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Tandem PCR-RFLP analysis helps distinguish among three Japanese gnomefish (Teleostei: Scombropidae: Scombrops)

Abstract

Scombrops boops and Scombrops gilberti are commercially important species inhabiting waters around the Japanese archipelago, and recently another undescribed species Scombrops sp. was found. Here, we developed a method using PCR-RFLP on cytochrome b gene sequences of known scombropids to distinguish among these taxa. Comparison of RFLP of the PCR products among scombropids produced a species-specific banding pattern, identifying them with close to 100% accuracy. Two misidentified specimens were identified correctly by the PCR-RFLP analysis developed previously using 16S rRNA sequences. These results showed that PCR-RFLP analysis, using 16S rRNA and cytochrome b sequences in tandem, correctly distinguishes among the three scombropids. We applied this method to 190 individuals collected around the Yonagunijima Island and got some insights into reproductive biology of the three species of Scombrops.

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References

  • Chen W, Ma X, Shen Y, Mao Y, He S (2015) The fish diversity in the upper reaches of the Salween River, Nujiang River, revealed by DNA Barcoding. Sci Rep 5: 17437

    CAS  Article  Google Scholar 

  • Dhar B, Ghosh SK (2015) Genetic assessment of ornamental fish species from North East India. Gene 555: 382–392

    CAS  Article  Google Scholar 

  • Hebert PD, Ratnasingham S, deWard JR (2003a) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Biol Sci 270: S96–S99

    CAS  Google Scholar 

  • Hebert PD, Cywinska A, Ball SL, deWard JR (2003b) Biological identifications through DNA barcodes. Proc Biol Sci 270: 313–321

    CAS  Article  Google Scholar 

  • Itoi S, Saito T, Shimojo M, Washio S, Sugita H (2007) Identification of Girella punctata and G. leonina by PCR-RFLP analysis. ICES J Mar Sci 64: 328–331

    Article  Google Scholar 

  • Itoi S, Takai N, Naya S, Dairiki K, Yamada A, Akimoto S, Yoshihara K, Sugita H (2008) A species identification method for Scombrops boops and Scombrops gilberti based on polymerase chain reaction-restriction fragment length polymorphism analysis of mitochondrial DNA. Fish Sci 74: 503–510

    CAS  Article  Google Scholar 

  • Itoi S, Odaka J, Yuasa K, Akeno S, Nakajima A, Suenaga A, Noda T, Akimoto S, Myojin T, Ikeda Y, Masuda Y, Takai N, Yoshihara K, Sugita H (2010) Distribution and species composition of juvenile and adult scombropids (Teleostei, Scombropidae) in Japanese coastal waters. J Fish Biol 76: 369–378

    CAS  Article  Google Scholar 

  • Itoi S, Odaka J, Noguchi S, Noda T, Yuasa K, Muraki T, Tanabe T, Takai N, Yoshihara K, Sugita H (2011) Genetic homogeneity between adult and juvenile populations of Scombrops gilberti (Percoid, Scombropidae) in the Pacific Ocean off the Japanese Islands. Fish Sci 77: 975–981

    CAS  Article  Google Scholar 

  • Itoi S, Mochizuki Y, Tanaka M, Oyama H, Tsunashima T, Yamada R, Shishido H, Masuda Y, Nakai S, Takai N, Fukushima H, Abe K, Kojima T, Sugita H (2018) Species composition of the genus Scombrops (Teleostei, Scombropidae) in the waters around the Japanese Archipelago: detection of a cryptic species. Mitochondrial DNA A DNA Mapp Seq Anal 29: 1293–1300

    CAS  PubMed  Google Scholar 

  • Khedkar GD, Jamdade R, Naik S, David L, Haymer D (2014) DNA barcodes for the fishes of the Narmada, one of India’s longest rivers. PLoS One 9: e101460

    Article  Google Scholar 

  • Ma H, Ma C, Ma L (2012) Molecular identification of genus Scylla (Decapoda: Portunidae) based on DNA barcoding and polymerase chain reaction. Biochem Syst Ecol 41: 41–47

    CAS  Article  Google Scholar 

  • Mochizuki K (1979) Age and growth of the two Japanese scombropids, Scombrops boops and S. gilberti. Jpn J Ichthyol 26: 62–68

    Google Scholar 

  • Mochizuki K (1984) Family Scombropidae. In: Masuda H, Amaoka K, Araga C, Uyeno T, Yoshino T (eds) The Fishes of the Japanese Archipelago. Tokai University Press, Tokyo, p 152

    Google Scholar 

  • Mochizuki Y, Yamada R, Shishido H, Masuda Y, Nakai S, Takai N, Itoi S, Sugita H (2017) Complete mitochondrial genome of an undescribed gnomefish of the genus Scombrops (Teleostei, Scombropidae) from southern waters off Kyushu Island, Japan. Mitochondrial DNA B Resour 2: 106–108

