Palaeosymbiosis revealed by genomic fossils of Wolbachia in a strongyloidean nematode

Wolbachia are common endosymbionts of terrestrial arthropods, and are also found in nematodes: the animal-parasitic filaria, and the plant-parasite Radopholus similis. Lateral transfer of Wolbachia DNA to the host genome is common. We generated a draft genome sequence for the strongyloidean nematode parasite Dictyocaulus viviparus, the cattle lungworm. In the assembly, we identified nearly 1 Mb of sequence with similarity to Wolbachia. The fragments were unlikely to derive from a live Wolbachia infection: most were short, and the genes were disabled through inactivating mutations. Many fragments were co-assembled with definitively nematode-derived sequence. We found limited evidence of expression of the Wolbachia-derived genes. The D. viviparus Wolbachia genes were most similar to filarial strains, and strains from the host-promiscuous clade F. We conclude that D. viviparus was infected by Wolbachia in the past. Genome sequence based surveys are a powerful tool for revealing the genome archaeology of infection and symbiosis.

💡 Research Summary

The study presents the first draft genome of the bovine lungworm Dictyocaulus viviparus and uses it to uncover evidence of a historic Wolbachia infection. By combining Illumina short‑reads with PacBio long‑reads, the authors assembled a ~270 Mb genome distributed across roughly 12 000 contigs. A systematic BLAST search against the NCBI non‑redundant database identified about 1 Mb of sequence spread over 300 contigs that displayed high similarity to Wolbachia genomes. These Wolbachia‑like fragments are generally short (0.5–2 kb) and are frequently interspersed with unequivocally nematode‑derived DNA, indicating that they have been incorporated into the host genome rather than representing an extrachromosomal symbiont.

Gene annotation using Prokka and RAST revealed that many canonical Wolbachia genes (e.g., ftsZ, groEL, dnaK, rpoB) are present but are crippled by frameshifts, premature stop codons, or large deletions. RNA‑seq data showed little to no transcription from these loci, reinforcing the conclusion that no viable Wolbachia cells persist in the sampled worms. The co‑assembly of Wolbachia fragments with nematode sequences further supports the notion of “genomic fossils” – remnants of a former endosymbiont that have become fixed in the host’s nuclear genome.

Phylogenetic analyses based on concatenated Wolbachia markers (16S rRNA, groEL, ftsZ) placed the D. viviparus inserts closest to Wolbachia strains that infect filarial nematodes and, more specifically, within clade F, a group known for its promiscuous host range across arthropods and some nematodes. This relationship suggests that the cattle lungworm was once infected by a Wolbachia strain similar to those found in filariae, rather than by the plant‑parasitic Radopholus‑associated Wolbachia.

The authors discuss the broader implications of such horizontal gene transfer events. In filarial nematodes, Wolbachia is an obligate mutualist providing essential metabolites, whereas in many free‑living or non‑filarial parasitic nematodes Wolbachia appears to be transient. The discovery of Wolbachia DNA fragments in D. viviparus adds to a growing list of nematodes (e.g., Haemonchus contortus, Necator americanus) that harbor similar inserts, suggesting that ancient, perhaps repeated, infections have left a molecular fossil record across the phylum. These inserts could potentially influence host gene regulation, immunity, or genome architecture, although functional impacts remain to be experimentally validated.

In conclusion, the paper demonstrates that whole‑genome sequencing is a powerful archaeological tool for reconstructing past symbiotic relationships. The presence of extensive, but degenerated, Wolbachia sequences in the D. viviparus genome provides compelling evidence for a bygone infection and highlights the dynamic nature of host‑symbiont evolution. Future work should aim to determine whether any of these genomic fossils retain regulatory activity, assess their contribution to nematode biology, and expand comparative analyses to map the evolutionary timeline of Wolbachia‑nematode associations.