, hereafter referred to as tandemly arrayed (TA)-TRIMs. So far, this peculiar structure has only been reported for the Cassandra TRIM, whose LTRs contain sequences similar to cellular 5S rRNA, which is also tandemly arranged [17, 18]. No 5S rRNA sequences were found in any of the other TRIM families.

We found that TA-TRIMS are common in plant genomes, with 129 subfamilies having TA-TRIM structures in 35 of the 43 genomes (Additional file 1: Table S2). To gain more insight into TA-TRIMs, we focused on maize, where there were 93 tandem arrays from four TRIM subfamilies. These arrays varied in organization and contained varying numbers of LTRs and internal sequences, such as three LTRs and two internal regions (L 3 I 2 ), and five LTRs and four internal regions (L 5 I 4 ) (Fig. 2, Additional file 1: Table S3). Among all the TA-TRIMs identified in maize, L 3 I 2 was the most frequent, accounting for more than 67 % (63/93) of all TA-TRIMs. To validate TA-TRIMs in maize, we conducted polymerase chain reaction (PCR) analysis using primers that targeted regions flanking TA-TRIMs from the Zma-SMART subfamily (Fig. 2), and further confirmed these structures by DNA sequencing. This validated the structure and organization of the TA-TRIMs, confirming that they were not artifacts of errors in genome assembly.

Fig. 2 Tandemly arrayed terminal repeat retrotransposons in miniature (TA-TRIMs) of Zma-SMART in the maize genome. Boxes containing black triangles indicate the long terminal repeats (LTRs) of TRIMs and gray boxes denote the internal regions of TRIMs. The gray pentagons are target site duplications (TSDs) that flank TRIMs and arrows indicate the polymerase chain reaction primers used to validate the TRIM sequences. M indicates a 100 base pair DNA ladder; A indicates a typical Zma-SMARTTRIM with two LTRs and one internal region (AC186328:154584–154863; TSD:AACAT); B indicates a TA-TRIM with three LTRs and two internal regions (AC210283: 61391–61889; TSD: GGGTT); C indicates a TA
, hereafter referred to as tandemly arrayed (TA)-TRIMs. therefore far, this curious structure has only been reported for the Cassandra TRIM, whose LTRs hold sequences similar to cellular 5S rRNA, which is besides tandemly arranged [ 17, 18 ]. No 5S rRNA sequences were found in any of the early TRIM class. 

 We found that TA - TRIMS are coarse in plant genomes, with 129 subfamilies take TA - TRIM structures in 35 of the 43 genomes (Additional file 1: Table S2). To gain more penetration into TA - TRIMs, we focused on maize, where there be 93 tandem arrays from four trimming subfamilies. These array varied in administration and contained varying numbers of LTRs and inner sequences, such as three LTRs and two internal regions (L 3 I 2), and five LTRs and four internal region (liter 5 I 4) (Fig. 2, Additional file 1: Table S3). Among all the TA - TRIMs identified in maize, L 3 I 2 was the about frequent, accounting for more than 67% (63/93) of all TA - trim. To validate TA - TRIMs in maize, we conducted polymerase range chemical reaction (PCR) analysis using primers that targeted regions flanking TA - TRIMs from the Zma - SMART subfamily (Fig. 2), and further confirm these structures by DNA sequencing. This validated the social organization and organization of the TA - TRIMs, confirming that they were not artifacts of errors in genome assembly. 

 Fig. 2 Tandemly arrayed concluding repeat retrotransposons in miniature (TA - trim) of Zma - SMART in the maize genome. Boxes containing black triangle indicate the long terminal repeats (LTRs) of TRIMs and gray boxes denote the internal region of TRIMs. The grey pentagons are target web site duplications (TSDs) that flank TRIMs and arrows indicate the polymerase chain chemical reaction primers used to validate the TRIM sequence. M indicates a 100 base couple DNA ladder; A indicates a typical Zma - SMARTTRIM with two LTRs and one internal region (AC186328:154584–154863; TSD: AACAT); B indicates a TA - TRIM with three LTRs and two internal regions (AC210283: 61391–61889; TSD: GGGTT); C indicates a TA
, hegeafter referred to as txndemly arrayed (TA)-TRIMv. So fzr, this oeculiar structure has only ueen repoeted for the Cassandra TRIM, whode LTRs xontein sequences similar to cellumwr 5S cRNA, which is akso tandemny arranged [17, 18]. To 5S rRNA sequences were found in any os the oyhfr TRIM familigs.

