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A method for identifying nine tuna and tuna-like species (tribe Thunnini) by using high-resolution melting analysis based on genotyping single nucleotide polymorphisms in mitochondrial DNA

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Abstract

Tuna and tuna-like fishes (tribe Thunnini) are pelagic species that are important worldwide for their ecological and economic value. Understanding the ecology of Thunnini at the early life stages is necessary for proper resource management and conservation. However, the morphological similarity among Thunnini species and the often physically damaged larval and juvenile samples makes unambiguous species identification difficult. Using molecular techniques is one way to deal with these issues, and here we applied high-resolution melting (HRM) analysis for species identification of Thunnini fishes. We developed two species identification sets using HRM analysis based on genotyping species-specific single nucleotide polymorphisms in the mitochondrial genomes of nine species. To validate the effectiveness of the two HRM sets, we screened 312 individuals from 11 Thunnini and one Sardini species. The melting curves from the two sets of HRM analysis showed six perfectly species-specific and three nearly species-specific patterns, with the success rate of species identification ranging from 0.90 to 1.00. Thus, our findings indicate that these two HRM sets are powerful tools that can be used to identify the nine Thunnini species. The ability to identify these species will not only enhance ecological research into their early life stages but also improve the traceability of their fish products.

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Acknowledgements

This study was supported by the Fisheries Agency of Japan and the Japan Fisheries Research and Education Agency.

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Authors and Affiliations

  1. School of Marine Science and Technology, Department of Marine Biology, Tokai University, 3-20-1 Orido, Shimizu, Shizuoka, 424-8610, Shizuoka, Japan

    Hirohiko Takeshima, Kotomi Yamaura, Natsumi Kuboshima, Miyu Hiramatsu, Chisato Kameya & Kenji Nohara

  2. Research Center of Marine Bioresources, Department of Marine Bioscience, Fukui Prefectural University, 49-8-2, Katsumi, Obama, 917-0116, Fukui, Japan

    Hirohiko Takeshima

  3. Fisheries Resources Institute, Demersal Fish Resources Division, 1-5939-22, Suido, Chuo, Niigata, 951-8121, Niigata, Japan

    Kay Sakuma

  4. Fisheries Resources Institute, Demersal Fish Resources Division, 116 Katsurakoi, Kushiro, 085-0802, Hokkaido, Japan

    Satoru N. Chiba

  5. Fisheries Resources Institute, Highly Migratory Resources Division, 2-12-4, Fukuura, Kanazawa-ku Yokohama, Kanagawa, 236-8648, Japan

    Atsushi Tawa

  6. Fisheries Resources Institute, Fisheries Data Sciences Division, 2-12-4, Fukuura, Kanazawa-ku Yokohama, 236-8648, Kanagawa, Japan

    Nobuaki Suzuki

Authors
  1. Hirohiko Takeshima
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  2. Kotomi Yamaura
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  3. Natsumi Kuboshima
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  4. Miyu Hiramatsu
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  5. Chisato Kameya
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  6. Kenji Nohara
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  7. Kay Sakuma
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  8. Satoru N. Chiba
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  9. Atsushi Tawa
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  10. Nobuaki Suzuki
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Contributions

H.T., K.Y., N.K., M.H., and K.N. designed the study. K.N. and N.S. provided funding for the research. S.N.C. and A.T. organized the collection of samples. K.Y., N.K., M.H., and C.K. performed the DNA analyses. H.T. and K.S. wrote the draft of the manuscript. N.S. supervised the process to write the manuscript. All authors finalized the manuscript.

Corresponding author

Correspondence to Hirohiko Takeshima.

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Fig. S1

. Aligned sequences of the partial tRNA-Glu to Cytb gene from 12 Thunnini species and the primers and unlabeled-probe designed for the tribe set of the high-resolution melting analysis

Fig. S2

. Aligned sequences of the partial COI gene from eight Thunnus species and the primers and unlabeled-probes designed for the genus set of the high-resolution melting analysis

Fig. S3

. Aligned sequences of the partial COII gene from eight Thunnus species and the primers designed for the genus set of the high-resolution melting analysis

Table S1

. List of available whole mitochondrial genome sequences of 12 Thunnini species and the accession numbers of the International Nucleotide Sequence Database Collaboration database.

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Takeshima, H., Yamaura, K., Kuboshima, N. et al. A method for identifying nine tuna and tuna-like species (tribe Thunnini) by using high-resolution melting analysis based on genotyping single nucleotide polymorphisms in mitochondrial DNA. Conservation Genet Resour 15, 153–159 (2023). https://doi.org/10.1007/s12686-023-01315-5

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