Table 1 Overview of dictyostelid retrotransposon properties and integration preferences
From: Convergent evolution of tRNA gene targeting preferences in compact genomes
Name | Consensus length (bp) | LTR length (bp) | Copy number in genome a | tRNA gene-specific | Distance to tRNA gene (bp) | |||
|---|---|---|---|---|---|---|---|---|
total | full length b | solo LTR | 5’ of tDNA (%) c | 3’ of tDNA (%) c | ||||
LTR retrotransposons | ||||||||
Dd-Skipper-1 | 6998 | 390 | 60 | 2 | 10 | no | – | – |
Dp_Skipper-1 | 7485 | 388 | 12 | 1 | 6 | no | – | – |
Dl_Skipper-1 | 4763 | 251 | 7 | 2 | 2 | no | – | – |
Pp_Skipper-1 | 5589 | 226 | 14 | 1 | 10 | yes | – | – |
Df_Skipper-1 | 5120 d | n.d. e | 5 | 0 | n.d. e | no | – | – |
Pf_Skipper-1.1 | 5296 | 259 | 6 | 1 | 0 | no | – | – |
Pf_Skipper-1.2 | 6983 | 382 | 3 | 0 | 1 | no | – | – |
Pf_Skipper-1.3 | 7081 | 363 | 7 | 1 | 6 | no | – | – |
Dd-Skipper-2 f | 6178 | 208 | 8 | 0 | 0 | no | – | 8–23 (4) |
Dp_Skipper-2 | 5676 | 315 | 23 | 3 | 5 | yes | – | 7–133 (5) |
Pp_Skipper-2 | 3675 d | n.d. e | 9 | 0 | n.d. e | yes | – | 54–136 (9) |
Df_Skipper-2 | 5708 | 312 | 12 | 7 | 5 | yes | – | 26–97 (11) |
Dd_DGLT-A | 5054 | 265 | 20 | 0 | 5 | yes | 13–33 (18) | – |
Dp_DGLT-A.1 | 5436 | 492 | 15 | 1 | 9 | yes | 13–16 (6) | – |
Dp_DGLT-A.2 | 6114 | 389 | 9 | 2 | 5 | yes | 15 (1) | – |
Dp_DGLT-A.3 | 5589 | 563 | 8 | 1 | 6 | yes | 10–11 (2) | – |
Dp_DGLT-A.4 g | 3447 d | 206 | 30 | 0 | 20 | yes | 16–34 (4) | – |
Dp_DGLT-A.5 g | 3440 d | 354 | 32 | 0 | 32 | yes | 10–19 (15) | – |
Dl_DGLT-A.1 | 4895 | 163 | 10 | 1 | 4 | yes | 63–64 (4) | – |
Dl_DGLT-A.2 | 5112 | 206 | 7 | 1 | 2 | yes | 55–65 (2) | – |
Pp_DGLT-A.1 | 7295 | 601 | 23 | 1 | 13 | no | – | – |
Pp_DGLT-A.2 | 6160 | 393 | 12 | 2 | 6 | no | – | – |
Pp_DGLT-A.3 | 5942 | 212 | 11 | 2 | 3 | no | – | – |
Pp_DGLT-A.4 g | 3650 d | n.d. e | 10 | 0 | n.d. e | yes | 14–24 (3) | – |
Pf_DGLT-A | 8367 | 168 | 2 | 1 | 1 | no | – | – |
Non-LTR retrotransposons | ||||||||
Dd_TRE3-A | 5229 | – | 67 | 13 | – | yes | – | 14–228 (60) |
Dd_TRE3-B | 5279 | – | 43 | 9 | – | yes | – | 34–188 (39) |
Dd_TRE3-C | 4734 | – | 29 | 2 | – | yes | – | 14–305 (29) |
Dd_TRE3-D | 1559 d | – | 11 | 0 | – | yes | – | 49–285 (11) |
Dp_TRE3-A | 5150 | – | 56 | 2 | – | yes | – | 69–161 (18) |
Dp_TRE3-B | 5210 | – | 9 | 2 | – | yes | – | 98–154 (2) |
Dp_TRE3-C | 1620 d | – | 37 | 0 | – | yes | – | 67–450 (15) |
Dl_TRE3-A | 4386 | – | 17 | 2 | – | yes | – | 23/87 (7) |
Pp_TRE3-A | 4515 | – | 35 | 4 | – | yes | – | 26–138 (10) |
Pp_TRE3-B | 4741 | – | 38 | 2 | – | yes | – | 57–151 (11) |
Df_TRE3-A | 1867 d | – | 14 | 0 | – | yes | – | 29–404 (11) |
Dd_TRE5-A | 5647 | – | 102 | 5 | – | yes | 37–90 (98) | – |
Dd_TRE5-B | 5971 | – | 25 | 1 | – | yes | 34–82 (25) | – |
Dd_TRE5-C | 879 d | – | 18 | 0 | – | yes | 38–95 (18) | – |
Dl_TRE5-A h | 7405 | – | 30 | 1 | – | no | – | – |
Pp_TRE5-A | 1169 d | – | 21 | 0 | – | yes | 38–74 (12) | – |
Df_TRE5-A.1 | 2587 d | – | 56 | 1 | – | yes | 45–88 (20) | – |
Df_TRE5-A.2 | 1275 d | – | 20 | 0 | – | yes | 31–98 (18) | – |
Df_TRE5-A.3 | 2941 d | – | 7 | 0 | – | yes | 39–67 (6) | – |
Df_TRE5-B | 1534 d | – | 27 | 0 | – | yes | 44–90 (9) | – |
Dp_NLTR-A | 7438 | – | 28 | 1 | – | yes | 2–6 (16) | – |
Pp_NLTR-B | 5550 d | – | 3 | 0 | – | yes | 39–64 (3) | – |
Pp_NLTR-C | 3536 d | – | 12 | 1 | – | no | – | – |