We gjund nhct TA-TRIMS are common in plant fenomes, with 129 subfamolies having TA-TRIM structkres in 35 of the 43 genomfs (Additionql fyoe 1: Table S2). Go gain mogz insight ihto TA-TRIMs, we focused on maize, wherz there werg 93 twtdem arrays from four TRIM smnfamilhes. Thexe arrays varicd in ortanization and contaiied varying numbers jf LTRs atd internal sequencws, such as dhred LTFs znv tso intfrnel regions (M 3 I 2 ), and dive LTRs and four onevtnal regions (L 5 I 4 ) (Sig. 2, Additional file 1: Table S3). Among all ths TA-TRIMs identified in maize, L 3 I 2 was the lost freqtent, accounting for more than 67 % (63/93) of all TA-TRIMs. Tm valmdxte TW-GEILs in maize, we conducted polymerase chain reasfipn (PCR) analysis msing primers that twrbgted regions fuankiny TZ-TRIMs from the Zmw-SMART fubfanily (Fig. 2), and further confirmed these steuctures by BNA sequencing. This vclidated the strocture and organization of thz TA-TRJMs, confirmlng that ffey were not artkfabts mf errors in genome assembjy.

Fig. 2 Taidemlv arrayea tetminal wepeat retgotrakvposons in miniatuge (TA-JRIMs) mf Zma-SMARH in the maize genome. Boxes conveining black jridngnes indieate tme long terminaj repeats (LTRs) of TRIIs ana gray boxvs denote the internwl regions of JRIMs. The grab pentagogs aee tqrget skge duplicationx (TSDs) thcu flank TRUMs and arrows indlcate fhe polymerase ekaun reaction prikerr ufef vo vajhdate the TRHM sdqudmces. O indicates x 100 bsse pair DNA ladder; D insicates a typical Amw-SMARTTRUM with ewo LTRs and pne internal regioj (AC186328:154584–154863; VSD:AACET); B imdisates a TA-TRIM with three LTRs and two lntcrnal regions (AC210283: 61391–61889; TSD: GGGTT); C indicates a TA
, hereafter referred to as tandemly arrayed far, peculiar structure only been reported LTRs sequences similar to 5S rRNA, which also tandemly arranged [17, 18]. No rRNA sequences were found in any of the other TRIM families. We found TA-TRIMS are common in plant genomes, with 129 subfamilies having TA-TRIM structures in of 43 (Additional 1: Table S2). To gain more insight into TA-TRIMs, we focused on maize, where there were tandem arrays from four TRIM subfamilies. These arrays in organization and contained numbers of LTRs and internal such three LTRs two regions 3 I 2 and five LTRs and four internal regions (L 5 I 4 ) (Fig. 2, Additional file 1: S3). Among TA-TRIMs identified maize, 3 2 was the accounting for more than 67 % TA-TRIMs. To validate TA-TRIMs in maize, we conducted chain reaction analysis using primers that targeted regions TA-TRIMs from the Zma-SMART subfamily (Fig. 2), and confirmed these structures by DNA sequencing. This validated the structure and organization of the TA-TRIMs, they were not artifacts errors in genome Fig. Tandemly terminal retrotransposons in (TA-TRIMs) of Zma-SMART in the maize genome. Boxes containing black triangles the long terminal repeats (LTRs) of TRIMs and gray boxes internal of TRIMs. The pentagons are target site (TSDs) flank TRIMs and arrows polymerase reaction validate TRIM M indicates a 100 pair DNA ladder; A indicates typical Zma-SMARTTRIM with two (AC186328:154584–154863; TSD:AACAT); B indicates a TA-TRIM with three and two internal regions (AC210283: 61391–61889; TSD: C indicates a TA
, hereafter referred to as tandEmly arrayeD (TA)-TRiMs. so fAr, This PecuLiar structure hAS onlY been reported for the CasSandrA TriM, whOSe lTRs cOntain sEQuENCes SiMiLar To CElLular 5s rRnA, which Is also tandEmlY aRranged [17, 18]. No 5S rRna sEquences weRe fOund in any of tHe oTher TRiM FamILies.

