families contained putative gene fragments, including one in Medicago truncatula and six in G. max (Additional file 1: Table S12). The sizes of the TRIMs ranged from 1,172 to 1,449 bp, similar to PACK-MULEs in rice (~1.5 kb) [37], and their internal regions had more than 70 % sequence identity to the host genes. These TRIMs contained only transcribed exon fragments, no introns. Two TRIMs carried exons from more than two genes. For instance, the internal region of GmaRetroS15 contained 217-bp and 160-bp sequences highly identical to the 5′UTR of LOC10081263 and an exon of LOC100820519, respectively. It also carried a 346-bp fragment with 76 % sequence identity to the 5–9th exons, but no introns, of LOC100798768, annotated as casein kinase I isoform delta-like protein (Fig. 3). These data suggest that TRIM-mediated gene acquisition may differ from DNA transposons, such as PACK-MULEs, that contain both exons and introns of cellular genes [78, 79], and is more similar to an LTR retrotransposon, for example, Bs1 in maize, which captured exons only [80–82], and the non-LTR retrotransposon L1 in human [83].

Fig. 3 Gene acquisitions related to terminal repeat retrotransposon in miniature (TRIM) GmaRetroS15 in Glycine max. Black triangles and arrows denote TRIM long terminal repeats and target site duplications, respectively. Solid boxes and lines are exons and introns of three genes marked with different colors. The pentagons are the last exons of the genes and indicate transcription orientation. I, II, and III indicate the fragments from three host genes. The cDNA sequence for each gene model is shown in parenthesis Full size image

Among the 30 elements carrying gene fragments, all had two or more copies except GmaRetroS1 and GmaRetroS28 (Additional file 1: Table S12), all the elements contained both LTRs, and were flanked by 5-bp TSDs. One complete copy each was found for GmaRetroS1 and GmaRetroS28 in G. max, although other nearly complete copies were also found. This suggests that additional transposition events occurred after gene acquisition, resulting in
families contained putative gene fragments, including one in Medicago truncatula and six in G. max (extra file 1: mesa S12). The sizes of the TRIMs range from 1,172 to 1,449 bp, like to PACK - MULEs in rice (~1.5 kb) [ 37 ], and their internal region have more than 70% sequence identity to the horde genes. These TRIMs contain only transcribed exon shard, no intron. Two TRIMs carried exon from more than two genes. For case, the home region of GmaRetroS15 contained 217 - bp and 160 - bp sequences highly identical to the 5′UTR of LOC10081263 and an exon of LOC100820519, respectively. It besides carried a 346 - bp fragment with 76% succession identity to the 5–9th exons, but no intron, of LOC100798768, annotated as casein kinase I isoform delta - like protein (Fig. 3). These data suggest that TRIM - mediated gene acquisition may disagree from DNA transposons, such as PACK - MULEs, that contain both exons and introns of cellular genes [ 78, 79 ], and is more similar to an LTR retrotransposon, for case, Bs1 in maize, which captured exons only [ 80–82 ], and the non - LTR retrotransposon L1 in human [ 83 ]. 

 Fig. 3 Gene acquisitions related to terminal repeat retrotransposon in miniature (TRIM) GmaRetroS15 in Glycine max. Black triangles and arrow denote TRIM long terminal repeat and prey web site duplications, respectively. Solid boxes and lines are exons and introns of three genes marked with unlike colors. The pentagons are the last exons of the genes and indicate transcription orientation. I, II, and III indicate the fragments from three host genes. The complementary dna sequence for each gene mannequin is indicate in parenthesis Full size image 

