Phylogenetic analysis of SB and ZB elements. Bootstrapped (1000 replicates) phylogenetic trees were inferred using the maximum likelihood method in IQ-TREE (v. 1.6.12) [34]. Reference families were DD34E/Tc1, DD36E/IC, DD37E/TRT, DD41D/VS, DD39D, and DD34D/mariner, DD37D/maT. DD37D/maT was used here as an outgroup. SB and ZB elements form a separate branch individually. The red and green parts in the figure represent the two branches that make-up SB elements, namely cluster SB and cluster SB-like, and the orange and blue parts in the figure represent the two branches that make-up ZB elements, namely cluster ZB and cluster ZB-like, with a confidence level of 100. See Supplementary Figure S1 for details.

Sequence identities between ZB and SB elements among species. Sequence identities were measured by pairwise comparison of representative sequences of SB and ZB elements. The numbers in the heatmap are the percentage of the average values of the sequences’ identities of the two types of transposons in the corresponding row and column, and “n” represents the number of each type of transposon sequence (A–D). The average values of sequence identities were measured by pairwise comparison of representative sequences of CDS (A), DBD (B), DDE (C), and TIR (D) of ZB and SB elements.

Taxonomic distribution of SB and ZB elements. (A) Taxonomic distribution of SB and ZB elements in the Metazoa, including cluster SB, cluster SB-like, cluster ZB, and cluster ZB-like. The numbers following the animal panels represent the number of species for which the corresponding transposon was detected in that lineage. (B) Taxonomic distribution of SB and ZB elements in the Actinopterygii. This graph was drawn based on statistics (Supplementary Table S3). The numbers in the table represent the distribution of SB and ZB species in this order. The darker the color, the more species containing the corresponding transposon in that order. (C) Overlapping species of SB and ZB. The numbers in the figure represent the number of species that possess several types of transposons in this column.

Structural organization of SB and ZB elements. (A) Alignment of the DBD domains of SB and ZB transposases. Representative species containing complete transposons were selected for each cluster. Sal-Saltru (Salmoniformes, Salmo trutta), Sal-Oncmyk (Salmoniformes, Oncorhynchus mykiss), Spa-Spaaur (Spariformes, Sparus aurata), Cic-Oreaur (Cichliformes, Oreochromis aureus), Cha-Astmex (Characiformes, Astyanax mexicanus), Per-Ethspe (Perciformes, Etheostoma spectabile), Cyp-Xipmac (Cyprinodontiformes, Xiphophorus maculatus), Cyp-Danrer (Cypriniformes, Danio rerio), Ble-Salfas (Blenniiformes, Salarias fasciatus), Cic-Astcal (Cichliformes, Astatotilapia calliptera), Cyp-Pacpla1 (Cyprinodontiformes, Pachypanchax playfairii), Anu-Bufbuf (Anura, Bufo bufo), and Gym-Micuni (Gymnophiona, Microcaecilia unicolor). Letters in different colors represent HTH patterns, and rectangles in different colors represent GRPR of different transposons. (B) Alignment of the DDE domains of SB and ZB transposases. The red rectangles represent the DDE domain, the pink rectangles represent linkers. (C) Structural organization of SB and ZB elements. Orange arrows and green arrows represent TIRs, and different colors represent different TIRs. The grey light column represents HTH motifs, the yellow circles represent NLS, the orange light column represents catalytic domains, and the red-light column represents transposons.

The alignment logo for SB and ZB elements. (A) The Weblogo server (http://weblogo.threeplusone.com/create.cgi, accessed on 16 March 2022) was used to create the logo representation of the first 20 bp of the TIR 5′ sequences. (B) Integration sites of four transposons. The sequence logos show the majority regular consensus sequence of the genomic insertion site in a 40 bp window centered on the target TA dinucleotide.

Taxonomic distribution and HT events of ZB and SB elements. This refers to the HT events jointly supported by two cytoplasmic ribosomal proteins (L3 and L4) in eukaryotic species (detailed information of species was listed in Supplementary Tables S5 and S6). (A) The number and proportion of species involved in HT events for the four transposons. (B) Venn of species number involved in HT events of ZB, ZB-like, SB, and SB-like. (C) Species number involved in HT events in Actinopterygii. (D) Species number involved in HT events in Metazoa.