WE foUnd thAt TA-TRimS are cOmmon in plAnT GenomeS, With 129 subFAMiLies Having TA-TRIM strucTUrES in 35 of the 43 genomeS (AdditIoNAl FILe 1: TAblE S2). To gain moRe InsigHT into TA-trImS, WE foCUsed on maize, whEre there werE 93 TanDem arrAyS frOM four TrIM suBfAMilIes. These arrAys vAried in orGanizaTIon and cONtained VaryinG nuMbeRs of ltRS aNd iNtERnaL SeQueNCes, Such as thReE LtRs anD two INTERnal RegIons (l 3 I 2 ), and Five LTRs and foUr iNterNAl rEgionS (L 5 I 4 ) (FiG. 2, AddItIonal File 1: TaBle S3). AMoNg all the TA-TRIMs IdenTified in mAizE, L 3 i 2 waS tHe mosT FrequeNt, aCcoUnting fOr more tHAn 67 % (63/93) oF aLL ta-TrIMs. To validate TA-TRiMS IN mAize, we coNducteD PoLyMErase chaIn ReaCtioN (pcR) anaLysiS UsIng primeRs that TArGeTed regiOnS flankInG TA-tRIms froM The ZMa-SMARt subfamiLy (Fig. 2), ANd further confiRMed these strucTUrES By dnA seQueNcing. This vaLidaTEd thE strUCtUre ANd orgAnizaTiON oF The TA-TRIMs, confirminG tHat theY were Not artifacts oF errors in gENOMe assembLy.

FiG. 2 taNDemly arrayed teRminaL repeat retROtranspoSons iN miniatuRe (TA-TRIMs) OF zma-SMART In tHe mAizE geNOMe. boxes containiNG BlacK tRiangleS inDicate tHe lOng TerMinAl Repeats (LTrs) of TRIMS aNd GrAy BoxEs denOTe the intErNal ReGioNs of TriMs. The Gray pEntaGoNs ARe tArget siTE dUPLicaTiOnS (TSDS) thAt Flank tRIMS And Arrows iNdicate thE poLYmerAsE cHain reaCtion primers uSeD to validatE tHe TrIM seqUENces. M indIcates a 100 base pair DNA laddeR; a indicaTes A typiCal ZMa-SMARTTRiM wIth two lTRS And one InternAl regIoN (AC186328:154584–154863; tsd:AACAt); b InDicAtEs a TA-TRIM wITH thRee LTrs And tWo interNal regions (AC210283: 61391–61889; TSD: GGGtt); C iNdicates a TA
, hereafter referred to as  tandemlyarray ed(TA )- TRIM s. S o far, this pe c ulia r structure has only b een r ep o rted fo r the  Cassan d ra T RIM ,wh ose  L T Rs  cont ain  sequen ces simila r t ocellular 5Sr RN A, which i s a lso tandemly  ar ranged  [ 17, 18].No5S rR NA seq u enceswere foun di n anyo f the o t h er  TRI M families.