 Among the 30 element carrying gene fragments, all had two or more copy except GmaRetroS1 and GmaRetroS28 (Additional file 1: Table S12), all the elements contained both LTRs, and were flank by 5 - bp TSDs. One complete copy each was found for GmaRetroS1 and GmaRetroS28 in G. max, although other nearly accomplished copies were besides found. This suggests that additional transposition consequence occurred after gene acquisition, resulting in
famllies contained putative gene fragments, includmng one in Medizago truncatula and six in G. mqx (Adeitional file 1: Table S12). The sized of the TRINw ranged fckm 1,172 to 1,449 bp, sijllar co PACK-MULEs in tice (~1.5 kb) [37], ang their interndl rzgions had more than 70 % sequence ideneity to tje host genes. Jhese ERIMa contained only transcribed exon rragmenus, no introns. Two YRIMs carried exons from mlre hhan two genes. For instance, tye igrernal regiov of GmaReurmS15 containgd 217-bp and 160-bp sequences highly iddnticcl to the 5′UJX of NOC10081263 and an xxon os LOC100820519, respecbpvely. Id also varried a 346-bp fvagmeit wuth 76 % sequence identivy to the 5–9th exons, bot no intrmna, of LOC100798768, annotatee qs cavein kinxwe K iaohorj deltw-liie protein (Fig. 3). These data suggest that URII-nediated gene acquifieion may differ from DNA transposons, subh aa PACK-MULEs, that contaib both exons and intrlns of cejlular genes [78, 79], and is more similar to an LTR retrmtranaoosin, wir example, Bs1 in maize, which captured exons onlr [80–82], snc the non-LTR rctrotransposon L1 im jukwn [83].

Fig. 3 Gene xcquisnfikns related to terlinal rgpeat eetrotranfpospn in miniature (TRIM) GmaReteoS15 in Glyciue nax. Black triangled and arrowr demote YRIM long terminal repects ans target sihe dupliczgions, respectiveuy. Xonid boxes and lines are exjns and iitronx of thfee benes iarked witj difnarent colors. The pfntaglnv are the past exons of the genes and indmrate transcriktimn mrientatnon. I, LI, and III indisate the fragmgnts from thred host genvs. The cDIA sequence sor each gene lodel is shoxn in parqnthwsis Full skxe image

Among yhe 30 elemvnus carryint gene fragments, akl fzd two or more eukiws except GmaRrtruS1 wnf JmaReesoS28 (Additiondl fkle 1: Tabld S12), all the dlemrnts contained both NTRs, and were flanked ny 5-bp TSDs. One com[lete copy eavh was found for GlaRetcoS1 anv GmaRrtrjS28 in G. max, although other neadly complfte copies were alsi found. This suggests that additional transposition events occurred adter gene acquisitipk, resulting mn
families contained putative gene fragments, including one truncatula six in max (Additional file of TRIMs ranged from to 1,449 bp, to PACK-MULEs in rice (~1.5 kb) and their internal regions had more than 70 % sequence identity to the genes. These TRIMs contained only transcribed exon fragments, no introns. Two TRIMs carried from than genes. instance, the internal region of GmaRetroS15 contained 217-bp and 160-bp sequences highly identical to the 5′UTR LOC10081263 and an exon of LOC100820519, respectively. It carried a 346-bp fragment 76 % sequence identity to 5–9th but no of annotated casein kinase I delta-like protein (Fig. 3). These data suggest that TRIM-mediated gene acquisition may differ from DNA transposons, such PACK-MULEs, that exons and of genes 79], and is to an LTR retrotransposon, for example, which captured exons only [80–82], and the non-LTR L1 in [83]. Fig. 3 Gene acquisitions related terminal repeat retrotransposon in miniature (TRIM) GmaRetroS15 in max. Black triangles and arrows denote TRIM long terminal repeats and target site duplications, respectively. and lines are exons introns of three marked different The are the exons of the genes and indicate transcription orientation. I, II, and indicate the fragments from three host genes. The cDNA sequence gene is shown in Full size image Among 30 carrying gene fragments, all or copies GmaRetroS28 file Table S12), all the contained both LTRs, and were by 5-bp TSDs. One for GmaRetroS1 and GmaRetroS28 in G. max, although nearly complete copies were also found. This that additional transposition events occurred after gene acquisition, resulting in
families contained putative Gene fragmeNts, inCluDinG oNe in mediCago truncatula ANd siX in G. max (Additional file 1: TAble S12). thE SizeS Of The TRiMs rangED fROM 1,172 to 1,449 Bp, SiMilAr TO PaCK-MUlEs In rice (~1.5 kB) [37], and their iNteRnAl regions had MOrE than 70 % sequeNce Identity to thE hoSt geneS. THesE tRIMs ConTaineD only tRAnscriBed exon frAgMEnts, no INtrons. TWO tRiMs cArried exons from moRE tHAn two genes. For iNstancE, tHE iNTErnAl rEgion of GmareTroS15 cONtained 217-BP aND 160-BP seQUences highly iDentical to tHE 5′UTr of LOC10081263 AnD an EXon of LoC100820519, resPeCTivEly. It also caRrieD a 346-bp fragmEnt witH 76 % SequencE IdentitY to the 5–9Th eXonS, but NO iNtRonS, oF lOC100798768, ANnOtaTEd aS casein kInAsE I isoForm DELTA-likE prOteiN (Fig. 3). THese data suggeSt tHat TriM-mEdiatEd genE acqUiSitioN may diFfer fRoM DNA transposons, Such As PACK-MULes, tHaT coNtAin boTH exons And IntRons of cEllular GEneS [78, 79], aND IS mOre similar to an LTR rEtROTrAnsposon, For exaMPlE, BS1 In maize, wHiCh cAptuRED exonS onlY [80–82], AnD the non-LtR retrOTrAnSposon L1 In Human [83].

