Reads length distribution of raw sequence reads after filtering by read length. Three biological replicate libraries per group of F₁ generation (5.5 hpf embryos) from parents exposed to 8.7 mGy/h of γ-radiation (F₁-γ) and control parents (F₁-C).

General statistics of reads mapping to zebrafish genome (GRCz10). Three biological replicate libraries per group of F₁ generation (5.5 hpf embryos) from parents exposed to 8.7 mGy/h of γ-radiation (F₁-γ) and control parents (F₁-C). Total clean reads represent the number of reads after QC analysis and filtering. Filtered reads indicate the number of reads after size filtering. Total mapped reads indicate the number of reads mapped to zebrafish reference genome after size filtering. Multimapping reads < 5 include reads aligning to < 5 genomic locations. Multimapping reads > 5, indicate reads mapped to > 5 genomic locations. Unmapped reads show the amount of reads which could not be aligned to the genome. Asterisks represent significant differences p < 0.0001, Chi-square with Yates correction of continuity.

Distribution of mapped reads (zebrafish genome reference GRCz10) onto genomic features. F₁ generation of embryos (5.5 hpf) from parents 1 year after exposure to 8.7 mGy/h γ-radiation (F₁-γ) and control parents (F₁-C). Values derived from three replicates in each group (n = 3). Asterisks denote statistical differences with p < 0.001, multiple t tests (FDR 99%). (A) miRNA total (total of reads mapping to microRNAs (miRNA)), miRNA danio_rerio (zebrafish miRNAs), miRNA other (miRNAs from other species), Mt_tRNA (mitochondrial transference RNA), piRNA (piwi-interacting RNA), no-annotation (mapped reads, which could not be assigned to any genomic feature), protein_coding (protein coding transcripts), rRNA (ribosomal RNA), tRNA (genomic transference RNA), others (sum of all reads mapping to genomic features presented in (B). (B) snoRNA (small nucleolar RNA), lincRNA (long intergenic non-coding RNA), Mt_rRNA (mitochondrial ribosomal RNA), snRNA (small nuclear RNA), misc_RNA (miscellaneous RNA), scaRNA (small cajal-body-spacific RNA), sRNA (bacterial small RNA).

Differential expression analysis of miRNAs (A), piRNA clusters (B), lincRNAs (C), and snRNAs (D) in F₁ generation of embryos (5.5 hpf) from parents exposed to 8.7 mGy/h γ-radiation (F₁-γ) and non-exposed control parents (F₁-C). Differentially expressed genes are represented as red dots. Expression values are shown as log2 of fold changes (X-axis). Y-axis represents the negative log10 of the p values (n = 3).

mRNA targets of let-7g involved in apoptosis network and showing the involvement of members of the miRNA biosynthesis pathway as well as other genes. This network predicts activation of apoptosis as shown by the orange edges between nodes. Arrowed blue lines predict inhibition. Green nodes indicate down-regulated genes.

Analysis of piRNA signatures in clusters predicted in F₁ generation of embryos (5.5 hpf) from parents exposed to 8.7 mGy/h γ-radiation (F₁-γ) and non-exposed control parents (F₁-C) (n = 3). A) Read length distribution. B) Per base distribution analysis. C) 5′10nt overlap distribution. Asterisk indicates significant differences (p < 0.05; paired t test). D) Read length analysis of reads with 5′ 10nt overlapping (ping-pong signatures; average Z score F₁-C = 44.2, and F₁-γ = 42.9; p < 0.01).

Expression and biological processes of genes within the co-expression network of DElincRNAs in the generation F₁ of embryos (5.5 hpf) from parents exposed to 8.7 mGy/h γ-radiation (F₁-γ). Gene expression values from our parallel differential expression data (GSE98539)⁹. (A) DElincRNAs expression level compared to modulated and unmodulated genes within the co-expression network. Modulated genes represent differentially expressed (FDR < 0.05), unmodulated genes represent not differentially expressed (FDR > 0.05). Asterisks indicate significant differences (**** p < 0.0001, * p < 0.05, Kruskal–Wallis and Dunn’s multiple comparison test, n = 3). (B) Overrepresented GO terms under the category biological processes from modulated genes in A (FDR < 0.05 Benjamini–Hochberg).