Additional files Additional file 1. Graphical overview of analysis workflow. Additional file 2. Ratio of LTR count to the internal sequence count of annotated RLX. 33 Additional file 3. Comparison of TE distribution in gene introns in PITA (P.taeda v.2.0, annotated filtered gene set) and PILA (P.lambertiana v.1.01, high quality gene set). 34 35 Additional file 4. GO annotation of genes with significantly enriched repeats in their vicinity. p=0.001 was considered if calculated t>5.04 (df=8); p=0.05 if t>2.31 (df=8). 5' 3' 5' 3' 1- 5' 2- 3' 2- 5' 3- 3' 3- 5' 4- 3' 4- Total Sum (0- LTR ID Biological process Molecular function 0- 0- 1- t 2kb 3kb 3kb 4kb 4kb 5kb 5kb sum 1kb) 1kb 1kb 2kb DNA integr.; nucl.acid bind.; zinc ion bind.; PtRLG_956:11940-13280* transmem.tr.; prot.kinase act.; ATP bind.; prot.phosph. transmem.transp.act 19 18 2 1 1 1 1 3 1 2 49 31,78 37 response to jasmonic 4 iron, 4 sulfur cluster binding; 5'- acid; transition ion 3' RNA polymerase activity;acid homeostasis; phosphatase activity; alcohol chromosome dehydrogenase (NAD) activity; condensation; fruit antioxidant activity; channel development; flower activity; chitin binding; cysteine- development; leaf type peptidase activity; D- development; arabinono-1,4-lactone oxidase monopolar cell growth; activity; fatty-acyl-CoA reductase cytidine deamination; (alcohol-forming) activity; flavin lignin metabolic adenine dinucleotide binding; PtRXX_3321:1127-1384 process; coA met proc; histone-lysine N- glutamat met.proc; methyltransferase activity; lysine monoterpene met.proc.; N-methyltransferase activity; histone methylation; UDP-glycosyltransferase activity; xyloglucan met.proc.; xyloglucan:xyloglucosyl reg.of gene expr.; reg.of transferase activity; lipoate trichome synthase activity; copper ion morphogenesis; binding; polysaccharide binding; negative reg.of catalytic magnesium ion binding. act.; metal ion tr.; drug transmembrane tr. 93 98 67 44 24 17 14 15 20 13 405 13,08 191 DNA integr.; cell RNA-dir. DNA pol.; zinc ion growth; DNA duplex bind.; ammon.transmem.tr.; flavin unwinding; DNA adenine dinucl.bind.; DNA bind.; recomb.; cellulose glucose bind.; prot kinase act.; microfibril org.; prot.bind.; hexokinase act.; ATP PtRLX_2602:13209- carbohydr. Phosph.; bind.; ATP-dep. 5-3 DNA 13943*not filtered RNA-dep DNA helicase act.; oxred act.; ubiquitin- biosynth.; prot.transf.act.; prot.ubiquitination; cell.glucose homeost.; prot.phosph. 18 16 4 5 4 5 1 3 9 7 72 10,54 34 2602 body >500bp hit 4 6 7 6 11 20 26 31 28 36 2602LTR f 0 2 3 3 10 8 4 6 7 5 DNA integr; proteolysis; prot.bind.; asp-type endopep.act.; PtRLX_3422_C:5374-6581* defense resp.; signal zinc ion bind.; ADP bind.; transduction. Nucl.acid bind. 22 20 14 9 8 10 11 12 11 13 130 10,26 42 Ox-re process; drug terpene synthase act.; heme transmembrane binding; protein heterodimer.act.; transport; cellular Mg ion bind.; ATP bind.; DNA resp.to jasmonic acid bind.; D-arabinono-1,4-lactone stimulus; protein oxidase; prot. Ser/thr kinase act.; PtRLC_348:6034- phosphorylationl oxidoreduct. Act; iron ion bind.; 6951(unknrep) monoterpene drug transmem.tr.act.; zinc ion biosynthetic process; bind.; monooxygenase act.; lipid catabol.proc.; coenzyme bind.; flavin adenine dinucl.bind.; antiporter act.; hydrolase act. 13 14 6 10 8 4 5 4 0 2 66 9,19 27 phoph.; ammonium prot.bind.; heme bind.; iron ion transmem.tr.; ox-red bind.; zinc ion bind.; DNA bind.; PtRLC_315_B:6291-7362* proc.; RNA-dep. DNA ammonium transmem.tr.act.; (3 genes) biosynth. Proc.; DNA RNA-dir.DNA pol.; kinase act.; integr. trans-octaprenyltransferase act.. 22 26 7 11 12 8 5 11 5 6 113 7,78 48 DNA repair; proteolysis; nucl.acid bind.; zinc ion bind.; RNA-dep.DNA esp.