Korean Journal of Ichthyology (한국어류학회지)

The Ichthyological Society of Korea (한국어류학회)
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Evidence of Intrusion of a Rare Species, Peristedion liorhynchus, into Korean Waters Based on High-throughput Sequencing of the Mixed Fish Eggs

희귀종 남방황성대(Peristedion liorhynchus)의 한국해 유입 증거 혼합 어란의 대용량 염기서열 분석법(high-throughput sequencing)으로 발견

  • Choi, Hae-young (Oceanic Climate & Ecology Research Division, Korea Institute of Ocean Science & Technology) ;
  • Chin, Byung-sun (Department of Marine Biotechnology, Anyang University) ;
  • Park, Gyung-soo (Department of Marine Biotechnology, Anyang University) ;
  • Kim, Sung (Oceanic Climate & Ecology Research Division, Korea Institute of Ocean Science & Technology)
  • 최해영 (한국해양과학기술원 해양생태연구센터) ;
  • 진병선 (안양대학교 강화캠퍼스 해양바이오시스템공학과) ;
  • 박경수 (안양대학교 강화캠퍼스 해양바이오시스템공학과) ;
  • 김성 (한국해양과학기술원 해양생태연구센터)
  • Received : 2022.02.15
  • Accepted : 2022.03.02
  • Published : 2022.03.31
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Abstract

The appearance of larvae of a rare species, Peristedion liorhynchus, in Korean waters is suggestive of spawning or adult intrusion. We conducted high-throughput sequencing (HTS) on 31,776 pelagic fish eggs collected from 123 stations off the Korean Peninsula during May to August in 2013, 2014 and 2017. A total of 21,621,874 HTS reads were mapped onto the P. liorhynchus COX1 reference sequence. Three consensus sequences (313 bp) were constructed from the three samples, respectively, off Uljin and Goeje Islands in May and off Ulsan in July. These samples were formed a clade with P. liorhynchus in the maximum likelihood tree of Peristedion. The average genetic distance within the P. liorhynchus clade (0.0054±0.0046) was less than that among clades (0.1475±0.0396). The results indicate that the HTS analysis of mixed fish eggs is useful for monitoring the intrusion of rare species such as P. liorhynchus in Korean waters.

한국 근해에서 희귀종 남방황성대(Peristedion liorhynchus) 치어의 출현은 이 종의 산란이나 성체의 유입 가능성을 암시한다. 우리는 2013, 2014, 2017년 5~8월 한국 연안의 123개 정점에서 수집한 어란 31,776개의 미토콘드리아 COX1 유전자에 대해 대용량 염기서열 분석(high-throughput sequencing, HTS)을 실시하였다. 확보한 21,621,874개 리드(reads)를 남방황성대(P. liorhynchus) COX1 참조염기서열(reference sequence)에 매핑(mapping)하여 이 종과 유전적 유사성이 높은 일치서열(consensus sequence)(313 bp)을 거제도와 울진(5월), 울산(7월) 주변해에서 발견하였다. 이 일치서열은 황성대속 maximum-likelihood tree에서 남방황성대 계통군에 속하였다. 남방황성대 계통군의 평균 유전적 거리(0.0054±0.0046)는 황성대속 내 계통군 간 평균 유전적 거리(0.1475±0.0396)보다 적었다. 이는 HTS 기반의 혼합 어란 분석을 남방황성대와 같은 희귀종 모니터링에 적용할 수 있음을 시사한다.

Keywords

Acknowledgement

본 논문은 한국해양과학기술원의 연구 과제(PEA0012)와 해양수산부와 해양환경공단이 주관하는 "국가해양생태계종합조사"의 자료를 이용하여 작성하였습니다. 국가해양생태계종합조사는 매년 입찰에 의하여 조사 기관이 선정되므로 조사 연도에 따라 자료 생산 기관이 상이하여 연구자 및 조사 기관을 전부 특정할 수 없어 본 논문의 저자에서는 생략하였습니다. 본 과제의 현장 조사 및 시료 분석에 기여하신 다수의 연구자와 조사 선박을 운영하여 주신 분들께 감사드립니다.

