Rampant loss of universal metazoan genes revealed by a chromosome-level genome assembly of the parasitic Nematomorpha

Parasites may manipulate host behavior to increase the odds of transmission or to reach the proper envi-ronment to complete their life cycle.1,2 Members of the phylum Nematomorpha (known as horsehair worms, hairworms, or Gordian worms) are large endoparasites that affect the behavior of their arthropod hosts. In terrestrial hosts, they cause erratic movements toward bodies of water,3-6 where the adult worm emerges from the host to find mates for reproduction. We present a chromosome-level genome assembly for the freshwater Acutogordius australiensis and a draft assembly for one of the few known marine spe-cies, Nectonema munidae. The assemblies span 201 Mbp and 213 Mbp in length (N50: 38 Mbp and 716 Kbp), respectively, and reveal four chromosomes in Acutogordius, which are largely rearranged compared to the inferred ancestral condition in animals. Both nematomorph genomes have a relatively low number of genes (11,114 and 8,717, respectively) and lack a high proportion (-30%) of universal single-copy meta-zoan orthologs (BUSCO genes7). We demonstrate that missing genes are not an artifact of the assembly process, with the majority of missing orthologs being shared by the two independent assemblies. Missing BUSCOs are enriched for Gene Ontology (GO) terms associated with the organization of cilia and cell pro-jections in other animals. We show that most cilium-related genes conserved across eukaryotes have been lost in Nematomorpha, providing a molecular basis for the suspected absence of ciliary structures in these animals.