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Complete genome of Vibrio japonicus strain JCM 31412 T and assessment of the Nereis clade of the genus Vibrio

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Abstract

Clade-based taxonomy has become a recognised means of classifying members of the family Vibrionaceae. A multilocus sequence analysis (MLSA) approach based on eight housekeeping genes can be used to infer phylogenetic relationships, which then groups species into monophyletic clades. Recent work on the Vibrionaceae clades added newly described species and updated existing relationships; the Nereis clade currently includes Vibrio nereis and Vibrio hepatarius. A publication characterising Vibrio japonicus as a novel species placed it within the Nereis clade, but this strain was not included in a recently published taxonomic update because a genome sequence was not available for phylogenetic assessment. To resolve this discrepancy and assess the taxonomic position of V. japonicus within the updated clades, we sequenced the complete genome of V. japonicus JCM 31412 T and conducted phylogenetic and genomic analyses of this clade. Vibrio japonicus remains within the Nereis clade and phylogenomic, average nucleotide identity (ANI), and average amino acid identity (AAI) analyses confirm this relationship. Additional genomic assessments on all Nereis clade members found gene clusters and inferred functionalities shared among the species. This work represents the first complete genome of a member of the Nereis clade and updates the clade-based taxonomy of the Vibrionaceae family.

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Data availability

The complete genome sequence for V. japonicus JCM 31412 T is deposited in DDBJ/ENA/GenBank under the accession numbers CP102096-CP102098. Raw reads are deposited in the SRA under the accession numbers SRX16997812 and SRX16997813.

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Acknowledgements

The authors thank Nancy Shough (Southern Oregon University, SOU) for technical support, and the editor and reviewers for their efforts to improve the quality and presentation of this work. We gratefully acknowledge the computing resources provided on the High-Performance Computing Cluster operated by Research Technology Services at the George Washington University.

Funding

This work was supported by startup funds from the GWU to J.H.S., from SOU to P.V., and from UNCW to B.U. The funders had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; or decision to submit the manuscript for publication.

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Author notes

  1. Patrick Videau

    Present address: Bayer Environmental Science, Cary, NC, USA

Authors and Affiliations

  1. Department of Biological Sciences, The George Washington University, Washington, DC, USA

    Maximillian D. Shlafstein & Jimmy H. Saw

  2. Department of Biology, Southern Oregon University, Ashland, OR, USA

    Sarah A. Emsley & Patrick Videau

  3. Microbiology Graduate Program, University of Delaware, Newark, DE, USA

    Rachel M. Loughran

  4. Instructure, Salt Lake City, Utah, USA

    Samantha M. O’Hanlon

  5. Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA

    Blake Ushijima

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Contributions

B.U., J.H.S., and P.V. designed the experiments; M.D.S., S.A.E, R.M.L., J.H.S., and P.V. conducted the experiments; M.D.S., S.M.O., J.H.S., and P.V. prepared the figures, B.U., P.V., and J.H.S. contributed methodology and validation; M.D.S., P.V., and J.H.S. wrote the manuscript and all authors analysed the data and reviewed the manuscript.

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Correspondence to Patrick Videau or Jimmy H. Saw.

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Shlafstein, M.D., Emsley, S.A., Loughran, R.M. et al. Complete genome of Vibrio japonicus strain JCM 31412 T and assessment of the Nereis clade of the genus Vibrio. Antonie van Leeuwenhoek 116, 129–141 (2023). https://doi.org/10.1007/s10482-022-01784-y

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