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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
  1. aTotal copy numbers refer to both full-length and partial sequences
  2. bFull-length copies with intact open reading frames
  3. cDistances are listed only for retrotransposons found in the direct neighborhood of tRNA genes; in cases where other tRNA gene-specific retrotransposons have integrated at the same tRNA gene and therefore upstream of a previously inserted element, distances of the original insertion to the target could not be determined. The number of elements used for determination of target distances are shown in parentheses
  4. dNo full-length consensus available
  5. eNo LTR sequences detectable
  6. fPrevious name DGLT-B (GenBank AF474004) [17]
  7. gNo ORFs for phylogenetic analysis; classification as DGLT-A according to integration preference
  8. hClassified as TRE5 by similarity of RT sequence (compare Fig. 5)