References

  1. Amplicon PCR, Clean-Up PCR and Index PCR. 2013. 16S Metagenomic Sequencing Library Preparation. https://support.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf.
  2. Ballenghien, M., N. Faivre and N. Galtier. 2017. Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions. BMC Biol., 15: 1-16. https://doi.org/10.1186/s12915-016-0343-5
  3. Choi, H.Y., J. Oh and S. Kim. 2018. Genetic identification of eggs from four species of Ophichthidae and Congridae (Anguilliformes) in the northern East China Sea. PloS One, 13: e0195382. https://doi.org/10.1371/journal.pone.0195382
  4. Clark, K., I. Karsch-Mizrachi, D.J. Lipman, J. Ostell and E.W. Sayers. 2016. GenBank. Nucleic Acids Res., 44: D67-D72. https://doi.org/10.1093/nar/gkv1276
  5. Delrieu-Trottin, E., L. Liggins, T. Trnski, J.T. Williams, V. Neglia, C. Rapu-Edmunds, S. Planes and P. Saenz-Agudelo. 2018. Evidence of cryptic species in the blenniid Cirripectes alboapicalis species complex, with zoogeographic implications for the South Pacific. Zookeys, 810: 127-138. https://doi.org/10.3897/zookeys.810.28887
  6. Duke, E.M. and R.S. Burton. 2020. Efficacy of metabarcoding for identification of fish eggs evaluated with mock communities. Ecol. Evol., 10: 3463-3476. https://doi.org/10.1002/ece3.6144
  7. Froese, R. and D. Pauly. (eds). 2020. FishBase. World Wide Web electronic publication. www.fishbase.org, version (12/2020).
  8. Gloerfelt-Tarp, T. and P.J. Kailola. 1984. Trawled fishes of southern Indonesia and northwestern Australia. Australian Development Assistance Bureau (ADAB), Directorate General of Fisheries, Indonesia (DGF), and German Agency for Technical Cooperation (GTZ), Jakarta, 407.
  9. Han, S.H., M.J. Kim and C.B. Song. 2015. Molecular identification and distribution pattern of fish eggs collected around Jejudo Island. Korean J. Ichthyol., 27: 284-292.
  10. Harada, A.E., E.A. Lindgren, M.C. Hermsmeier, P.A. Rogowski, E. Terrill and R.S. Burton. 2015. Monitoring spawning activity in a southern California marine protected area using molecular identification of fish eggs. PloS One, 10: e0134647. https://doi.org/10.1371/journal.pone.0134647
  11. Hebert, P.D., A. Cywinska, S.L. Ball and J.R. Dewaard. 2003. Biological identifications through DNA barcodes. Proc. R. Soc. B: Biol. Sci., 270: 313-321. https://doi.org/10.1098/rspb.2002.2218
  12. Houde, E.D. 1987. Fish early life dynamics recruitment variability. America Fisheries Society Symposium, 2: 17-29.
  13. Ikeda, T., A. Hirai, S. Tabata, Y. Onishi and S. Mito. 2014. In: An atlas of early stage fishes in Japan. 2nd edition (Okiyama M. editor), 108 pp. Tokyo: Tokai University Press.
  14. Jang, S.H., J.K. Kim and H.J. Ryu. 2020a. Morphological description and molecular identification of juvenile Peristedion liorhynchus (Peristediidae, Pisces) from Jeju-do Island, Korea. Korean J. Fish. Aquat. Sci., 53: 794-799. https://doi.org/10.5657/KFAS.2020.0794
  15. Jang, S.H., J.K. Kim and J.H. Ryu. 2020b. First report on the occurrence of eggs of the small yellow croaker Larimichthys polyactis from Chilsan-do Island, Jeollanam-do, Korea. Korean J. Fish. Aquat. Sci., 53: 650-655. https://doi.org/10.5657/KFAS.2020.0650
  16. Jang, Y.S., K.Y. Kim and S. Kim. 2015. The complete mitochondrial genome of the Hwanghae Rockfish Sebastes koreanus(Scorpaenidae, Scorpaeniformes). Mitochondrial DNA, 26: 834-835. https://doi.org/10.3109/19401736.2013.855916
  17. Kaschner, K., K. Kesner-Reyes, C. Garilao, J. Segschneider, J. Rius-Barile, T. Rees and R. Froese. 2019. AquaMaps: Predicted range maps for aquatic species. World Wide Web electronic publication, www.aquamaps.org, version 10/2019 (final).
  18. Kim, G. and Y. Song. 2021. Identification of freshwater fish species in Korea using environmental DNA technique-from the experiment at the freshwater fish ecological learning center in Yangpyeong, Gyeonggi Do. J. Environ. Impact Assess., 30: 1-12. https://doi.org/10.14249/EIA.2021.30.1.1
