TABLE 4.
Results of annotation at the supercluster and cluster level.
| Sequence type | Repeat family | Genomic proportion (%)a |
||||||||||
| IntA | IntC | PreA | PreC | PalA | PalF | PicF | PicB | Hyb2 | Hyb3 | Hyb4 | ||
| Ty1/Copia retrotransposons | Ale | 0.149 | 0.149 | 0.177 | 0.176 | 0.147 | 0.151 | 0.192 | 0.152 | 0.159 | 0.160 | 0.154 |
| Angela | 4.199 | 4.202 | 4.474 | 4.409 | 4.202 | 4.334 | 4.408 | 4.397 | 4.351 | 4.319 | 4.363 | |
| (2.740) | (2.829) | (3.055) | (2.864) | (3.196) | (3.319) | (3.426) | (3.050) | (2.799) | (2.951) | (2.845) | ||
| Bianca | 0.163 | 0.163 | 0.155 | 0.164 | 0.165 | 0.169 | 0.160 | 0.172 | 0.164 | 0.166 | 0.169 | |
| Ikeros | 0.032 | 0.030 | 0.015 | 0.000 | 0.015 | 0.017 | 0.000 | 0.018 | 0.017 | 0.016 | 0.017 | |
| SIRE | 16.399 | 16.776 | 14.043 | 14.151 | 15.940 | 15.734 | 14.873 | 14.022 | 14.874 | 14.929 | 15.535 | |
| (7.442) | (7.328) | (6.926) | (6.466) | (5.981) | (7.335) | (7.719) | (6.134) | (6.571) | (6.114) | (6.654) | ||
| TAR | 0.337 | 0.277 | 0.257 | 0.254 | 0.258 | 0.267 | 0.292 | 0.276 | 0.265 | 0.266 | 0.255 | |
| Tork | 0.367 | 0.359 | 0.470 | 0.346 | 0.359 | 0.351 | 0.354 | 0.351 | 0.360 | 0.431 | 0.356 | |
| total Ty1/Copia | 21.646 | 21.956 | 19.591 | 19.500 | 21.086 | 21.023 | 20.279 | 19.388 | 20.190 | 20.287 | 20.849 | |
| (11.230) | (11.135) | (11.055) | (10.270) | (10.120) | (11.609) | (12.143) | (10.153) | (10.335) | (10.104) | (10.450) | ||
| Ty3/Gypsy retrotransposons | chromovirus/Tekay | 31.687 | 30.830 | 33.006 | 31.413 | 33.114 | 36.522 | 32.350 | 32.104 | 32.849 | 31.884 | 32.571 |
| (10.227) | (10.843) | (11.456) | (10.583) | (9.570) | (10.049) | (10.997) | (10.980) | (10.156) | (9.983) | (11.269) | ||
| chromovirus/CRM | 0.014 | 0.029 | 0.032 | 0.064 | 0.023 | 0.027 | 0.000 | 0.063 | 0.026 | 0.095 | 0.039 | |
| non-chromovirus/OTA/Athila | 1.773 | 1.472 | 1.355 | 1.502 | 1.668 | 1.699 | 1.380 | 1.528 | 1.667 | 1.567 | 1.622 | |
| (1.756) | (1.457) | (1.335) | (1.483) | (1.652) | (1.699) | (1.363) | (1.510) | (1.667) | (1.548) | (1.602) | ||
| non-chromovirus/OTA/Ogre_Tat/TatV | 0.571 | 0.527 | 0.463 | 0.441 | 0.482 | 0.512 | 0.445 | 0.453 | 0.500 | 0.482 | 0.491 | |
| (0.571) | (0.527) | (0.375) | (0.441) | (0.398) | (0.512) | (0.445) | (0.239) | (0.500) | (0.482) | (0.409) | ||
| total Ty3/Gypsy | 34.045 | 32.858 | 34.856 | 33.420 | 35.287 | 38.760 | 34.175 | 34.148 | 35.042 | 34.028 | 34.723 | |
| (12.568) | (12.856) | (13.198) | (12.571) | (11.643) | (12.287) | (12.805) | (12.792) | (12.349) | (12.108) | (13.319) | ||
| pararetrovirus | 0.069 | 0.055 | 0.000 | 0.000 | 0.050 | 0.031 | 0.017 | 0.042 | 0.021 | 0.029 | 0.031 | |
| DNA transposons | EnSpm_CACTA | 0.175 | 0.178 | 0.145 | 0.177 | 0.163 | 0.265 | 0.284 | 0.168 | 0.151 | 0.189 | 0.160 |
