Table 1.
Plant transposable element (TE) classification compiled from [16] with updates from [23] for Copia lineages, ref. [20] for Gypsy LTR retrotransposons (LTR-RTs), ref. [24,25,26] for Penelope-like elements (PLEs), ref. [27] for long interspaced nuclear elements (LINEs), ref. [28,29] for short interspaced nuclear elements (SINEs), and [30,31] for Sola elements.
| Class | Order (Non-Autonomous TE Name) |
Superfamily | Family/Lineage | Plant Family Examples |
|---|---|---|---|---|
| Class I | LTR-Retrotransposons | Copia | Osser | Volvox canteri Osser |
| (retrotransposons) | (LARD) | Bryco | representatives in moss species | |
| (TRIM/SMART) | Lyco | representatives in clubmosses species (Lycopodiaceae) | ||
| Gymco-I | representatives in gymnosperms species | |||
| Gymco-II | representatives in gymnosperms species | |||
| Gymco-III | representatives in gymnosperms species | |||
| Gymco-IV | representatives in gymnosperms species | |||
| Ale/Retrofit | Oryza longistaminata Retrofit, Oryza sativa Hopscotch | |||
| Ivana | Oryza sativa Oryko1-1 and Ilona, Hordeum vulgare HORPIA, Nicotiana tabacum Queenti | |||
| Ikeros | Zea mays Sto-4 | |||
| Tork | Nicotiana tabacum Tnt1, Tto1 and Tnt2, Solanum lycopersicum Tork4, Ipomea batatas Batata | |||
| Alesia | low copy number representatives in many Angiosperms, close to the Ale lineage | |||
| Angela | Triticum aestivum Angela, Oryza sativa RIRE1, Hordeum vulgare BARE1 | |||
| Bianca | Triticeae Bianca, Arabidopsis thaliana RomaniAT5 | |||
| SIRE/Maximus | Solanum lycopersicum ToRTL1, Zea mays Opie-2, Glycine max SIRE1 | |||
| TAR | Oryza spp. Houba and Osr-1, Arabidopsis thaliana ATcopia95 | |||
| Gypsy (Chromovirus) | Galadriel | Solanum esculentum Galadriel, Musa Monkey, Tntom1 | ||
| Tekay | Hordeum vulgare Bagy-1, Arabidopsis thaliana Legolas Peabody, Oryza sativa RIRE3, Lilium henryi Del | |||
| Reina | Zea mays Reina, Arabidopsis thaliana Gloin or Gimli | |||
| CRM | Zea mays CRM (centromeric retrotransposon of maize), Beta vulgaris Beetle1, Oryza sativa RIRE7 | |||
| (Non-chromovirus) | Phygy | Phycomitrella patens Chr21 (4035670,4045566) | ||
| Selgy | Selaginella moellendorffii LTR-RT | |||
| Athila | Arabidopsis thaliana Athila4-1, Diaspora, Hordeum vulgare Bagy-2 | |||
| TatI | Selaginella moellendorffii LTR-RT | |||
| TatII | Picea abies, Picea glauca LTR-RTs | |||
| TatIII | Picea abies, Picea glauca LTR-RTs | |||
| Ogre/TatIV + TatV | Pisum sativum Ogre | |||
| Retand/TatVI |
Zea mays Cinful-1, Arabidopsis thaliana Tat4-1, Oryza sativa RIRE2, Sorghum bicolor
RetroSor1, Silene latifolia Retand |
|||
| Non-LTR retrotransposons PLE |
Penelope/Poseidon | Pinus taeda (loblolly pine) and Picea abies (Norway spruce) Dryad PLEs by horizontal transfer | ||
| EN(-)PLE | Selaginella moellendorffii spike moss, Pinus taeda and Picea abies EN(-)PLEs | |||
| LINE | L1 | Llb | sweet potato Llb, Beta vulgaris BvL1 | |
| LINE-CS | Cannabis sativa LINE-CS, Beta vulgaris Belline2, Belline5 | |||
| BNR | Beta vulgaris Belline1/BNR | |||
| PUR | Carica papaya L1-26_Cpa, Solanum tuberosum L1-3_Stu, Vitis vinifera | |||
| Cin4 | Zea mays Cin4 | |||
| Karma | Oryza sativa Karma | |||
| nubo | Oryza sativa LINE-1 or OSLINE1-4, Zea mays L1-2_ZM | |||
| RTE | plant RTE | Malus x domestica RTE-1_Mad, Solanum tuberosum RTE-1_Stu | ||
| SINE | tRNA | Nicotiana tabacum TS, Au, Solanales SolS-II, Brassicale BraS-I, SB families, mainly found in Angiosperm | ||
| Class II Subclass 1 |
TIR (MITE) | Tc1-Mariner | Stowaway (MITE): Sorghum bicolor Stowaway, Brassica BraSto | |
| hAT | Zea mays Ac/Ds, Antirrhinum majus Tam3, Nicotiana tabacum Slide | |||
| Sola | Physcomitrella Sola1, found also in Capsicum annuum and C. baccatum | |||
| (MULE) | MuDR-Foldback | Zea mays Mu, MULEs | ||
| PIF-Harbinger | Zea mays PIFa, Oryza sativa Pong; Tourist (MITE): mPing/Ping; mPIF/PIFa | |||
| CACTA | Zea mays En/Spm, Arabidopsis thaliana CAC1, Antirrhinum majus Tam1, Petunia hybrida PsI | |||
| Subclass 2 | Helitron | Helitron | Oryza sativa, Arabidopsis thaliana AthE1 Atrep, Ipomoea tricolor Hel-It1 |