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Additional file 11: Figure S10. Paralogous empty sites of PxSE1 (A) in P. xylostella and SfSE1 (B) in S. frugiperda. The nucleotides of TSD are indicated with the red background. The nucleotides of 3′ tail sequence are indicated with the gray background.

Additional file 6: Figure S6. Alignment of potential LINE transposons in 8 lepidopteran insects genome. PxLINE1 in P. xylostella (NW011952036.1: 552486–555,713), TaLINE1 in Tuta absoluta (SNMR 01038797.1: 8533–11852), McLINE1 in Melitaea cinxia (APLT01012314.1: 14517–16103), CcLINE1 in Conopomorpha cramerella (SJJU01072145.1: 61771–65266), GmLINE1 in Galleria mellonella (NHTH01000021.1: 4230671–4228043), ArLINE1 in Adela reaumurella (WYDE01048472.1: 2507–535), AhLINE1 in Adoxophyes honmai (BHDV01006067.1: 48096–49728), DpLINE1 in Dendrolimus punctatus (JAABVI010000027.1: 8196917–8193378).

Additional file 5: Figure S5. The 8 copies with high identity to PxLINE1.1 in P. xylostella (A) and the multiple sequence alignment of one copy (AHIO01028576.1: 13049_14357) and Mariner-8_BM (B).

Additional file 3: Figure S3. Multiple sequence alignment the consensus sequence of PxSE1 (A), PxSE2 (B), PxSE3 (C), PxSE4 (D), PxSE5 (E) and their empty site sequences. The nucleotides of TSD are indicated with the red words. The nucleotides of 3′ tail sequence are indicated with the gray background.

Additional file 10: Figure S9. The typical integration pattern of SINEs within genome of P. xylostella. (A) (B) and (C) are schematic diagrams of several copies inserted into the introns of LOC105382892, LOC105381513 and LOC105383359, respectively. (D) Statistics number of different SINE families inserted into the same gene.

Additional file 7: Figure S7. The origin analysis of ObSE2. (A) the alignment of 75-bp fragment at 5′-end of ObSE2 and 72-bp tRNA-related region of D. melanogaster. (B) the schematic representation of structure of ObSE2.

Additional file 2: Figure S2. The consensus sequence of tRNA and 5S rRNA related SINE transposons in insect genomes. Nucleotides in red font are 3′ tail sequences.

Additional file 4: Figure S4. Multiple sequence alignment and evolutionary divergence estimation between the consensus sequences of SINEs. The number of base differences per site from between sequences are shown. All ambiguous positions were removed for each sequence pair. Evolutionary analyses were conducted in MEGA7.0.

Additional file 1: Figure S1. Characteristic of PxSE1 in P. xylostella. (A) the sequence of PxSE1. The pink nucleotides are TSD sequence, gray background present A box and B box structure, green background is 3′tail sequence. (B) the homology search of PxSE1 in Repbase database.

Additional file 9: Figure S8. Examples for the relative age distribution of SINE families in other species based on the identity to the species-specific consensus. The abscissa showed that the identity between each consensus sequence and the copies. The ordinate showed that the copy numbers of sequence with the same identity.

Data S1. The Hel1 elements with degenerated remnants of Helitron coding sequences identified in insect and spider genome databases. Data S2. The reconstructed potential autonomous Hel1 Helitrons. (PDF 67 kb)

Data S4. The consensus sequences of 35 Helitron exemplars. Data S5. The sequences used for evolutionary analysis. (PDF 101 kb)