| hAT | 0.068 | 0.056 | 0.068 | 0.063 | 0.070 | 0.060 | 0.060 | 0.075 | 0.058 | 0.034 | 0.060 | |
| MuDR_Mutator | 0.152 | 0.159 | 0.149 | 0.184 | 0.159 | 0.195 | 0.090 | 0.073 | 0.160 | 0.092 | 0.089 | |
| (0.132) | (0.159) | (0.148) | (0.167) | (0.159) | (0.195) | (0.090) | (0.073) | (0.160) | (0.092) | (0.089) | ||
| PIF_Harbinger | 0.262 | 0.284 | 0.286 | 0.284 | 0.241 | 0.253 | 0.123 | 0.283 | 0.279 | 0.256 | 0.249 | |
| total DNA transposons | 0.657 | 0.677 | 0.648 | 0.708 | 0.633 | 0.773 | 0.557 | 0.599 | 0.648 | 0.571 | 0.558 | |
| (0.636) | (0.677) | (0.647) | (0.691) | (0.633) | (0.773) | (0.557) | (0.599) | (0.648) | (0.571) | (0.558) | ||
| Helitron | 0.160 | 0.155 | 0.105 | 0.133 | 0.143 | 0.125 | 0.101 | 0.146 | 0.126 | 0.124 | 0.128 | |
| satellite DNA | satellite CL18 b (23+21 bp) | 0.405 | 0.349 | 0.369 | 0.424 | 0.471 | 0.414 | 0.477 | 0.485 | 0.417 | 0.452 | 0.405 |
| satellite CL160 (89 bp) | 0.129 | 0.125 | 0.118 | 0.089 | 0.113 | 0.119 | 0.088 | 0.114 | 0.108 | 0.121 | 0.124 | |
| satellite CL82 (369 bp) | 0.086 | 0.000 | 0.163 | 0.200 | 0.077 | 0.103 | 0.120 | 0.106 | 0.192 | 0.112 | 0.108 | |
| satellite CL229 (46bp) | 0.042 | 0.000 | 0.000 | 0.000 | 0.023 | 0.014 | 0.021 | 0.021 | 0.024 | 0.025 | 0.025 | |
| satellite CL201 (172bp) | 0.000 | 0.000 | 0.026 | 0.028 | 0.000 | 0.000 | 0.031 | 0.013 | 0.025 | 0.014 | 0.027 | |
| satellite CL217 (126bp) | 0.023 | 0.029 | 0.000 | 0.011 | 0.016 | 0.021 | 0.013 | 0.018 | 0.014 | 0.017 | 0.023 | |
| total satellite DNA | 0.685 | 0.503 | 0.676 | 0.752 | 0.700 | 0.671 | 0.749 | 0.758 | 0.781 | 0.741 | 0.712 | |
| 45S rDNA | 0.331 | 0.225 | 0.576 | 0.380 | 0.394 | 0.561 | 0.619 | 0.297 | 0.458 | 0.442 | 0.331 | |
| 5S rDNA | 0.027 | 0.000 | 0.052 | 0.024 | 0.029 | 0.028 | 0.021 | 0.024 | 0.031 | 0.030 | 0.023 | |
| unclassified repeats | 13.918 | 13.445 | 14.613 | 14.562 | 12.211 | 8.952 | 13.447 | 14.202 | 13.918 | 14.836 | 13.755 | |
| (45.831) | (44.267) | (44.806) | (44.658) | (46.821) | (44.839) | (42.954) | (44.793) | (46.465) | (46.939) | (45.557) | ||
| small uncharacterized clusters | 11.336 | 11.817 | 11.436 | 11.938 | 10.856 | 11.264 | 10.779 | 11.707 | 10.797 | 10.733 | 10.717 | |
| singlets | 17.128 | 18.311 | 17.450 | 18.582 | 18.612 | 17.811 | 19.256 | 18.690 | 17.988 | 18.179 | 18.172 | |
aValues in regular font represent results of annotation at the supercluster level; results at the cluster level are indicated in italics and in parentheses. Annotations at the cluster level are only reported when they differ from the ones at the supercluster level.bcomplex structure with nested repeats including two minisatellites (see Belyayev et al., 2018).