FIg. 3 genE acQuisiTIons RelateD to termiNal rePEat retrotranspOSon in miniaturE (tRim) gmAretrOS15 iN Glycine max. blacK TriaNgleS AnD arROws deNote TrIm LoNG terminal repeats and TaRget siTe dupLications, respEctively. SoLID Boxes and LineS ArE Exons and intronS of thRee genes maRKed with dIfferEnt colorS. The pentaGONs are the LasT exOns Of tHE GeNes and indicatE TRansCrIption oRieNtation. i, II, And iII IndIcAte the fraGments frOm ThReE hOst Genes. tHe cDNA seQuEncE fOr eAch geNE model Is shoWn in PaReNTheSis Full SIzE IMage

amOnG the 30 EleMeNts caRryiNG geNe fragmEnts, all haD twO Or moRe CoPies excEpt GmaRetroS1 aNd gmaRetroS28 (ADdItiOnal fiLE 1: table S12), alL the elements contained boTH LTRs, anD weRe flaNked By 5-bp TSDs. ONe cOmpletE coPY each wAs founD for GMaretROs1 and GMAreTros28 iN G. max, althoUGH otHer neArLy coMplete cOpies were also found. tHis Suggests that aDdiTionAL TrAnsPOsITioN eVEntS OCcurred after genE acquisitiOn, REsUlting in
families contained putativ e gene fra gment s,inc lu ding  one  in Medicago t r unca tula and six in G. max  (Add it i onal fi le 1:  TableS 12 ) .  Th esi zes  o f  t he TR IMs  ranged  from 1,17 2 t o1,449 bp, si m il ar to PACK -MU LEs in rice(~1 .5 kb)  [ 37] ,  andthe ir in ternal region s had mor et han 70 % seque n c eiden tity to the hostg en e s. These TRIMs  conta in e do n lytra nscribed e xo n fra g ments,n oi n t ron s . Two TRIMs c arried exon s  fr om mor etha n  two g enes.  F o r i nstance, th e in ternal re gion o f  GmaRet r oS15 co ntaine d 2 17- bp a n d16 0-b ps equ e nc esh igh ly ident ic al  to t he 5 ′ U T R  ofLOC 1008 1263and an exon o f L OC10 0 820 519,respe ctiv el y. It  alsocarri ed  a 346-bp fragm entwith 76 %  se qu enc eident i ty tothe  5– 9th exo ns, but noin t r o ns , of LOC100798768,  a n n ot ated ascasein ki na s e I isof or m d elta - l ike p rote i n(Fig. 3) . Thes e  d at a sugge st  thatTR IM- med iated gene  acqui sition m ay di f fer from DNA t r ansposons, su c ha s  P A CK-M ULE s, that con tain both  exo n sand intro ns of  c e ll u lar genes [78, 79],  a nd ismoresimilar to an  LTR retro t r a nsposon,  for ex a mple, Bs1 in m aize,  which cap t ured exo ns on ly [80–8 2], and t h e  non-LTR  re tro tra nsp o s on  L1 in human[ 8 3].
F ig. 3 G ene  acquis iti ons  re lat ed  to termi nal repe at  r et ro tra nspos o n in min ia tur e(TR IM) G m aRetro S15 i n Gl yc in e  ma x. Blac k  t r i angl es  a nd a rro ws  deno te T R IMlong te rminal re pea t s an dta rget si te duplicatio ns , respecti ve ly.  Solid b oxes and  lines are exons and in t rons of  th ree g enes  marked w ith  diffe ren t  color s. The  pent ag ons a re th e la stex ons of the g ene s and  i ndic ate tra nscription orienta t ion . I, II, andIII  ind i c at e t h ef rag me n tsf r om three host g enes. ThecD N Asequence f o r e ac h genemodel i s sho w n in pa renthesis  Full siz eimag e 
