Extended Data Fig. 5: The Hox gene complement and expression in O. fusiformis.

a, Orthology assignment of O. fusiformis Hox genes through maximum likelihood phylogenetic inference. Bootstrap support values are shown for major gene groups. Of: O. fusiformis. b, Volcano plot of the mitraria to competent larva transition, highlighting the marked upregulation of Hox genes. LFC: log₂(fold-change). P-values were derived from the described DESeq2 pipeline and Benjamini-Hochberg-adjusted. c, Chromosomal location of the Hox cluster and Post1 gene in O. fusiformis (top) and schematic comparison of Hox cluster organisation in annelids and a mollusc (bottom). Arrows denote direction of transcription. d, Schematic representation to scale of the genomic loci and intron–exon composition of Hox genes in O. fusiformis. e, Heatmaps of Hox gene expression during the development of C. teleta, O. fusiformis and the echiuran annelid Urechis unicinctus. In the two annelid species with planktotrophic larvae, Hox genes only become expressed at the larval stage (dotted vertical line), and not during embryogenesis, as observed in C. teleta. f, Whole mount in situ hybridisation of Hox genes in the gastrula (lateral views) and in the mitraria larva, pre-competent larva, and juvenile stages of O. fusiformis (ventral views). The area encircled by a dotted white line at the pre-competent stage highlights a region of probe trapping from ingested food content. bp: blastopore; mo: mouth. Representative results of three independent analyses. g,h Schematic representations of the expression of Hox genes in the trunk rudiment of the competent larva (g) and juvenile trunk (h). A: anterior; P: posterior. Drawings are not to scale, and schematic expression domains are approximate. Scale bars in f, 50 µm in gastrulae and larvae, and 100 µm in juvenile.