Analyses ofXenorhabdus griffiniaegenomes reveal two distinct sub-species that display intra-species variation due to prophages

Abstract

AbstractNematodes of the genusSteinernemaand theirXenorhabdusbacterial symbionts are lethal entomopathogens that are useful in the biocontrol of insect pests, as sources of diverse natural products, and as research models for mutualism and parasitism.Xenorhabdusplay a central role in all aspects of theSteinernemalifecycle, and a deeper understanding of their genomes therefore has the potential to spur advances in each of these applications. Here, we report a comparative genomics analysis ofXenorhabdus griffiniae, including the symbiont ofSteinernema hermaphroditumnematodes, for which genetic and genomic tools are being developed. We sequenced and assembled circularized genomes for threeXenorhabdusstrains: HGB2511, ID10 and TH1. We then determined their relationships to otherXenorhabdusand delineated their species via phylogenomic analyses, concluding that HGB2511 and ID10 areXenorhabdus griffiniaewhile TH1 is a novel species. These additions to the existingX. griffiniaelandscape further allowed for the identification of two subspecies within the clade. Consistent with otherXenorhabdus, the analysedX. griffiniaegenomes each encode a wide array of antimicrobials and virulence-related proteins. Comparative genomic analyses, including the creation of a pangenome, revealed that a large amount of the intraspecies variation inX. griffiniaeis contained within the mobilome and attributable to prophage loci. In addition, CRISPR arrays, secondary metabolite potential and toxin genes all varied among strains within theX. griffiniaespecies. Our findings suggest that phage-related genes drive the genomic diversity in closely relatedXenorhabdussymbionts, and that these may underlie some of the traits most associated with the lifestyle and survival of entomopathogenic nematodes and their bacteria: virulence and competition. This study establishes a broad knowledge base for further exploration of not only the relationships betweenX. griffiniaespecies and their nematode hosts but also the molecular mechanisms that underlie their entomopathogenic lifestyle.