    Article  Google Scholar 

  • Noguchi S, Itoi S, Takai N, Noda T, Myojin T, Yoshihara K, Sugita H (2012) Population genetic structure of Scombrops boops (Percoid, Scombropidae) around the Japanese archipelago inferred from the cytochrome b gene sequence in mitochondrial DNA. Mitochondrial DNA 23: 233–239

    Article  Google Scholar 

  • Oyama H, Itoi S, Ueda H, Mochizuki Y, Tanaka M, Ito T, Shishido H, Masuda Y, Takai N, Sugita H (2019) Genetic difference between African and Japanese scombropid populations based on cytochrome c oxidase subunit I gene sequences. Mitochondrial DNA B Resour 4: 1016–1020

    Article  Google Scholar 

  • Palumbi S, Martin A, Romano S, McMillan WO, Stice L, Grabowski G (1991) The simple fool’s guide to PCR, ver 2. Department of Zoology and Kewalo Marine Laboratory, University of Hawaii, Honolulu

    Google Scholar 

  • Poey F (1860) Poissons de Cuba. Mem Hist Nat Isla Cuba 2: 115–356

    Google Scholar 

  • Sato S (1940) Supplementary notes on the fishes from Akkeshi Bay. J Fac Sci Hokkaido Imp Univ Ser VI Zool 7: 99–106

    Google Scholar 

  • Shao K-T (1987) First record of Scombropidae (Pisces: Percoidei) from Taiwan. Bull Inst Zool Acad Sin 26: 191–194

    Google Scholar 

  • Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7: 539

    Article  Google Scholar 

  • Steinke D, Zemlak TS, Boutillier JA, Hebert PD (2009) DNA barcoding of Pacific Canada’s fishes. Mar Biol 156: 2641–2647

    Article  Google Scholar 

  • Steinke D, Connell AD, Hebert PDN (2016) Linking adults and immatures of South African marine fishes. Genome 59: 959–967

    Article  Google Scholar 

  • Takai N, Kozuka Y, Tanabe T, Sagara Y, Ichihashi M, Nakai S, Suzuki M, Mano N, Itoi S, Asahina K, Kojima T, Sugita H (2014) Habitat use of the gnomefishes Scombrops boops and S. gilberti in the northwestern Pacific Ocean in relation to reproductive strategy. Aquat Biol 21: 109–120

    Article  Google Scholar 

  • Tsunashima T, Itoi S, Abe K, Takigawa T, Inoue S, Kozen T, Ono N, Noguchi S, Nakai S, Takai N, Huang M-C, Sugita H (2016a) The complete mitochondrial genome of the gnomefish Scombrops boops (Teleostei, Perciformes, Scombropidae) from the Pacific Ocean off the Japanese Islands. Mitochondrial DNA A DNA Mapp Seq Anal 27: 785–786

    CAS  Article  Google Scholar 

  • Tsunashima T, Yamada R, Abe K, Noguchi S, Itoi S, Nakai S, Takai N, Sugita H (2016b) Phylogenetic position of Scombropidae within teleostei: the complete mitochondrial genome of the gnomefish, Scombrops gilberti. Mitochondr DNA A DNA Mapp Seq Anal 27: 3446–3448

    CAS  Google Scholar 

  • Ward RD, Costa FO, Holmes BH, Steinke D (2008) DNA barcoding of shared fish species from the North Atlantic and Australasia: minimal divergence for most taxa, but Zeus faber and Lepidopus caudatus each probably constitute two species. Aquat Biol 3: 71–78

    Article  Google Scholar 

  • Yasuda F, Mochizuki K, Kawajiri M, Nose Y (1971) On the meristic and morphometric differences between Scombrops boops and S. gilberti. Jpn J Ichthyol 18: 118–124

    Google Scholar 

  • Zhu SR, Fu JJ, Wang W, Li JL (2013) Identification of Channa species using the partial cytochrome c oxidase subunit I (COI) gene as a DNA barcoding marker. Biochem Syst Ecol 51: 117–123

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank H. Imai for his cooperation in the collection of specimens. This study was supported in part by Research Grants for 2016–2018 from Nihon University College of Bioresource Sciences (S.I., S.N. and N.T.), and the Japan Science Society for 2016 (28-721, Y.M.).

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Correspondence to Shiro Itoi.

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Itoi, S., Tanaka, M., Mochizuki, Y. et al. Tandem PCR-RFLP analysis helps distinguish among three Japanese gnomefish (Teleostei: Scombropidae: Scombrops). Ichthyol Res 67, 197–202 (2020). https://doi.org/10.1007/s10228-019-00705-w

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  • DOI: https://doi.org/10.1007/s10228-019-00705-w

Keywords

  • Cryptic species
  • Cytochrome b
  • Gnomefishes
  • Species identification
  • Tandem PCR-RFLP
  • 16S rRNA