If these first four classification levels are generally well accepted, the need of extra levels to reach the TE family level is still unclear and may vary according to the TE considered. For example, the superfamily subgroups “chromovirus” or “non-chromovirus” have been introduced for Gypsy LTR-RTs [20]. An increase in family/lineage number or even new superfamilies will probably arise with the accumulation of genome sequencing data and the improvement of bioinformatic pipelines for TE detection and annotation. This hierarchical classification also does not include some non-autonomous TEs, i.e., TEs that are still able to transpose but need extra-function in trans coming from another TE element (phylogenetically related or not). This includes LARDs (large retrotransposon derivatives), TRIMs (transposon in miniature) and SMARTs (small LTR-retrotransposon) for Class I TEs, and MITEs (miniature inverted-repeats transposable elements), SNACs (small non-autonomous CACTA) or MULEs (Mu-like elements) for class II TEs. Many such non-autonomous elements share enough sequence similarity/motifs to be easily linked to a candidate “helper” autonomous TE family, as reported in rice with the isolation of the complete RIRE2 Gyspy retrotransposon displaying a high LTR sequence similarity to sequence extremities of the defective Dasheng retrotransposon [21]. Another example is the description of both complete and truncated—but nevertheless active—CACTA Caspar elements in Triticeae ^[16][22][16,22]. Some other non-autonomous TEs may not present any clear feature allowing them to be classified, as some non-autonomous short TIR-harboring Tes that may share only a few bases homology with the autonomous helper [16]. In the classification we propose, we choose to include the non-autonomous SINES as a full order, as these TEs do not correspond to deleted versions of autonomous class I TEs.

Table 1 and Figure 1 present, respectively, the up-to-date classification and structures of plant transposable elements adapted from Wicker et al. [16]. It is important to note that only a subset of existing TE superfamilies in all living organisms (as reported in repbase https://www.girinst.org/repbase/update/browse.php accessed on 10 March 2022) has been detected in land plants (~30% of class II superfamilies, and ~17% of class I—representing 20% of all described superfamilies). Plant TEs fall into six different orders, four orders corresponding to class I elements (LTR-RTs, Penelope-like elements (PLE), long interspaced nuclear elements (LINEs), short interspaced nuclear elements (SINEs)) and two orders including elements of class II (terminal inverted repeat (TIR) transposons, Helitrons) (Table 1).

Figure 1. Structure and organization of plant transposable element superfamilies (adapted from [16]). Schemes are not to scale. Protein coding domains: APE = apurinic endonuclease, CHR = chromodomain, EN = endonuclease, GAG = capsid protein, HEL = helicase, INT = integrase, PROT = proteinase, RH = RNAse H, RPA = replication protein A, RT = reverse transcriptase. eORF = extra open reading frame (unknown function), Tpase = transposase (* with DDE motif), YR = tyrosine recombinase, Y2 = YR with YY motif, ◊ = different possible locations of an additional cellular-like ribonuclease H (aRH) specific of the Tat lineages (see Table 1). Optional protein-coding domains only present in some superfamily lineages are indicated in brackets. Some structural features are also represented. Terminal repeats in the same or reverse orientation are indicated by black arrows, and purple rectangles refer to diagnostic sequences present in non-coding sequences. Specific base termination of some TEs are also indicated. PBS = primer binding site, PPT = poly purine tract. Interrupted line in Helitron representation means that the region may contain one or more additional ORFs.

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][24,25,26] for Penelope-like elements (PLEs), ref. [27] for long interspaced nuclear elements (LINEs), ref. ^[28][29][28,29] for short interspaced nuclear elements (SINEs), and ^[30][31][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,
		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

In plants, class II elements (subclass 1) belonging to the TIR order (also called DNA transposons) fall into six superfamilies, based on the structure and sequence of their transposase and on the sequence of their terminal inverted repeats (TIRs) (Figure 1). Transposase is the protein catalyzing their transposition, while TIRs harbor key sequences recognized by the DNA-binding domains of the transposase during a transposition event. Some TIR elements also harbor additional coding sequences, as the maize MuDR, and plant CACTA or PIF/Harbinger elements [16]. Most of these superfamilies are also characterized by specific target site duplications (TSDs) lengths, generated after the filling of DNA nicks generated by the transposase on the integration site. Their transposition is not always strictly conservative and could lead to an increase of copy number if it occurs before a DNA replication fork [32].

Replicating plant TEs fall into two major groups: (1) Helitrons (class II-subclass 2, see Table 1) replicate through a rolling-circle (RC) mechanism from one DNA strand, without generating TSDs, by using a RepHel protein with a RC replication initiator (Rep) and DNA helicase (Hel) domains, in association with an ssDNA-binding “replication protein A” (RPA) [33]. (2) Class I retrotransposons replicate from RNA templates by reverse transcription using a TE-encoded reverse transcriptase (RT) and use at least one additional protein to mediate their insertion into their host genome, such as endonuclease (EN) or DDE integrase (INT). We do not include the DIRS superfamily as a member of land plants, as DIRS elements have only been found in green algae until now [34].

Among the four retrotransposon orders present in plants, SINEs occupy a particular place, as these small non-coding and non-autonomous elements of a few hundred base pairs exploit the transposition machinery of LINEs to ensure their amplification. Plant SINEs are derived from tRNAs [28]. They are transcribed by polymerase III, harbor short degenerated internal promoters (A and B boxes), and display mostly A tail at the 3′-end. Apart from these small structural domains, SINEs display a high sequence diversity that hinders their detection and characterization. Recently, a 37 pb Angio-domain located in the 3′-end has been reported in many Angiosperm SINEs [29].

