Polypodium hydriforme is an enigmatic parasite that belongs to the phylum Cnidaria. Its taxonomic position has been debated: whereas it was previously suggested to be part of Medusozoa, recent phylogenomic analyses based on nuclear genes support the view that P. hydriforme and Myxozoa form a clade called Endocnidozoa. Medusozoans have linear mitochondrial (mt) chromosomes, whereas myxozoans, as most metazoan species, have circular chromosomes. In this work, we determined the structure of the mt genome of P. hydriforme, using Illumina and Oxford Nanopore Technologies reads, and showed that it is circular. This suggests that P. hydriforme is not nested within Medusozoa, as this would entail linearization followed by recirculation. Instead, our results support the view that P. hydriforme is a sister clade to Myxozoa, and mt linearization in the lineage leading to medusozoans occurred after the divergence of Myxozoa + P. hydriforme. Detailed analyses of the assembled P. hydriforme mt genome show that: (1) it is encoded on a single circular chromosome with an estimated size of ∼93,000 base pairs, making it one of the largest metazoan mt genomes; (2) around 78% of the genome encompasses a noncoding region composed of several repeat types; (3) similar to Myxozoa, no mt tRNAs were identified; (4) the codon TGA is a stop codon and does not encode for tryptophan as in other cnidarians; (5) similar to myxozoan mt genomes, it is extremely fast evolving.

Computational and Statistical Genomics Branch Division of Intramural Research National Human Genome Research Institute National Institutes of Health Bethesda MD 20892 USA

Department of Ecology and Evolutionary Biology University of Kansas 1200 Sunnyside Avenue Haworth Hall Lawrence KS 66045 USA

Faculty of Science University of South Bohemia Branišovská 31 370 05 České Budějovice Czech Republic

GeoGenetics Centre Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark

Institute of Parasitology Biology Centre Academy of Sciences of the Czech Republic Branišovská 31 370 05 České Budějovice Czech Republic

School of Zoology George S Wise Faculty of Life Sciences Tel Aviv University Tel Aviv 6997801 Israel

The Steinhardt Museum of Natural History and National Research Center Tel Aviv University Tel Aviv 6997801 Israel

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