Table 1.
A summary of the major characteristics of each MULE group identified in the phylogenetic analysis performed in this study (shadings as illustrated in Additional file 1)
| Group No. | Group Name | Host phyla | TSD length | TIR length | ORF number | Zn finger type | Other motifs/ORFs |
|---|---|---|---|---|---|---|---|
| Outgroup | Rehavkus | Arthropoda and Annelida | 9 bp | 26–400 bp | 1 | PHD finger | Minisatellite in Cterm |
| 1 | TvMULE | Parabasalia | 9–11 bp | 20–38 bp | 1 | FLYWCH for 1 | FAR1 |
| 2 | Phantom-Ca | Ascomycota | 9 bp | 34 bp | 1 | – | – |
| 3 | Curupira | Platyhelminthes | 9 bp | None | 1 | SWIM | – |
| 4 | MULE-Ag | Mucoromycota | amino acid sequence | – | – | – | – |
| 5 | MULE-Mucorales | Mucoromycota | 10 bp | 40 bp | 1 | SWIM | – |
| 6 | MULE-Co | Filozoa | Not indicated in RepBase | None | 2 | – | The second ORF is unknown |
| 7 | Ghost sub-group Cnidaria | Cnidaria | Not indicated in Repbase | 177 bp and amino acid sequences | 1 | – | – |
| 7 | Ghost | Arthropoda | Not identified | None and amino acid sequences | 1 | SWIM | – |
| 8 | Spectre | Arthropoda | 8 bp | 76 bp | 1 | C2H2 | – |
| 9 | MULE-Ov | Platyhelminth | amino acid sequences only | – | – | – | – |
| 10 | MULE-Pi | Oomycota | amino acid sequences only | – | – | – | – |
| 11 | MULE1_EI | Amoebozoa | 9 bp | 187 bp | 1 | – | |
| 12 | MULE-Ei | Amoebozoa | amino acid sequences only | – | – | – | |
| 13 | EMULE | Amoebozoa | amino acid sequences only | – | – | – | – |
| 14 | MuDR-6_HM | Cnidaria | Not indicated in RepBase | None | 1 | – | Ovarian Tumour Gene |
| 15 | MULE-Cg | Mollusca | Not indicated in RepBase | 48 bp and 296 bp | 1 | – | – |
| 16 | MULE-Phytophthora_1 sub-group Sm | Platyhelminthes | 9 bp | 42–46 bp | 1 | SWIM and FLYWCH | – |
| 16 | MULE-Phytophthora_1 | Oomycota | Not indicated in RepBase | None, except one with 71 bp | 1 or 2 | SWIM only in MuDR-5 | SET for 14 members |
| 17 | MuDRx-Phytophthora | Oomycota | 9 bp | 40–80 bp | 1 | FLYWCH | – |
| 18 | MULE-Tv | Parabasalia | 9 bp | 100 bp and 31 bp | 1 | – | – |
| 19 | MULE-Mollusca | Mollusca | Not indicated in RepBase | None and amino acid sequences | 1 | – | – |
| 20 | Phantom | Platyhelminthes, Crustacea, Arthropoda, Tunicata and Ichnovirus | Not indicated/8-10 bp | 18–613/None | 1 or 2 | None or FLYWCH or SWIM | Mini-satellite after the transposase ORF (aphids) |
| 21–34 | MULE-Trichinella | Annelida | Not indicated | None and amino acid sequences | 1 | – | – |
| 35 | Hop sub-group MULE-Cglob | Ascomycota | Not indicated in RepBase | 51 bp and amino acid sequences | 1 | CCHC | – |
| 35 | sub-group Mutyl | Ascomycota | 9–10 bp | 22 bp | 2 | C2H2 | Second ORF called MutB in antisens |
| 35 | sub-group plants, Phytophthora, Pucciniaand Fungi | Magnoliophyta, Oomycota, Basidiomycota and Ascomycota | Not indicated in RepBase | 30–220 bp and amino acid sequences | 1 | CCHC, C2H2 and SWIM | FAR1 in half the members |
| 35 | sub-group Fungi | Ascomycota | Not indicated in RepBase | 85–99 bp and amino acid sequences | 1 or 2 | CCHC | – |
| 36 | Jittery sub-group MULE-Cc | Rhodophyta | Not indicated in RepBase | 192 bp and 500 bp | 1 | SWIM | Various inserts, potentially host derived |
| 36 | sub-group Dicots and Monocots | Magnoliophyta | Not indicated/8 bp | 39–292 bp, none and amino acid seq | 1 | SWIM or CCHC in Cterm | FAR1 in Nterm |
| 37 | MULE-Diatoms | Stramenopiles | No TSD and not indicated | 123–124 bp and amino acid sequences | 1 | SWIM | – |
| 38 | MULE-Cc | Rhodophyta | 9 bp and not indicated | 244 and 640 bp | 1 | SWIM | – |
| 39 | MULE-Phytophthora_2 | Oomycota | Not indicated in RepBase | 81, 67 bp and amino acid sequences | 1 | SWIM and CCHC | – |
| 40 | MuDR-4_Sm | Platyhelminth | Not indicated in RepBase | 53 bp | 1 | SWIM | – |
| 41 | MULE-Cm | Magnoliophyta | amino acid sequences only | – | – | – | – |
| 42 | MULE-Solanaceae_1 | Magnoliophyta | 9 bp and not indicated | None and amino acid sequences | 1 | SWIM | unknown ORF and PMD (antisens) |
| 43 | MULE-Capsicum | Magnoliophyta | amino acid sequences only | – | – | – | – |
| 44 | MULE-Solanaceae_2 | Magnoliophyta, one Oomycota | 9 bp and not indicated | None and amino acid sequences | – | – | – |
| 45 | VANDAL | Magnoliophyta | 9 bp and not indicated | 46–174 bp and amino acid sequences | 1 | SWIM and CCHC | PMD and/or DUF in half the members |
| 46 | MuDR-9_OS | Magnoliophyta | 9 bp | 45 bp | 1 | SWIM | PMD |
| 47 | MULE-Monocots | Magnoliophyta | Not indicated in RepBase | 14–421 bp and amino acid sequences | 1 | SWIM or CCHC | PMD in most, sometimes antisense |
| 48 | MDR | Magnoliophyta | Not indicated/9 bp | 32–373 bp and amino acid sequences | 1 | SWIM | PMD in most, sometimes antisense |
| 49 | MUDRAVI2 | Magnoliophyta | Not indicated/9 bp | 80–290 bp and amino acid sequences | 1 or 2 | SWIM or CCHC | PMD in most, often antisense |
| 50 | MUDR | Magnoliophyta | Not indicated/9–10 bp | 30–320 bp and amino acid seq | 1 or 2 | SWIM (CCHC for MuDR-13B_Atr and MuDRB_PT) | PMD in antisense for most of them |
| 50 | sub-group Phytophthora | Oomycota | Not indicated in RepBase | 40–55 bp | 1 | SWIM (C3HC4 ring finger for 37_Pi) | FAR1 in MULE-1_Pi and MuDR-2_Pso |
| 50 | sub-group MUDRAVI | Magnoliophyta | Not indicated/9 bp | 63–447 bp and amino acid sequences | 1 | SWIM and C2H2 for two members | – |