Extended Data Fig. 4: Dot-plots showing conserved syntenies between amphioxus and selected invertebrates.

Dots represent mutual best hits between amphioxus and the genomes of the Crown Of Thorns sea star Acanthaster planci, the soil nematode Caenorhabditis elegans, and the starlet sea anemone Nematostella vectensis. The N. vectensis and A. planci genomes are not yet assembled into chromosomes, and only scaffolds containing 20 or more genes (counting only mutual-best-hit vs. amphioxus) are shown. Scaffolds are sorted based on clustering using similarity of their CLG content. Vertical dashed lines are as shown in and Fig. 1, with the same CLG-based coloring, showing that the partitioning of amphioxus found using jawed vertebrates is also consistent with diverse invertebrates, and that sea star and sea anemone scaffolds can be grouped according to conserved synteny with amphioxus. C. elegans chromosomes arose by fusion, translocation, and mixing of the ancestral bilaterian units that are still retained in amphioxus.