Pdx and Cdx genes are part of the ParaHox gene cluster, hypothesized to pattern the gut and anus. The goal was to examine the downstream molecular effects of mutation to Pdx and Cdx homeobox genes in amphioxus, Branchiostoma floridae. Frameshift mutations were made in Pdx and Cdx using TALENs and stable heterozygous lines generated. Heterozygous animals for each mutation were crossed (separately for Pdx and Cdx) , and larvae reared until phenotypes were evident: 5 gill slits for Pdx -/- and 2-3 gill slits (34h or 42h) for Cdx -/-. Approximately 100 to 300 larvae were collected for each sample: 3 samples each of Pdx -/- mutants, Pdx wild type (mix of +/+ and +/-), Cdx -/- mutants, Cdx wild type (mix of +/+ and +/-). These data were used to uncover downstream genetic pathways affected by each gene and also demonstrated a predominant effect of gut-associated genes.