 |
| mobile_element/Class_I/LTR/Ty1_copia/Ale | 0.00 | 0.00 | 0.01 |
| mobile_element/Class_I/LTR/Ty1_copia/Angela | 0.00 | 6.08 × 10−3 | 0.11 |
| rDNA/45S_rDNA | 0.37 | 0.26 | 0.31 |
| rDNA/5S_rDNA | 0.01 | 5.27 × 10−3 | 0.06 |
| satellite | 1.64 | 0.12 | 0.36 |
| unknown in analyzed clusters | 3.93 | 2.99 | 1.48 |
| Total in analyzed clusters | 45.66 | 58.36 | 55.84 |
| unknown small clusters that were not analyzed | 14.45 | 10.60 | 11.05 |
| non-clustered reads (low/single) | 39.89 | 31.04 | 33.11 |
| total | 100.00 | 100.00 | 100.00 |