First in family Rhabdiasidae: the reference-guided genome assembly of an invasive parasite, the cane toad lungworm (Rhabdias pseudosphaerocephala)

Rhabdias pseudosphaerocephala is a well-studied invasive nematode parasite of amphibians. However, there are several outstanding questions about R. pseudosphaerocephala that are best answered using genomic data. This species differs phenotypically across its invasive range. These differences are challenging to interpret because this species is part of a complex that is diverse and cryptic in its home-range, and we do not know how many species from this complex originally colonised Australia. For this reason, it is unknown whether the phenotypic differences across the introduced range are due to intraspecific differentiation between populations or due to the presence of multiple species. In addition, there is little consensus in the placement of Rhabdiasidae family within the phylum Nematoda, making it difficult to perform comparative analyses with other nematodes. Within this paper, we assemble a reference genome for R. pseudosphaerocephala, the first assembly of any Rhabdiasidae species. We then use resequencing data to address outstanding questions about this species. Specifically, we combine population genetic and phylogenetic analyses to determine that there is likely only a single R. pseudosphaerocephala lineage within Australia, and identify that the invasive range population is closely related to home rage isolates that infect similar host species. We present compelling evidence for a genetic bottleneck following introduction to Australia and genetic differentiation occurring between invasive range populations. We then use genome-scale phylogenomic analysis to place the Rhabdiasidae family in the suborder Rhabditina. Ultimately, this paper brings the study of Rhabdiasidae into the genomic era, and sheds light on its ancient and modern evolutionary history.