  19. Kim, S., C.G. Kim, J. Oh, B.J. Kim, H.S. Seo, W.S. Kim and Y.H. Lee. 2008. Genetic similarity between the South Atlantic and the western North Pacific Maurolicus (Stomiiformes: Actinopterygii) taxa, M. walvisensis Parin & Kobyliansky and M. japonicus Ishikawa: evidence for synonymy? J. Fish. Biol., 72: 1202-1214. https://doi.org/10.1111/j.1095-8649.2007.01786.x
  20. Kumar, S., G. Stecher, M. Li, C. Knyaz and K. Tamura. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evolution, 35: 1547-1549. https://doi.org/10.1093/molbev/msy096
  21. Leray, M., J.Y. Yang, C.P. Meyer, S.C. Mills, N. Agudelo, V. Ranwez, J.T. Boehm and R.J. Machida. 2013. A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front. Zoology, 10: 1-14. https://doi.org/10.1186/1742-9994-10-1
  22. Lin, H.Y., M.Y. Chiu, Y.M. Shih, I.S. Chen and M.A. Lee. 2016. Species composition and assemblages of ichthyoplankton during summer in the East China Sea. Cont. Shelf Res., 126: 64-78. https://doi.org/10.1016/j.csr.2016.07.016
  23. May, J.L. and J.G.H. Maxwell. 1986. Trawl fish from temperate waters of Australia. CSIRO Division of Fisheries Research, Tasmania, 492.
  24. Monkolprasit, S., S. Sontirat, S. Vimollohakarn and T. Songsirikul. 1997. Checklist of fishes in Thailand. Office of environmental policy and planning, Bangkok, Thailand, 353.
  25. National list of species of Korea. 2020. National Institute of Biological Resources, online at http://kbr.go.kr accessed on February 21 2022.
  26. Nei, M. and S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York.
  27. Ochiai, A. and T. Yatou. 1984. Peristediidae. In: The fishes of the Japanese Archipelago. Masuda, H., K. Amaoka, C. Araga, T. Uyeno and T. Yoshino. Editors, Tokai University Press, Tokyo, Japan, 301-364.
  28. Oh, J. and S. Kim. 2015. Morphological and molecular characterization of separated pelagic eggs from Lophius litulon (Lophiiformes; Lophiidae). J. Fish Biol., 86: 1887-1891. https://doi.org/10.1111/jfb.12701
  29. Okiyam, M.(Editor). 2014. An atlas of early stage fishes in Japan. 2nd edition. 1639pp. Tokyo: Tokai University Press.
  30. Paxton, J.R., J.E. Gates, D.J. Bray, M.F. Gomon and D.F. Hoese. 2006. Triglidae. armoured gurnards, armoured sea robins, gurnards, sea robins, searobins. In: zoological catalogue of Australia. Vol. 35. Fishes. Part 2. Actinopterygii: acanthopterygii (in part): mugiliformes to perciformes (Zoarcoidei to Labroidei). Hoese, D.F., D.J. Bray, J.R. Paxton and G.R. Allen. (Editors)., ABRS & CSIRO Publishing, Melbourne, Australia, pp. 921-930.
  31. Richards, W.J. 1999. Triglidae. In: FAO Species Identification Guide for Fishery Purposes. The Living Marine Resources of the Western Central Pacific. Vol. 4. Bony Fishes Part 2 (Mugilidae to Carangidae). Carpenter, K.E. and V.H. Niem (Editors). FAO, Rome, Italy, pp. 2359-2382.
  32. Shao, K.T., J.S. Yang, K.C. Chen and Y.S. Lee. 2001. An identification guide of marine fish eggs from Taiwan. Institute of Zoology, Academia Sinica and Taiwan Power Company, 179.
  33. Song, C.U., H. Choi, M.S. Jeon, E.J. Kim, H.G. Jeong, S. Kim, C.G. Kim, H. Hwang, D.W. Purnaningtyas, S. Lee, S.I. Eyun and Y.H. Lee. 2021. Zooplankton diversity monitoring strategy for the urban coastal region using metabarcoding analysis. Sci. Rep., 11: 1-13. https://doi.org/10.1038/s41598-020-79139-8
  34. Takeuchi, A., T. Iijima, W. Kakuzen, S. Watanabe, Y. Yamada, A. Okamura, N. Horie, N. Mikawa, M.J. Miller, T. Kojima and K. Tsukamoto. 2019. Release of eDNA by different life history stages and during spawning activities of laboratory-reared Japanese eels for interpretation of oceanic survey data. Sci. Rep., 9: 1-9. https://doi.org/10.1038/s41598-018-37186-2
  35. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22: 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  36. Tsukamoto, K., S. Chow, T. Otake, H. Kurogi, N. Mochioka, M.J. Miller, J. Aoyama, S. Kimura, S. Watanabe, T. Yoshinaga, A. Shinoda, M. Kuroki, M. Oya, T. Watanabe, K. Hata, S. Ijiri, Y. Kazeto, K. Nomura and H. Tanaka. 2011. Oceanic spawning ecology of freshwater eels in the western North Pacific. Nat. Commun., 2: 1-9.