-type endopeptidase act.; N- biosynth.proc; DNA acetyltransferase act.; PtRLG_893:12732-13729* integr; prot.ubiquitination; nucl.acid phosphodiester bond hydr.; 80 108 28 13 1 0 2 1 1 2 236 6,41 188 DNA integr.; asp-type endopep.act.; PtRLG_501:7808-8807* (1 proteolysis; xyloglucan xyloglucan:xyloglucosyl gene) met.proc.; cell wall org.; transf.act.; nucl.acid bind.; zinc cell wall bio.; ieon bind; 35 26 4 1 2 9 5 5 1 3 91 5,97 61 DNA integration; aspartic-type endopeptidase act.; vacuolar transport; phosphatase act.; ATP bind.; PtRLG_478:5197- proteolysis; nucl.acid bind.; prot.bind.; 6610(7genes in flanks, 2 prot.phosph.; ion coenzyme bind.; zinc ion bind; genes in introns, 1 homolog transm.tr.; ionotrophic ADP bind.; ionotroph. Protein pita-pila dopo) glutamate sign.pathw.; kinase act.; Glutamate receptor ox-red pr.; fatty acid act.; oxidoreductase act.; biosynt.proc; 11 13 12 8 5 4 3 8 0 2 66 5,59 24 cell devision; terpene synth.act.; cell.glucan met.proc.; xyloglucan:xyloglucosyl reg.of transcription transf.act.; monooxygenase act.; DNA-templ.; heme binding; zinc ion bind.; PtRLG_930:5353- prot.phosph.; cell.resp.to DNA bind.; RNA-dir. DNA pol.; 6339(RnaseH domain, sim to jasm.acid.stimulus; ox- prot.heterodimer.act.; Mg.ion copia-16Pab; one short red proc.; microtubule bind.; prot.kinase act.; hydrolase probable RE, but only 1-2 severing; monoterpene act.; microtubule-severing genes) biosynth.proc.; cell ATPase act.; iron ion bind.; ATP cycle; DNA integr,.; bind. RNA-dep. DNA bio.proc. 14 19 4 5 6 5 5 2 1 1 62 5,22 33 cell wall modif.; sucrose synth.act.; peptidyl-tyrosine xyloglucan:xyloglucosyl tr.act.; phosph.; ox-red. Proc.; NAD+ bind.; ADP bind.; recognition of pollen; prot.tyrosine kinase act.; cell.glucan met.proc.; pectinesterase act.; zinc ion bind.; PtRLG_987:4530-4963 (new response to biotic ATP bind.; iron ion bind.; re cpia, sim to co-25) stimulus; DNA integr.; protochlorophyllide red.act.; proteolysis; oxred act.; Mg.ion bind.; transmem.tr.; sucrose prot.bind.; hydrolase act.; heme met.proc.; defence resp.; bind.; dioxygenese act.; trehalose bio.proc.; transmem.tr.act.; ser-type signal transduction. endopept.act. 20 14 6 4 2 2 4 11 0 0 63 4,46 34 GDP-mannose NADH biosynth.proc.; dehydrogenase(ubiquinone) act.; ammonium metalloendopeptidase act.; transmem.tr.; ATP electron transfer act.; iron-sulfur synth.coupled electron cluster bind.; RNA-dir.DNA pol PtRLG_476_C:6048-7057 tr.; plant-type cell wall act.; ammonium transmem.tr.act.; org.; RNA-dep. DNA zinc ion bind.; ATP bind.; kinase biosynth.proc; act.; heme bind.; nucl.acid bind.; proteolysis; ox-red act.; iron ion bind.; carbohydrate met.proc; prot.bind.; mannose-6-phoshatase DNA integr. isomerase act.; 10 11 9 13 4 8 11 4 3 5 78 3,93 21 DNA