Figure S1. Insertion of a novel Helitron element into downstream region of a SINE element in C. suppressalis genome. The SINE and Helitron sequences are highlighted in blue and pink, respectively. The nucleotides highlighted in purple are the target site duplication (TSD) of SINE. Figure S2. Characteristic of Csup_Hel1A. (a), Multiple alignment of 30-bp end sequences as well as the flanking host nucleotides at the 5′- and 3′-end from Csup_Hel1A elements. The alignment was graphically edited using TeXshade package. (b), Predicted secondary structure of 30-bp region at the 3′-end of Csup_Hel1A consensus sequence. Figure S3. The distribution of Csup_Hel1A-like Helitrons in insect and spider genomes. Taxa showing Hel1A-like Helitrons are colored taxonomically, with Lepidopteran insects in red, Diptera insects in purple, Hymenoptera wasps in yellow, Araneae species in green. Figure S4. Multiple alignment of 126 bp region at the 5′-end consensus sequence of Hel1 Helitrons. Figure S5. Multiple alignment (a) and genetic distance analysis (b) of 30-bp region at the 5′-end of consensus sequences of Ptep_Hel2Ca and Csup_Hel1Ab. Figure S6. Structural analysis of degenerated remnants potential autonomous Helitrons found in N. clavipes, P. tepidariorus, P. machaon, C. vestalis, H. vitripennis, A. rosae and T. cristinae. Figure S7. Multiple alignment (a) and genetic distance analysis (b) of Rep/helicase protein sequences of reconstructed potential autonomous Helitrons. Figure S8. The typical integration pattern of Hel1A within genomes of P. xuthus and P. rapae. (a), A copy of Pxut_Hel1Aa inserted into the coding sequence (CDS) of a gene. (b), A copy of Pxut_Hel1Ab inserted into intron. (c), Several copies of Prap_Hel1Aa inserted into introns and exons of the same gene. Figure S9. Identification of source loci and end junctions of insertions in Sfru_Hel1A. The end junction sequences are shaded. Figure S10. Multiple alignment of Pxut_Hel1Ab consensus sequence and core sequence in P. xuthus (a), Csup_Hel1Aa and Csup_Hel1Ab consensus sequences in C. suppressalis as well as core sequence in genome of P. xuthus (BBJE) and S. frugiperda (FJUZ) (b) and Csup_Hel1Ea consensus sequence and four short core sequences in C. suppressalis (c). Figure S11. Paralogous or orthologous empty sites of Prap_Hel1Aa in P. rapae, Cves_Hel1Aa in C. vestalis, Csup_Hel1Aa in C. suppressalis, and Mcin_Hel1Ca in Melitaea cinxia. The 4-letter project ID of WGS accession number and corresponding species are listed as following: LWME for P. rapae, JZSA for C. vestalis, ANCD for C. suppressalis, APLT for Melitaea cinxia, JXPT for Bactrocera oleae and AZMT for Microplitis demolitor. Figure S12. Multiple alignment of orthologous gene of calreticulin from P. rapae (EU826537.1) and C. vestalis (KX384605.1) (a), heat shock protein 70 from P. rapae (KJ573767.1) and C. vestalis (JX088378.1) (b), opsin from P. rapae (AB177984.1) and C. vestalis (KY368220.1) (c), consensus sequences of Prap_Hel1Aa and Cves_Hel1Aa as well as a short copy of Prap_Hel1Aa (Prap0202, LWME01000202.1: 138955–138,682) (d) and Prap0202 and eight individual sequences of Cves_Hel1Aa including Cves_Hel1Aa.1(JZSA01006637.1: 22335–22,612), Cves_Hel1Aa.2 (JZSA01007293.1: 718–441), Cves_Hel1Aa.3 (JZSA01002845.1: 21212–21,486), Cves_Hel1Aa.4 (JZSA01005118.1: 18777–18,500), Cves_Hel1Aa.5 (JZSA01002791.1: 17198–17,475), Cves_Hel1Aa.6 (JZSA01001525.1: 718–441), Cves_Hel1Aa.7 (JZSA01000595.1: 12281–12,558) and Cves_Hel1Aa.8 (JZSA01006408.1: 3165–2888) (e). Figure S13. Phylogenetic analysis of all copies of Hel1 Helitrons in C. vestalis, P. rapae and C. suppressalis. The phylogenetic tree was constructed by the neighbor-joining method using MEGA 7.0 software. Figure S14. Detection of orthologous empty site of a short copy of Prap_Hel1Aa (Prap0202, LWME01000202.1: 138955–138,682) in P. rapae larvae collected from Yangzhou, China. Figure S15. Multiple alignment of sequences completely same as the consensus sequence of Prap_Hel1Aa in P. rapae. Figure S16. Multiple alignment of Emus_Hel1Ca and the consensus sequences of Bmor_Hel1Ca, Cvic_Hel1Ca (a) as well as Emus_Hel1Ca and the individual sequences of Bmor_Hel1Ca (Bmor_Hel1Ca.1, AADK01000158.1: 43487–43,268) and Cvic_Hel1Ca (Cvic_Hel1Ca.1, JXOT01107662.1: 1253–1516; Cvic_Hel1Ca.2, JXOT01181287.1: 382–645) (b). Figure S17. Multiple alignment (a) and genetic distance ananlysis (b) of Pgla_Hel1Ga and Hvit_Hel1Ga. Figure S18. Multiple alignment of Csup_Hel1Aa and Csup_Hel1Ab. Figure S19. Multiple alignment of Pxut_Hel1Aa and Pxut_Hel1Ab from P. xuthus. (PDF 3085 kb)