Additional file 1 of A computational investigation into the role of tRNAs encoded by Shigella phage Sf14

Supplementary Material 1. Supplementary figure S1: median RSCU values of the Sf14 and S. flexneri 2457 T genomes Stacked bar graph comparing the median RSCU values of each codon in Sf14 and host S. flexneri 2457T. Asterisks indicate the difference in RSCU is significant. Supplementary figure S2: average RSCU values for the S. flexneri 2457 T genome and all gene groups of interest Bar graphs showing the average RSCU values for all codons in 2457 T for (A) genome, (B) metabolism genes, (C) biosynthesis genes, (D) gene expression genes, (E) stress response and drug resistance genes, and (F) transport and miscellaneous genes. Supplementary figure S3: average RSCU values for Sf14 genome and all Sf14 gene groups Bar graphs showing the average RSCU values for all codons in Sf14 (A) genome, (B) early genes, (C) middle genes, (D) late genes, and (E) hypothetical genes. Supplementary figure S4: PCA plot of RSCU scores for all codons in the Sf14 and S. flexneri 2457 T gene groups Genes are assigned a color based on their group, as indicated in the key on the right. An unlabeled version of this plot is available in the text (Fig. 4). Some labels are hidden due to multiple overlapping observations. Supplementary figure S5: tAI values for both Sf14 and S. flexneri 2457 T genomes and host genes of interest Bar graphs depicting the tAI values for the (A) host genome, (B) host genes of interest, (C) Sf14 genome; (D) Boxplot of the distribution of tAI values in S. flexneri 2457 T and Sf14. Supplementary figure S6: Sf14-encoded tRNA mutation frequency by isotype and position (A) Bar graph of the mutation frequency for Sf14 tRNAs according to their isotype. (B) Bar graph of the frequency of mutations at each anticodon loop position. Supplementary figure S7: comparison of tRNA ∆G values between Sf14 and S. flexneri 2457 T Free energy (∆G) values for Sf14-encoded tRNAs and their counterparts in 2457T. Sf14 ∆G values are on the y-axis, and 2457 T ∆G values are on the x-axis. Supplementary figure S8: ∆∆G values (Sf14 – S. flexneri 2457 T) and the impact of mutation position on ∆∆G Dot plot of the mutation position (x-axis) of Sf14 mutated tRNAs as it relates to ∆∆G values (y-axis). Position “0” indicates no mutations were found. Supplementary figure S9: secondary structure of four representative mutated Sf14-encoded tRNAs Four Sf14-encoded tRNAs were modeled and compared to their host counterparts, with mutations in the anticodon loops highlighted in yellow. The tRNAs modeled were (A) tRNA-Leu-CAA, (B) tRNA-Leu-TAG, (C) tRNA-Phe-GAA, and (D) tRNA-Gln-TTG.