integr.; RNA-dep. transporter act.; ATP bind.; DNA bio.; intracell. nucl.acid bind.; ATPase act.; PtRLX_11_D:5833-6259 Prot.tr.; proteolysis.; polygalacturonase act.; asp-type prot.phosph.; endopep.; Ran GTPase bind.; carbohydrate met.proc. carbohydr.bind.; prot.kinase act. 15 10 6 2 6 1 2 2 2 6 52 3,84 25 36 pathogenesis; hexose DNA bind.; RNA-dir.DNAbio.; met.proc.; translation; heme bind.; isomerase act.; proteolysis; prot.kinase act.; ATPase act.; prot.phosph.; RNA- oxidored.act.; polygalacturonase dep.DNA bio.proc.; ox- act.; ATP bind.; L-ascorbic acid PtRLG_521:6056-7165 red. Proc.; intracellular bind.; iron ion bind.; zinic ion prot.tr.; DNA integr.; bind.; monooxygen.act.; asp-type transmem.tr.; endopep.act.; Ran GTPase bind.; transmem.tr.act.; stuctural constituent of ribosome; 36 25 8 13 10 7 14 8 13 10 144 3,81 61 intracellular prot.tr.; structural molecule act.(COPI vesicle-med.tr.; vesicle coat); prot.bind.; ammonium nucl..acid bind.; transmem.tr.act.; PtRLC_763:5801-6533 transmem.tr.; DNA RNA-directed DNA pol.act.; integr.; RNA-dep DNA ammonium transmem.act.; biosynt.proc.; 12 9 12 9 1 0 4 4 9 3 63 3,52 21 positive reg.of translation elongation factor act.; translational hydroquinone: oxygen termination; cell wall oxidored.act,.; oxidored.act.; macromol.cat.proc.; monooxgenase act.; ribosome floral organ dev.; bind.; pectinoesterase act.; ser.- flavonoid met.proc.; type andopept.; flavin adenine prot.phosph.; dinucl.bind.; prot.self-association; proteolysis; coenzyme A cytokin dehydr.act.; enzyme met.proc.; lignin inhibitor act.; prot.kinase act.; biosynth.proc.; defence cellulose synthetase (UDP- resp.; gametophyte dev.; forming) act.; NADPH act.; ADP cytokinin met.proc.; cell bind.; copper ion bind.; iron ion wall modif.; DNA bind.; chitinase act.; GTP binding; PtRYX_6:5006-5920 integr.; lignin methyltransf.act.; receptor ser/thre catabol.proc.; ox-red kinase bind.; polysaharide bind. proc.; positive reg.of translational proc.; small GTPase med. signal transduction; negative reg. of catalytic act.; methylation; response to biotic stimulus; translational frameshifting; reg. of meristem growth; cellulose biosynth.proc.; chitin catabol.proc.; 17 10 7 5 6 4 4 4 0 2 59 2,92 27 lignin cat.proc.; floral D-arabino-1,4-lactone ox.act.; organ dev.; proteolysis; histone-lys. N-metyltr. Act.; seq- cell wall spec.DNA bind.; ox-red act.; macromol.cat.proc.; NADP bind.; ionotr.glutamate ammonium mem.tr.; rec.act.; NADP bind; cell.oxidant detox.; G transl.elong.act.; ribosome bind.; prot.-coupled rec. Sign. chitin bind.; polysach.bind.; Pathway; actin filament terpene synth.act.; prot.self- org.; chitin cat.proc.; assoc.; prot.dimer.; cytokinin plant-type cell wall org.; dehydr.; ser-type endopep.act.; 1-3-beta-D-glucan fatty-acyl-CoA red. act.; G bio.broc.; coA prot.rec.act.; pectinesterase act.; met.proc.; celluloze histone bind.; flavin dinucl.bind.; bio.proc.; ox-red. proc.; 1,3-beta-D-glucan synth.act.; flavonoid met.proc.; monoox.act.; extracell. glutamate- cytokinin mrt. proc.; gated ion chanel act.; GTP bind.; DNA integr. DNA repl.; heme bind.; ATPase act.; enzyme purine inh.act.; ox-red act.; ammonium nucl.transmem.tr.; transmem.act.; polygalacturonase positive reg.