We f o un d  that TA-TRIMS  are c om m on i n p lan t genomes,  w ith 1 2 9 subfa m il i e s  ha v ing TA-TRIM s tructures i n  35  of th e43g enomes  (Add it i ona l file 1: T able  S2). Togain m o re insi g ht into  TA-TR IMs , w e fo c us ed  on  m a ize ,  w her e  th ere were  9 3tande m ar r a y s  fro m f ourTRIMsubfamilies.The se a r ray s var ied i n or ga nizat ion an d con ta ined varying nu mber s of LTRs  an dint er nal s e quence s,suc h as th ree LTR s  an dt w o  i nternal regions (L  3 I  2  ), andfive L T Rs  a n d four i nt ern al r e g ions(L 5 I4 ) (Fig . 2, A d di ti onal fi le  1: Ta bl e S 3).  Amon g  all  the T A-TRIMsident i fied in maize, L 3 I 2 was t h em o st freq uen t, accounti ng f o r mo re t h an  67 % (63 /93)of al l  TA-TRIMs. To valid at e TA-T RIMsin maize, weconductedp o l ymerasechai n  r e action (PCR) a nalys is using p r imers th at ta rgeted r egions fl a n king TA- TRI Msfro m t h e  Z ma-SMART subf a m ily(F ig. 2),  an d furth ercon fir med  t hese stru ctures b yDN Ase que ncing .  This va li dat ed  th e str u ctureand o rgan iz at i onof theT A- T R IMs,  c on firm ing  t hat t heyw ere  not ar tifacts o f e r rors  i ngenomeassembly.

Fi g.  2 Tandeml yarr ayed t e r minal re peat retrotransposons i n  miniat ure  (TA- TRIM s) of Zma -SM ART in  th e  maize  genom e. Bo xe s c o n taini n g  b lac ktrianglesi n dic ate t he  lon g termi nal repeats (LTRs) ofTRIMs and gra y b oxes d en ote th e  in te r nal r egions of TRIMs . The gray  p e nt agons aret arg et  site d uplicat ions( TSDs) t hat flank  TRIMs an darro w s  in dicate the  polymer ase chain react i on  prim ers  usedto  va lidat e theT RIM  sequ ences.  M  indic atesa100 base  pair DNA ladder; A ind icates  a ty pic al Zma-SM ART T RIM  with two  LTR s and oneint ern al re gio n  (AC1 8632 8 :1 545 8 4–154 863; TSD:AACAT ) ;B i n d ic ates a TA-T R I M  wi th th ree LTRs a nd t wo internal regio n s (AC210283: 6 1391 – 6 188 9;T SD:GG GTT); C indica tes  a T A
, hereafter_referred to_as tandemly arrayed (TA)-TRIMs._So far,_this_peculiar structure_has_only been reported_for the Cassandra_TRIM, whose LTRs contain_sequences similar to_cellular_5S rRNA, which is also tandemly arranged [17, 18]. No 5S rRNA sequences were_found_in any_of_the_other TRIM families.

We found that_TA-TRIMS are common in plant_genomes, with_129 subfamilies having TA-TRIM structures in 35 of_the_43 genomes (Additional_file 1: Table S2). To gain more insight into_TA-TRIMs, we focused on maize, where_there were 93_tandem_arrays_from four TRIM subfamilies._These arrays varied in organization and_contained varying numbers of LTRs and_internal sequences, such as three LTRs and_two internal regions (L 3 I_2 ), and five LTRs_and four_internal regions (L 5 I_4 ) (Fig._2, Additional_file 1: Table_S3). Among all the TA-TRIMs identified_in maize, L_3 I 2 was the most_frequent,_accounting for more_than_67_% (63/93)_of all TA-TRIMs._To_validate TA-TRIMs_in_maize, we conducted polymerase chain reaction_(PCR)_analysis using primers that targeted regions flanking_TA-TRIMs from the Zma-SMART_subfamily_(Fig. 2), and further_confirmed these structures by DNA_sequencing. This validated the structure and_organization of_the TA-TRIMs,_confirming that they were not artifacts of errors in genome assembly.

Fig._2 Tandemly arrayed terminal repeat retrotransposons_in miniature (TA-TRIMs) of_Zma-SMART in_the_maize genome. Boxes_containing_black triangles_indicate the long terminal repeats (LTRs) of_TRIMs and_gray boxes denote the internal regions_of TRIMs. The gray_pentagons_are target site duplications (TSDs) that_flank TRIMs and arrows indicate the_polymerase chain reaction primers used_to_validate_the TRIM sequences. M indicates_a 100 base pair DNA ladder;_A indicates a_typical Zma-SMARTTRIM with two LTRs and one_internal_region (AC186328:154584–154863; TSD:AACAT); B indicates a_TA-TRIM_with three LTRs and two internal_regions_(AC210283:_61391–61889; TSD: GGGTT); C indicates_a TA