Fig. 1: Characterization of TE-derived transcripts.

a Experimental and bioinformatics analysis pipeline to identify and classify TE-derived transcripts over zebrafish early embryonic development. Total RNA is extracted from 11 developmental stages (hpf hours post fertilization) and reversely transcribed into cDNA for PacBio RNA sequencing. Full-length (FL) circular consensus sequence (CCS) reads are used for transcript identification with TALON and both FL and Non-FL CCS reads are used for quantification. Gene and TE annotations are used for classifying all transcripts into TE-alone, TE-gene and gene subgroups. TE-alone, autonomously transcribed TE transcript; TE-gene, chimeric transcript of TE and gene; gene, TE-sequence-free transcripts. Manual curation is used for further polishing the TE-alone transcript annotation. b Number of identified loci and transcripts among three different types. c, d Categorization of 706 TE-alone transcripts based on TE type/family/subfamily/loci. e Characterization of chimeric TE-alone transcripts. f Transcriptional patterns among three TE types. Comparisons are conducted with differences in exon number, canonical splicing signal (GU-AG) and alternative splicing. g Number of TE-alone transcripts having core conserved domains. Pie charts show the classification of TE-alone transcripts due to the presence and absence of core domains. Gray color, no open reading frames (ORFs); light colors, having ORF but losing domains; dark colors, having all conserved domains. The percentages (%) indicate the proportions of TE-alone transcripts maintaining all conserved domains. Heatmap showing the details of domain presence and absence. Each column represents one domain, and each row represents one transcript (with complete ORF), with light colors indicating domain loss. TP transposase, APE apurinic endonuclease, RT reverse transcriptase, GAG capsid protein, AP aspartic proteinase, RH RNase H, INT integrase, ENV envelope protein²³.