Fig. 6

Transcriptome analysis of Pdx and Cdx mutant amphioxus embryos and larvae. a MA plot showing fold change in expression (log 2 scale) between wild type and Pdx mutant larvae in relation to mean expression level (read counts). Coloured dots are contigs meeting significance criteria. b MA plot showing fold change in expression (log 2 scale) between wild type and Cdx mutant embryos in relation to mean expression level (read counts). Coloured dots are contigs meeting significance criteria. c Violin plot comparing expression level (FPKM) between wild type (WT) and Pdx mutant larvae (KO) for selected GFP, ILP1 and ILPR contigs, showing downregulation of GFP and upregulation of ILPR in mutants. d Violin plot comparing expression level between wild type (WT) and Cdx mutant embryos (KO) for selected iLBP contigs, showing downregulation in mutants. e Linear regression showing colinear-like response in expression level fold change of Hox genes to Cdx mutation. f Proportional Venn diagram showing overlap between contigs classed as gut-enriched (blue) and those expressed differentially after Pdx mutation (orange) or Cdx mutation (green)