Additional file 1 of Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga

Additional file 1: Fig S1. Survival and fertility rates of A. vaga individuals exposed to desiccation and radiation stress. Percentage of survival (dark blue) and fertility rate of A. vaga exposed to desiccation, rehydration post 14 days desiccation, and 500 Gy of X-rays (low-LET) or Fe-ions (high-LET). The fertility is represented by three different histograms: fraction of individuals able to produce viable offspring (green), fraction of individuals unable to produce viable offspring but only sterile egg(s) (blue), fraction of individuals unable to lay egg or with premature dead (red). Survival rate was evaluated 2 days post rehydration or post radiation. To ensure reliable results, survival data were obtained from at least three replicates. Samples exposed to 500 Gy of iron ions were transported from Belgium to GSI and then returned to the authors' laboratory for analysis. To evaluate the impact of transportation on the samples, a control group labeled "Ctl transport" was also sent to GSI. This control group experienced similar conditions as the exposed samples but did not undergo radiation exposure. Fig S2. Volcano plots of differential genes over-expressed (OE) and under-expressed (UE) in A) A. vaga individuals entering desiccation, B) 2.5 h post desiccation and x-rays radiation. The percentage of the genome over- and under-expressed are written. Although a higher percentage of genes are under-expressed in B) the log2foldchange values are bigger in OE than UE genes. Fig S3. Number of genes with GO ids for a specific log2foldchange values identified as A) over-expressed (OE) genes in A. vaga rotifers entering desiccation, B) under-expressed (UE) genes in A. vaga rotifers entering desiccation, C) 906 OE genes in the core response to radiation 2.5 h post irradiation, D) 724 OE genes in the core response to irradiation 8 h post radiation. Fig S4. Gene Ontology enrichment analyses GO biological processes significantly enriched (chi-square test p-value < 0.05, min. 3 OE genes with the GO id) with genes being significantly A) under-expressed (framed in red, FDR < 0.01 and log2foldchange < -0.5 in DESeq2 and EdgeR) and B) over-expressed (framed in green, FDR < 0.01 and log2foldchange > 0.5 in DESeq2 and EdgeR) in A. vaga individuals entering desiccation (in gray) and 1.5 h post-rehydration after 14 days of desiccation (in yellow), and in the core response to radiation 2.5 h (pink) and 8 h (purple) post radiation. Fig S5. Expression of genes involved in Non-Homologous End-Joining (NHEJ) pathway differentially expressed post desiccation and/or radiation. The figure represents how the different proteins act in this DNA repair pathway and in which order. They are represented by different symbols. How the level of expression of genes (gene ids written on the right side of the figure) coding for these proteins change in the different conditions is represented by a heatmap of the log2foldchange. The color is not white when the gene is significantly (FDR < 0.01 with both DESeq2 and EdgeR) over- (log2foldchange > 0.5 in green) or under-expressed (log2foldchange < -0.5 in orange or red). The investigated conditions are: individuals entering desiccation (gray), after 14 days desiccation and 1.5 h rehydration (yellow), after desiccation and x-rays radiation (orange), after desiccation and Fe radiation (purple), after x-ray radiation without desiccation (blue). The investigated time points are represented as follow: 0 h (triangles), 1.5 or 2.5 h (circles), 8 h (squares), 24 h (pentagons). Heatmap of transcripts per millions (TPMs) for each gene is represented on the right side and with a different code representing the level of expression. Fig S6. Expression of genes involved in Homologous Recombination (HR) pathway differentially expressed post desiccation and/or radiation. The figure represents how the different proteins act in this DNA repair pathway and in which order. They are represented by different symbols. How the level of expression of genes (gene ids written on the right side of the figure) coding for these proteins change in the different conditions is represented by a heatmap of the log2foldchange. The color is not white when the gene is significantly (FDR < 0.01 with both DESeq2 and EdgeR) over- (log2foldchange > 0.5 in green) or under-expressed (log2foldchange < -0.5 in orange or red). The investigated conditions are: individuals entering desiccation (gray), after 14 days desiccation and 1.5 h rehydration (yellow), after desiccation and x-rays radiation (orange), after desiccation and Fe radiation (purple), after x-ray radiation without desiccation (blue). The investigated time points are represented as follow: 0 h (triangles), 1.5 or 2.5 h (circles), 8 h (squares), 24 h (pentagons). Heatmap of transcripts per millions (TPMs) for each gene is represented on the right side and with a different code representing the level of expression. Fig S7. Expression of genes involved in Nucleotide excision repair (NER) pathway differentially expressed post desiccation and/or radiation. The figure represents how the different proteins act in this DNA repair pathway and in which order. They are represented by different symbols. How the level of expression of genes (gene ids written on the right side of the figure) coding for these proteins change in the different conditions is represented by a heatmap of the log2foldchange. The color is not white when the gene is significantly (FDR < 0.01 with both DESeq2 and EdgeR) over- (log2foldchange > 0.5 in green) or under-expressed (log2foldchange < -0.5 in orange or red). Genes potentially involved in this pathway are indicated in the bottom of the figure. The investigated conditions are: individuals entering desiccation (gray), after 14 days desiccation and 1.5 h rehydration (yellow), after desiccation and x-rays radiation (orange), after desiccation and Fe radiation (purple), after x-ray radiation without desiccation (blue). The investigated time points are represented as follow: 0 h (triangles), 1.5 or 2.5 h (circles), 8 h (squares), 24 h (pentagons). Heatmap of transcripts per millions (TPMs) for each gene is represented on the right side and with a different code representing the level of expression. Horizontal transfer genes (HGT) are represented by the violet stars. Fig S8. Expression of genes involved in Mismatch repair pathway (MR) differentially expressed post desiccation and/or radiation. The figure represents how the different proteins act in this DNA repair pathway and in which order. They are represented by different symbols. How the level of expression of genes (gene ids written on the right side of the figure) coding for these proteins change in the different conditions is represented by a heatmap of the log2foldchange. The color is not white when the gene is significantly (FDR < 0.01 with both DESeq2 and EdgeR) over- (log2foldchange > 0.5 in green) or under-expressed (log2foldchange < -0.5 in orange or red). Genes potentially involved in this pathway are indicated in the bottom of the figure. The investigated conditions are: individuals entering desiccation (gray), after 14 days desiccation and 1.5 h rehydration (yellow), after desiccation and x-rays radiation (orange), after desiccation and Fe radiation (purple), after x-ray radiation without desiccation (blue). The investigated time points are represented as follow: 0 h (triangles), 1.5 or 2.5 h (circles), 8 h (squares), 24 h (pentagons). Heatmap of transcripts per millions (TPMs) for each gene is represented on the right side and with a different code representing the level of expression. Horizontal transfer genes (HGT) are represented by the violet stars.