Genomes of the entomopathogenic nematode<i>Steinernema hermaphroditum</i>and its associated bacteria

Abstract

As an entomopathogenic nematode (EPN),Steinernema hermaphroditumparasitizes insect hosts and harbors symbioticXenorhabdus griffinaebacteria. In contrast to other Steinernematids,S. hermaphroditumhas hermaphroditic genetics, offering the experimental scope found inCaenorhabditis elegans. To enable biological analysis ofS. hermaphroditum, we have assembled and analyzed its reference genome. This genome assembly has five chromosomal scaffolds and 83 unassigned scaffolds totaling 90.7 Mb, with 19,426 protein-coding genes having a BUSCO completeness of 88.0%. Its autosomes show higher densities of strongly conserved genes in their centers, as inC. elegans, but repetitive elements are evenly distributed along all chromosomes, rather than with higher arm densities as inC. elegans. Either when comparing protein motif frequencies between nematode species or when analyzing gene family expansions during nematode evolution, we observed two categories of genes preferentially associated with the origin ofSteinernemaorS. hermaphroditum: orthologs of venom genes inS. carpocapsaeorS. feltiae; and some types of chemosensory G protein-coupled receptors, despite the tendency of parasitic nematodes to have reduced numbers of chemosensory genes. Three-quarters of venom orthologs occurred in gene clusters, with the larger clusters comprising functionally diverse pathogenicity islands rather than paralogous repeats of a single venom gene. While assembling the genome ofS. hermaphroditum, we coassembled bacterial genomes, finding sequence data for not only the known symbiont,X. griffinae, but also for eight other bacterial genera. All eight genera have previously been observed to be associated withSteinernemaspecies or the EPNHeterorhabditis, and may constitute a "second bacterial circle" of EPNs. The genome assemblies ofS. hermaphroditumand its associated bacteria will enable use of these organisms as a model system for both entomopathogenicity and symbiosis.

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