Table 4 Classification and key characteristics of TE families in the genome of F. poae 2516. Elements below the length threshold for RIP are not included (MITE, ZIT1). Repetitive elements such as the rDNA tandem and two families of telomere linked RecQ helicases are not included. Nomenclature of TEs is as recommended in literature [73]. R retrotransposon, D DNA transposon, L long terminal repeat (LTR), T terminal inverted repeat (TIR), G Gypsy, C Copia, F Fot1/Pogo, T Tc1/mariner, M Mutator, A hAT, x unknown. n/a designates instances where a TIR/LTR could not be detected for a specific element
Core | Supernumerary | Size (bp) | LTR/TIR (bp) | Family | |||
|---|---|---|---|---|---|---|---|
Intact | RIP | Intact | RIP | ||||
Retrotransposons | |||||||
RLG_Maggy | 27 | 25 | 11 | - | 5684 | 240 | Gypsy/Ty3 like |
RLG_Skippy | 5 | 7 | 13 | - | 6561 | 379 | Gypsy/Ty3 like |
RLC_Ghost | - | 1 | 14 | - | 4900 | 195 | Copia/Ty1 like |
Rxx_marsu | - | - | 30 | - | 2234 | n/a | unknown |
DNA transposons | |||||||
DTF_Fot4 | 1 | - | - | - | 1852 | 48 | Pogo |
DTF_Fot8 | - | - | 1 | - | 2133 | 43 | Pogo |
DTF_Fot2 | - | 2 | 41 | - | 2220 | 90 | Pogo |
DTF_Fot3-A | - | 1 | 7 | - | 2212 | 75 | Pogo |
DTF_Fot3-B | - | 1 | 20 | - | 2200 | 73 | Pogo |
DTF_Fot3-C | - | - | 9 | - | 2203 | 73 | Pogo |
DTF_Fot5-A | 40 | 10 | 9 | - | 1865 | 51 | Pogo |
DTF_Fot5-C | - | 15 | 7 | - | 1865 | 51 | Pogo |
DTF_ESP4-A | - | - | 21 | - | 2909 | 98 | Pogo |
DTF_ESP4-B | 12 | 11 | 24 | - | 2868 | 90 | Pogo |
DTF_Drogon | 33 | - | 24 | - | 1934 | 51 | Pogo |
DTF_Viserion | 8 | 6 | 8 | - | 2885 | 84 | Pogo |
DTF_Rhaegal | - | 1 | 10 | - | 1854 | 36 | Pogo |
DTF_Balerion | - | - | 12 | - | 2749 | 79 | Pogo |
DTA_RLT1 | - | - | 17 | - | 2912 | 27 | hAT-like |
DTA_RLT2 | - | - | 11 | - | 2975 | 22 | hAT-like |
DTA_RLT3 | - | - | 12 | - | 2954 | n/a | hAT-like |
DTA_Hornet1 | - | 1 | 10 | - | 2613 | n/a | hAT-like |
DTA_Hornet2 | - | - | 22 | - | 2739 | n/a | hAT-like |
DTA_Hornet3 | - | - | 11 | - | 2965 | n/a | hAT-like |
DTA_Tfo1 | - | - | 20 | - | 2852 | 28 | hAT-like |
DTA_Tfo2 | - | - | 15 | - | 2838 | 26 | hAT-like |
DTA_Drifter | - | - | 23 | - | 2779 | n/a | hAT-like |
DTA_Obara | - | - | 13 | - | 3867 | 19 | hAT-like |
DTA_Nymeria | - | - | 36 | - | 2850 | 30 | hAT-like |
DTA_Obella | - | - | 5 | - | 2480 | 29 | hAT-like |
DTA_Sarella | - | - | 12 | - | 4236 | n/a | hAT-like |
DTM_Hop7 | 8 | 10 | 2 | - | 3449 | 81 | Mutator |
DTM_Hop4 | 1 | - | 7 | - | 2825 | 97 | Mutator |