Table 4. Main families and characteristics of transposable elements and other repeats in the L. maculans genome.
| Genome coverage | Size (bp) | LTR/TIR size (bp) | Number of copies | Number of complete copies | Complete/incomplete copies | Superfamily | |
|---|---|---|---|---|---|---|---|
| Class I (retrotransposons)* | |||||||
| LTR: 9 families. | 12.30 Mb (27.26%) | ||||||
| RLG_Olly | 3.06 Mb | 7,246 | 250 | 1,085 | 187 | 0.172 | Ty3/Gypsy |
| RLG_Polly | 2.97 Mb | 6,928 | 179 | 1,014 | 164 | 0.162 | Ty3/Gypsy |
| RLG_Rolly | 2.24 Mb | 11,875 | 235 | 594 | 46 | 0.077 | Ty3/Gypsy |
| RLC_Pholy | 3.10 Mb | 6,981 | 281 | 1,020 | 83 | 0.081 | Ty1/Copia |
| RLG_Dolly | 0.30 Mb | 6,620 | 228 | 85 | 30 | 0.353 | Ty3/Gypsy |
| RLC_Zolly-1and -2 | 0.16 Mb | 5,306 | 177 | 97 | 14 | 0.144 | Ty1/Copia |
| RLx_Jolly | 0.02 Mb | 803 | 259 | 57 | 5 | 0.088 | Unknown |
| RLx_Ayoly | 0.40 Mb | 10,397 | 217 | 164 | 8 | 0.049 | Unknown |
| RLG_Brawly | 0.05 Mb | 7,289 | None | 22 | 3 | 0.136 | Ty3/Gypsy |
| Class II (DNA transposons) | |||||||
| TIR: 10 families | 1.19 Mb (2.64%) | ||||||
| DTF_Elwe | 199.3 kb | 2,173 | 57 | 158 | 54 | 0.342 | Fot1-Pogo |
| DTM_Lenwe | 25.6 kb | 3,489 | 49 | 36 | 3 | 0.083 | Mutator |
| DTx_Olwe | 5.3 kb | 866 | 49 | 15 | 4 | 0.267 | Unknown |
| DTx_Valwe | 11.5 kb | 1,793 | 37 | 73 | 2 | 0.027 | Unknown |
| DTT_Finwe-1 | 2.7 kb | 529 | 29 | 7 | 4 | 0.571 | Tc1-Mariner |
| DTT_Finwe-2 | 10.8 kb | 523 | 29 | 31 | 11 | 0.355 | Tc1-Mariner |
| DTT_Finwe-3 | 7.4 kb | 806 | 29 | 15 | 4 | 0.267 | Tc1-Mariner |
| DTM_Sahana | 782.8 kb | 5,992 | None | 873 | 49 | 0.056 | Mutator |
| DTx_Gimli | 112.9 kb | 606 | None | 279 | 51 | 0.183 | Unknown |
| DTM_Ingwe | 33.4 kb | 3,582 | 37 | 48 | 1 | 0.021 | Mutator |
| Uncharacterized repeats (11 families) | 159.9 kb (0.35%) | ||||||
| rDNA repeats† | 767 kb (1.70%) | 7,800‡ | >100 | 50 | |||
| Telomeric repeats§ | 935.0 kb (2.07%) | ||||||
* Classification of TEs according to Wicker et al.16: the three-letter code refers to class (R, retrotransposon; D, DNA transposon), order (L, Long terminal repeat—LTR; T, terminal inverted repeat—TIR; P, Penelope-like element—PLE) and superfamily (G, Gypsy; C, Copia; P, Penelope; F, Fot1-Pogo; T, Tc1-Mariner; M, Mutator, x, unknown superfamily) followed by the family (or subfamily) name italicized.
†Including a rDNA-specific LINE element.
‡Excluding variable length short-tandem repeats flanking almost every rDNA repeat.
§Including telomere-associated Penelope-like retroelement RPP-Circe and RecQ telomere-linked helicase.