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Peer-reviewedCC BY 4.0Parasitology

Chromosome‑scale genome assembly of the bovine parasite Tritrichomonas foetus using short-read, long‑read and Pore‑C sequencing identifies conserved and lineage‑specific gene families relevant to host interaction

  • John Harvey Santos1
  • Antonino Cavallaro1
  • Elizabeth M. Ross1
  • Hannah Siddle1
  • Gry Boe-Hansen1,2
  • Ali Raza3
  • Loan Nguyen1
  • Ala Tabor1,4
4 affiliations
  1. 1Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
  2. 2School of Veterinary Science, The University of Queensland, Gatton, QLD, Australia
  3. 3School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
  4. 4School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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Abstract

Tritrichomonas foetus is the causative agent of bovine trichomonosis, a venereal disease that compromises cattle fertility and causes major economic losses. We report a chromosome-scale genome assembly of T. foetus isolate, TfOz5, from Queensland, Australia generated using Oxford Nanopore long-read sequencing and Pore-C chromatin conformation capture. The 137.7 Mb assembly spans 5 chromosomes with an N50 of 24 Mb. Repeat analysis revealed 43.6% repetitive content dominated by DNA transposons. Gene prediction identified 32 104 protein-coding genes of which 98.3% were assigned to orthogroups. Comparative analysis with the KV-1 genome detected 160 structural variants, including deletions (40.6%), insertions (22.5%), duplications (16.3%), inversions (13.1%) and translocations (7.5%). Across 9 Parabasalia species, we observed high gene family conservation and 305 species-specific orthogroups in TfOz5. Phylogenetic analysis confirmed the monophyletic cluster of T. foetus strains (K, KV-1 and TfOz5). Inter-species comparison with the human urogenital parasite Trichomonas vaginalis G3 revealed conserved gene sets between T. foetus TfOz5 and T. vaginalis G3 that were significantly enriched for core cellular functions (translation, cell cycle and mitochondria-related homology hits), while divergent genes highlighted species-specific host interactions. Trichomonas vaginalis G3 showed enrichment for proteolysis, regulation of DNA-templated transcription and symbiont–host adhesion, traits consistent with persistence in the human genital tract. Similarly, T. foetus TfOz5 host interactions align with long-term survival in the bovine reproductive niche. This chromosome-scale assembly provides a valuable genomic framework for investigating parasite evolution, identifying candidate genetic features associated with host adaptation and supporting the development of next-generation recombinant vaccines to control bovine trichomonosis.

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Cite

BibTeXRIS
BibTeX
@article{santos2026chromosomescale,
  title = {{Chromosome‑scale genome assembly of the bovine parasite Tritrichomonas foetus using short-read, long‑read and Pore‑C sequencing identifies conserved and lineage‑specific gene families relevant to host interaction}},
  author = {John Harvey Santos and Antonino Cavallaro and Elizabeth M. Ross and Hannah Siddle and Gry Boe-Hansen and Ali Raza and Loan Nguyen and Ala Tabor},
  journal = {Parasitology},
  year = {2026},
  month = aug,
  doi = {10.1017/s0031182026102716},
  url = {https://doi.org/10.1017/s0031182026102716},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Chromosome‑scale genome assembly of the bovine parasite Tritrichomonas foetus using short-read, long‑read and Pore‑C sequencing identifies conserved and lineage‑specific gene families relevant to host interaction
AU  - John Harvey Santos
AU  - Antonino Cavallaro
AU  - Elizabeth M. Ross
AU  - Hannah Siddle
AU  - Gry Boe-Hansen
AU  - Ali Raza
AU  - Loan Nguyen
AU  - Ala Tabor
PY  - 2026
DA  - 2026/08/11
JO  - Parasitology
DO  - 10.1017/s0031182026102716
UR  - https://doi.org/10.1017/s0031182026102716
AB  - Tritrichomonas foetus is the causative agent of bovine trichomonosis, a venereal disease that compromises cattle fertility and causes major economic losses. We report a chromosome-scale genome assembly of T. foetus isolate, TfOz5, from Queensland, Australia generated using Oxford Nanopore long-read sequencing and Pore-C chromatin conformation capture. The 137.7 Mb assembly spans 5 chromosomes with an N50 of 24 Mb. Repeat analysis revealed 43.6% repetitive content dominated by DNA transposons. Gene prediction identified 32 104 protein-coding genes of which 98.3% were assigned to orthogroups. Comparative analysis with the KV-1 genome detected 160 structural variants, including deletions (40.6%), insertions (22.5%), duplications (16.3%), inversions (13.1%) and translocations (7.5%). Across 9 Parabasalia species, we observed high gene family conservation and 305 species-specific orthogroups in TfOz5. Phylogenetic analysis confirmed the monophyletic cluster of T. foetus strains (K, KV-1 and TfOz5). Inter-species comparison with the human urogenital parasite Trichomonas vaginalis G3 revealed conserved gene sets between T. foetus TfOz5 and T. vaginalis G3 that were significantly enriched for core cellular functions (translation, cell cycle and mitochondria-related homology hits), while divergent genes highlighted species-specific host interactions. Trichomonas vaginalis G3 showed enrichment for proteolysis, regulation of DNA-templated transcription and symbiont–host adhesion, traits consistent with persistence in the human genital tract. Similarly, T. foetus TfOz5 host interactions align with long-term survival in the bovine reproductive niche. This chromosome-scale assembly provides a valuable genomic framework for investigating parasite evolution, identifying candidate genetic features associated with host adaptation and supporting the development of next-generation recombinant vaccines to control bovine trichomonosis.
SN  - 0031-1820
SN  - 1469-8161
ER  -