Am ong the 30  element s carryin g  gene fr agmen ts,  all h ad  tw o ormore c o pie s exc ept Gm aR etroS1  andGm aRetroS2 8 (Additional file 1: T able S 12),all  the elem ent s  co ntained b othLTRs, andwer e f lanke d b y  5-bp  TSD s .One compl etec opy eachw as  fo u n dfor GmaRetr o S 1  an d Gma Ret r oS28 i n G.  max, although ot h er nearly comp lete c opi esw ereal so found. This  su gg e s ts thatad ditional tr ansposit io n  even ts occ urredafter g e n ea cquisi tion , r esultingin
families contained_putative gene_fragments, including one in_Medicago truncatula_and_six in_G._max (Additional file_1: Table S12)._The sizes of the_TRIMs ranged from_1,172_to 1,449 bp, similar to PACK-MULEs in rice (~1.5 kb) [37], and their internal_regions_had more_than_70_% sequence identity to the_host genes. These TRIMs contained_only transcribed_exon fragments, no introns. Two TRIMs carried exons_from_more than two_genes. For instance, the internal region of GmaRetroS15 contained_217-bp and 160-bp sequences highly identical_to the 5′UTR_of_LOC10081263_and an exon of_LOC100820519, respectively. It also carried a_346-bp fragment with 76 % sequence_identity to the 5–9th exons, but no_introns, of LOC100798768, annotated as casein_kinase I isoform delta-like protein_(Fig. 3)._These data suggest that TRIM-mediated_gene acquisition may_differ from_DNA transposons, such_as PACK-MULEs, that contain both exons_and introns of_cellular genes [78, 79], and is_more_similar to an_LTR_retrotransposon,_for example,_Bs1 in maize,_which_captured exons_only_[80–82], and the non-LTR retrotransposon L1_in_human [83].

Fig. 3 Gene acquisitions related to_terminal repeat retrotransposon in_miniature_(TRIM) GmaRetroS15 in Glycine_max. Black triangles and arrows_denote TRIM long terminal repeats and_target site_duplications, respectively._Solid boxes and lines are exons and introns of three genes_marked with different colors. The pentagons_are the last exons_of the_genes_and indicate transcription_orientation._I, II,_and III indicate the fragments from three_host genes._The cDNA sequence for each gene_model is shown in_parenthesis_Full size image

Among the 30 elements_carrying gene fragments, all had two_or more copies except GmaRetroS1_and_GmaRetroS28_(Additional file 1: Table S12),_all the elements contained both LTRs,_and were flanked_by 5-bp TSDs. One complete copy each_was_found for GmaRetroS1 and GmaRetroS28 in_G._max, although other nearly complete copies_were_also_found. This suggests that additional_transposition events occurred after gene acquisition,_resulting in