Table 2.
Type, localization and characteristics of repeated elements in the RGA08 locus of M. balbisiana
| Name | Type | ID | Location | Length | 5' LTR | 3'LTR | TSD | Divergence time | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| (bp) | (bp) | length | TG | CA | length | TG | CA | (MY) | ||||
| RE1 | Copia-like element | MbP032N20c_te030 | 129477 | 2855 | - | - | - | - | - | - | - | - |
| RE1 | MbP036B13_te010 | 100745 | 2882 | - | - | - | - | - | - | - | - | |
| Clio | LARD | MbP032N20c_te010 | 28466 | 4441 | 382 | TG | CA | 382 | TG | CA | ATAC/ATAC | 0.294 |
| Clio | MbP032N20c_te040 | 148954 | 4441 | 382 | TG | CA | 382 | TG | CA | GGAG/GGAG | 1.189 | |
| Clio | MbP036B13_te020 | 120343 | 4441 | 382 | TG | CA | 382 | TG | CA | GGAG/- | ||
| Clio* | MbP036B13_te030 | 124784 | 1606 | - | - | - | - | - | - | - | ||
| Mooz | Copia-like element | MbP032N20c_te050 | 166534 | 3849 | 115 | - | - | 112 | - | - | - | - |
| Mooz | MbP032N20c_te060 | 225945 | 3346 | 231 | - | - | 447 | TG | CA | - | - | |
| Mooz | MbP036B13_te050 | 185390 | 3688 | 447 | TG | CA | 447 | TG | CA | CTTTG/CTTTC | 2.183 | |
| Mooz* | MbP036B13_te040 | 181339 | 2464 | 447 | TG | CA | - | - | - | CTTTG/- | ||
| RE5 | Copia-like element | MbP032N20c_te020 | 124026 | 4301 | 94 | TG | - | 171 | TG | CA | ACCAC/ACCAC | - |
LTR features (length, presence of TG and CA at their ends) and Target Site Duplication (TSD) were determined using LTR_FINDER followed by manual annotation. For complete elements with clearly identified TSD and with LTR length exceeding the empirical limit of 300 bp, divergence time was calculated based on the Kimura-2 parameter distance between LTRs with a substitution rate of 0.9 × 10-8 mutation per site per year. Stars indicate TE fragments. MY, million years.