Figure 5

Global transcriptome analysis of M. marinum Mma20 vs PBS and M. avium MAC 101 vs PBS groups. (A) Experimental scheme to collect samples for RNA deep sequencing. AB/TL zebrafish embryos were injected with ~250 CFU M. marinum Mma20 strain or ~4500 CFU M. avium MAC 101 strain at 28 hpf. The embryos in the control group were injected with sterile PBS with 2% PVP. The samples for RNAseq are taken from four independent sample sets with the injected larvae at 4 dpi. (B) Principal component analysis. The RNAseq samples clustered based on their groups, as showed by the solid ellipses grouping samples. (C) Overview of the distribution of DEGs fold change in zebrafish larvae infected with Mma20 or MAC 101. DEGs were assessed by FDR p-value < 0.05. Upregulated gene sets are shown in red and downregulated gene sets are shown in blue. The intensity of the color represents the fold change level. (D) Venn diagram shows the common and specific DEGs number between the 250 CFU Mma20- infected group and 4500 CFU MAC 101- infected group compared to the control. The Venn diagrams were made by the website: https://www.biovenn.nl/. (E) The top 10 gene ontology (GO) terms of biological process with lowest P value in the Mma20- infected larvae compared to the control group. (F) The top 10 GO terms of biological process with lowest P value in the MAC101-infected larvae compared to the control group. (G) Top 20 significantly enriched KEGG pathways in the Mma20- infected larvae compared to the control group. (H) Top 20 significantly enriched KEGG pathways in the MAC 101- infected larvae compared to the control group. The GO analysis and KEGG pathway enrichment analysis were performed by using DAVID. In (G, H), the size of circle represents the enriched gene numbers, bigger circle indicates more enriched genes were found in this pathway. The color of circle represents -log10 (P value).