Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species.
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, | |||
CACTA | Zea mays En/Spm, Arabidopsis thaliana CAC1, | |||
A | ||||
ntir | ||||
r | abidopsis thalian | |||
hinum m | ||||
a | CAC1, | |||
jus | ||||
A | ||||
Tam1, | Petu | |||
n | t | i | rrhinum m | |
a hybrid | ||||
a | jus | Tam1, | Petunia hybrida | PsI |
PsI | ||||
Subclass 2 | ||||
Helitron | Helitron | |||
Oryza sativa | ||||
, | ||||
Arabidopsis thaliana | ||||
AthE1 Atrep, | ||||
Ipomoea tricolor | ||||
Hel-It1 |