Fig. 3: Trunk development is delayed to pre-metamorphosis in O. fusiformis.

a, Representative images from three independent analyses of Hox gene expression by whole-mount in situ hybridization at the mitraria larva, pre-competent larva, and juvenile stages of O. fusiformis. Only Hox3 is expressed at the mitraria stage (white arrowhead). Hox genes show spatial collinearity along the anteroposterior axis at the developing trunk of the pre-competent larva (white arrowheads) and in the juvenile. Dotted lines in the competent larva panels indicate background from the midgut. Black arrowheads in the juvenile panels indicate head to trunk boundary. cs, chaetal sack; mg, mid gut. Scale bar, 50 µm (larval stages) or 100 µm (juvenile stage). b, Average expression dynamics of anterior (n = 1,655), and posterior and trunk genes (n = 407) expressed in corresponding adult tissues during O. fusiformis development. P values were derived from two-tailed Student’s t-tests and adjusted using the Bonferroni method for multiple testing correction. ***, P < 0.001; NS, not significant. Centre lines in boxplots are the median, box is the interquartile range (IQR), and whiskers are the first or third quartile ± 1.5× IQR. c, Correlation matrices of transcription factor binding score (TFBSs). The dotted black line highlights the high TFBS correlation and heterochrony between the mitraria and competent larvae of O. fusiformis and the stage 4tt larva of C. teleta. d, Sequence logo of the annelid archetype (top) shows substantial similarity to the human homologue (bottom). e, TFBS dynamics for the annelid HOX, CDX, and EVX motif during O. fusiformis and C. teleta development. f, Average TFBS dynamics of all motifs in the peaks of the Hox cluster. Curves are locally estimated scatterplot smoothings, coloured shaded areas represent standard error of the mean.