The genome of an enigmatic sea urchin parasite Echinomermella matsi Jones & Hagen, 1987 resolves its place among other invertebrate parasitic nematodes

Abstract

We present a genome of Echinomermella matsi (Nematoda: Plectida: Benthimermithidae), a body cavity parasite of the green sea urchin Strongylocentrotus spp. commonly found along the coast of Central and Northern Norway. Three assemblies were generated, one from multiple individuals using Oxford Nanopore long read data and two from two individuals using PacBio long read data. The genome of Echinomermella matsi is 65 Mb long consisting of 7 chromosomes, with nematode Benchmarking Using Single Copy Orthologue (BUSCO) completeness reaching 61%. The E. matsi chromosome complement corresponds to the proposed Rhabditida ancestral linkage groups. Phylogenetic analyses using newly generated 18S rRNA genes and a multigene dataset consisting of BUSCO protein coding genes, supported by morphological observations of juveniles, firmly place Echinomermella within the nematode order Plectida, alongside nematode parasitoids of marine invertebrates, Trophomera or Neocamacolaimus. As a result, the generally free-living order Plectida includes at least three independently evolved lineages of nematodes symbiotic with various groups of aquatic and terrestrial invertebrates and with unicellular organisms. This, and the fact that Plectida is the closest sister lineage to Rhabditida as a whole, and one node away from the exclusively animal parasitic Spirurina, makes this lineage a valuable model for study of evolution of animal parasitism in the aquatic environment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/699767v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@d44b08org.highwire.dtl.DTLVardef@18a3310org.highwire.dtl.DTLVardef@1e79dforg.highwire.dtl.DTLVardef@d33b3b_HPS_FORMAT_FIGEXP M_FIG C_FIG Article summaryThe researchers generated a genome of Echinomermella matsi, a body cavity parasite of the green sea urchin, using PacBio and Oxford Nanopore long read sequencing. The genome is 65 Mb long, shows 61% of nematode BUSCO completeness, and consists of 7 chromosomes. Single and multiple gene phylogenies place Echinomermella within mostly free-living Plectida as one of the three independently evolved parasitic lineages. The authors suggest Echinomermella to be a valuable model to study evolution of animal parasitism in the aquatic environment. The genome can be used to develop biocontrol strategies of Echinomermella in mariculture of green sea urchin.