Additional file 1: of Characterization of a novel Helitron family in insect genomes: insights into classification, evolution and horizontal transfer

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)