The second non-LTR retrotransposon order present in plants, LINEs, contains elements belonging to the L1 and the RTE (retrotransposable element) superfamilies (Table 1 and Figure 1), which are two of the five known superfamilies of LINEs detected in eukaryotes [16]. RTE and L1 LINEs have one or two open reading frames (ORFs), respectively, and code for proteins required for retrotransposition, such as an endonuclease (EN), a RT, and often a ribonuclease H (RNase H (RH)). The L1 ORF1 is involved in the binding, protection and transport of the RNA intermediate used for retrotransposition. At their 3′-end lies a stretch of (A)_n for L1 or (GTT)_n for RTE involved in the reverse transcription initiation. A recent study shows that plant LINEs extracted from 23 genomes fall into only seven L1 and one RTE families/lineages/subclades [27]. As the reverse transcription starts from the 3′-end of LINEs and does not always reach the 5′-end, many incomplete daughter copies can be generated.

Between their bordering direct repeats 5′-LTR and 3′-LTR, autonomous LTR-retrotransposons (LTR-RTs) code for structural capsid-like (GAG) and functional (POL) proteins needed for their retrotransposition cycle (RT = reverse transcriptase, RH, INT = integrase), resembling the replication cycle of retroviruses. Only two out of the five superfamilies found in eukaryotes are represented in plants [16]. Plant LTR-RTs are further classified into Copia/Ty1 or Gypsy/Ty3 superfamilies according to the order of their coding pol domains. Recently, a systematic survey of plant LTR-RTs in 80 plant genomes refined the classification by introducing 16 lineages/families into the Copia/Ty1 superfamily and 14 lineages/families into the Gypsy/Ty3 group (six with a chromo-domain and eight without) [20]. Two Gypsy lineages, Chlamyvir and Tcn1, having only representatives in algae and non-Viridiplantae species, have not been included in Table 1. Non-autonomous derivatives of variable size (from a few hundred bp up to 25 kb) have been characterized in plants, containing between both LTRs a DNA sequence of variable length, either non-coding or reminiscent of some retrotransposon internal domains. Large internal sequences (>4 kb) define LARDs (large retrotransposon derivatives), and short ones (<4 kb) are often called TRIM (terminal repeat retrotransposon in miniature) [16].

Retrotransposons belonging to the Penelope-like elements (PLE) order are also found in some plant genomes, but with a patchy distribution. PLE encode an RT domain related to telomerase, a highly specialized class of non-mobile RTs responsible for chromosome end maintenance in most eukaryotes. Some PLEs also carry a second EN domain with a specific GIY-YIG motif. PLEs are bordered by repeats in direct or reverse orientation and are often subjected to 5′ truncation upon retrotransposition, as non-LTR retrotransposons. EN(+)PLEs (Dryads elements belonging to the Penelope/Poseidon group) and EN(-)PLEs have been found in some Conifer genomes (Table 1, Figure 1), and some of them were presumably derived from a horizontal transfer (HT) event [26].

The accumulation of sequenced genomes and TE detection pipelines allow the analysis and comparison of TE composition and diversity across plant genera. Figure 2 presents a heatmap of genomic percentage of four types of TEs—LTR-RTs, LINEs, SINEs and TIR DNA transposons—across 74 Angiosperm species displaying variable genome sizes (Data collected from [35] in the Supplementary Tables S1 and S2 of this article). Among the different types of TEs, LTR-RTs (Copia/Ty1 and Gypsy/Ty3) occupy the largest proportion of these genomes, the highest being up to 80% in Zea mays. Such an increase can result from rapid amplification of only a few families. For example, Oryza australiensis has undergone a recent burst of transposition involving only three families (one Copia = RIRE1 and two Gypsy = Wallabi and Kangourou), which compose 60% of its genome [36]. Genomes of the legume tribe Fabeae are also dominated by the Ty3/Gypsy Ogre family/lineage, that accounts for 57% of genome size variation on average in this clade [37]. The predominance of one type of LTR-RT may vary depending on the taxa considered. For example, in Gossypium species, Copia LTR-RTs have accumulated in the small genome of G. raimondii (880 Mb), while Gypsy LTR-RTs (mainly Gorge3) have proliferated in large genomes lineages of G. herbaceum 1667 Mb) and G. exiguum (2460 Mb) [38]. Plant species belonging to the same order (see Brassicales, Poales, Figure 2) might display different TE compositions and genome sizes. Some plant species also harbor specific TE composition as shown in Figure 2, with dominance of LINEs retrotransposons or TIR DNA transposon for the aquatic plant coontail Ceratophyllum demersum (33.6% of total genome size) and the small herbaceous plant Trichopus zeylanicus (~27.3% of total genome size). Non-LTR-retrotransposons have been shown to be abundant (~11.7%) in other plant genomes, such as Arachis ipaenis, one of the peanut parental genomes [39].

Figure 2. Transposable elements (TE) profiles in some land plant genomes. Species are clustered according to their TE profiles. TE percentages, plant orders and genome size estimations from 74 land plant species have been collected from [35] (data collected in Supporting information, Tables S1 and S2 from [35]). Some plant orders as Poales or Brassicales have been highlighted in colors (green and red respectively) in order to underline the diversity of TE composition between species belonging to the same plant order. Plant belonging to different orders as Dioscoreales and Ceratophyllales (in blue) can share close TE composition.