Additional file 2 of Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa

Additional file 2: Supplementary Table 1. Number of reads per organism. Number of reads in each library (‘reads processed’) and number and fraction of reads mapped to each organism by Kallisto. Column ‘tmt’ indicates treatment, i.e. uninfected (H0) or H. defensa-infected aphid hosts (infecting strains H15, H402, H76 or H85). ‘Batch’ indicates which libraries were grouped during RNA extraction and library preparation. The library that was excluded from analysis is marked with **. Read counts marked with * are most likely a result of index hopping. Supplementary Table 2. Read assignment to taxa. Fraction of reads assigned to different taxa by Kraken. Fractions were averaged over all libraries of each treatment, except for treatment H15 for which the strongly contaminated library H15R1 was listed separately from the other three libraries (H15*). Aphid hosts were uninfected (H0) or infected (infecting strains H15, H402, H76 or H85) by H. defensa. As this table contains only taxa of specific interest, the read fractions are not expected to add up to 100%. Fractions below 0.01 were not extracted from the Kraken output, which is indicated by “ 0.5 are indicated by coloured backgrounds. Supplementary Table 6. Differential expression of aphid genes (reduced model). Results of differential expression analysis comparing gene expression of aphids infected with H. defensa H15 to aphids infected with H. defensa H85. P-values adjusted for multiple testing (padj) 0.5 are indicated by coloured backgrounds. Supplementary Table 7. Differential expression of H. defensa genes (full model). Results of differential expression analysis comparing gene expression of H. defensa strains H15, H76 or H402 to H. defensa strain H85 (full model with all strains). P-values adjusted for multiple testing (padj) 0.5 are indicated by coloured backgrounds. Supplementary Table 8. Differential expression of B. aphidicola genes. Results of differential expression analysis comparing gene expression of B. aphidicola in aphid hosts infected with H. defensa (H15, H76, H85 or H402) to uninfected aphid hosts (H0). P-values adjusted for multiple testing (padj) 0.5 are indicated by coloured backgrounds. For each gene, read counts in each replicate are indicated. Supplementary Table 9. Correlation of aphid gene expression. Correlation coefficient and p-values of aphid gene modules with H. defensa titre and toxin type. Coloured: Correlation has a p-value of < 0.01. If no GO-terms are enriched in a module, the value in ‘associated GO-terms’ is set to ‘NA’. a) WGCNA analysis with aphid and H. defensa genes. b) Correlation analysis with aphid and H. defensa genes. Supplementary Table 10. Correlation of H. defensa gene expression. Correlation coefficient and p-values of H. defensa gene modules with H. defensa titre and toxin type. Coloured: Correlation has a p-value of < 0.01. If no GO-terms are enriched in a module, the value in ‘associated GO-terms’ is set to ‘NA’. a) WGCNA analysis with aphid and H. defensa genes. b) Correlation analysis with aphid and H. defensa genes. c) Correlation analysis with B. aphidicola and H. defensa genes. Supplementary Table 11. Correlation of B. aphidicola gene expression. Correlation coefficient and p-values of B. aphidicola gene modules with H. defensa titre and toxin type. Coloured: Correlation has a p-value of < 0.01. If no GO-terms or KEGG pathways are enriched in a module, the values in ‘associated GO-terms’ and ‘associated KEGG pathways’ is set to ‘NA’. a) WGCNA analysis with B. aphidicola and H. defensa genes. b) Correlation analysis with B. aphidicola and H. defensa genes. Supplementary Table 12. Origin of aphid clones. Collection date, site and host plant for the aphid clones used as donors and recipients during the transfections that created the infected A06–407 sublines. Supplementary Table 13. Accession numbers of H. defensa assemblies. Protein fasta files from genome assemblies of H. defensa were downloaded from NCBI and provided to Prokka for gene prediction and to BUSCO for phylogenetic analyses. Supplementary Table 14. Accession numbers of contaminant bacterial genomes. Coding DNA sequences (CDS) from genome assemblies of the most frequent contaminant bacteria were downloaded from NCBI and provided to Kallisto during mapping.