Sea anemone genomes reveal ancestral metazoan chromosomal macrosynteny

Cnidaria (sea anemones, jellyfish, corals and hydra) form a close sister group to Bilateria. Within this clade, the sea anemone Nematostella vectensis has emerged as a slow evolving model for investigating characteristics of the cnidarian-bilaterian common ancestor, which diverged near the Cambrian explosion. Here, using long read sequencing and high throughput chromosome conformation capture, we generate high quality chromosome-level genome assemblies for N. vectensis and the closely related edwardsiid sea anemone, Scolanthus callimorphus. In both cases we find a robust set of 15 chromosomes comprising a stable linkage group detectable within all major clades of sequenced cnidarian genomes. Further, both genomes show remarkable chromosomal conservation with chordates. In contrast with Bilateria, we report that extended Hox and NK gene clusters are chromosomally linked but do not retain a tight spatial conservation. Accordingly, there is a lack of evidence for topologically associated domains, which have been implicated in the evolutionary pressure to retain tight microsyntenic gene clusters. We also uncover ultra-conserved noncoding elements at levels previously undetected in non-chordate lineages. Both genomes are accessible through an actively updated genome browser and database at https://simrbase.stowers.org