Skip to main content

Advertisement

SpringerLink
Log in

The Jawa and Bali Island Marine Fish Molecular Identification to Improve 12S rRNA-tRNA Valin-16S rRNA Partial Region Sequences on the GenBank Database

  • Published:
Thalassas: An International Journal of Marine Sciences Aims and scope Submit manuscript

Abstract

The molecular approach provides an alternative method of easy identification of marine finfish, quickly and has high accuracy. This study represents the molecular identification based on the 12S rRNA and 16S rRNA partial region (12S–16S rRNA PR) then confirm by Cytochrome C Oxidase I (COI) of commercial marine fish of Jawa and Bali, Indonesia. We examined 169 samples and identified 78 new 12S–16S rRNA PR sequences confirmed by the COI region representing 136 genera, 50 families, and 12 orders. Carangids were dominated and followed by Lutjanids, Scombrids, and Serranids. We highlight the importance of implementing molecular identification of marine resources for complementing biodiversity assessment in Indonesian marine ecosystems. This study represents the first step toward the environment DNA (e-DNA) analysis in Java and Bali marine ecosystem using the 12S–16S rRNA PR.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Antoro S, Na-Nakorn U, Koedprang W (2006) Study of genetic diversity of orange-spotted grouper, Epinephelus coioides, from Thailand and Indonesia using microsatellite markers. Mar Biotechnol 8:17–26

    Google Scholar 

  • Arai, T., Aoyama, J., Limbong, D. & Tsukamoto, K. 1999. Species composition and inshore migration of the tropical eels Anguilla spp. recruiting to the estuary of the Poigar River, Sulawesi Island. Marine Ecology Progress Series, 299–303

  • Ariyanti Y (2012) Aplikasi DNA Barcode pada Penentuan Spesies Ikan Danau Laut Tawar, Nangroe Aceh Darussalam

  • Baldwin CC, Mounts JH, Smith DG, Weigt LA (2009) Genetic identification and color descriptions of early life-history stages of Belizean Phaeoptyx and Astrapogon (Teleostei: Apogonidae) with comments on identification of adult Phaeoptyx. Zootaxa 2008:1–22

    Google Scholar 

  • Bellwood DR, Meyer CP (2009) Endemism and evolution in the coral triangle: a call for clarity. J Biogeogr 36:2010–2012

    Google Scholar 

  • Bernardi G, Vagelli A (2004) Population structure in Banggai cardinalfish, Pterapogon kauderni, a coral reef species lacking a pelagic larval phase. Mar Biol 145:803–810

    Google Scholar 

  • Bernardi G, Holbrook SJ, Schmitt RJ (2001) Gene flow at three spatial scales in a coral reef fish, the three-spot dascyllus, Dascyllus trimaculatus. Mar Biol 138:457–465

    Google Scholar 

  • Boore JL, Medina M, Rosenberg LA (2004) Complete sequences of the highly rearranged molluscan mitochondrial genomes of the scaphopod Graptacme eborea and the bivalve Mytilus edulis. Mol Biol Evol 21:1492–1503

    Google Scholar 

  • Carreras-Carbonell J, Pascual M, Macpherson E (2007) A review of the Tripterygion tripteronotus (Risso, 1810) complex, with a description of a new species from the Mediterranean Sea (Teleostei: Tripterygiidae). Sci Mar 71:75–86

    Google Scholar 

  • Cawthorn D-M, Steinman HA, Witthuhn RC (2012) Evaluation of the 16s and 12s rrna genes as universal markers for the identification of commercial fish species in south africa. Gene 491:40–48

    Google Scholar 

  • Chow S, Ueno Y, Toyokawa M, Oohara I, Takeyama H (2009) Preliminary analysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals. Mar Biotechnol 11:301–306

    Google Scholar 

  • Collette B, Carpenter K, Polidoro B, Juan-Jordá M, Boustany A, Die D, Elfes C, Fox W, Graves J, Harrison L (2011) High value and long life—double jeopardy for tunas and billfishes. Science 333:291–292

    Google Scholar 

  • Comitini S, Hardjolukito S (1986) Economic benefits and costs of alternative arrangements for tuna fisheries development in the exclusive economic zone: the case of Indonesia. Ocean management 10:37–55

    Google Scholar 

  • Croce O, Lamarre M, Christen R (2006) Querying the public databases for sequences using complex keywords contained in the feature lines. BMC bioinformatics 7:45

    Google Scholar 

  • Dahruddin H, Hutama A, Busson F, Sauri S, Hanner R, Keith P, Hadiaty R, Hubert N (2017) Revisiting the ichthyodiversity of Java and Bali through DNA barcodes: taxonomic coverage, identification accuracy, cryptic diversity and identification of exotic species. Mol Ecol Resour 17:288–299

    Google Scholar 

  • Das S, Deb B (2015) DNA barcoding of fungi using ribosomal ITS marker for genetic diversity analysis: a review. Int J Pure Appl Biosci 3:160–167

    Google Scholar 

  • DJPT (2011) Statistika Perikanan Tangkap Indonesia 2010. Kementrian Kelautan dan Perikanan, Jakarta

    Google Scholar 

  • Douady CJ, Dosay M, Shivji MS, Stanhope MJ (2003) Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol Phylogenet Evol 26:215–221

    Google Scholar 

  • Dulvy NK, Baum JK, Clarke S, Compagno LJ, Cortés E, Domingo A, Fordham S, Fowler S, Francis MP, Gibson C (2008) You can swim but you can't hide: the global status and conservation of oceanic pelagic sharks and rays. Aquat Conserv Mar Freshwat Ecosyst 18:459–482

    Google Scholar 

  • Giusti A, Armani A, Sotelo CG (2017) Advances in the analysis of complex food matrices: species identification in surimi-based products using next generation sequencing technologies. PLoS One 12:1–18

    Google Scholar 

  • Handy SM, Deeds JR, Ivanova NV, Hebert PD, Hanner RH, Ormos A, Weigt LA, Moore MM, Yancy HF (2011) A single-laboratory validated method for the generation of DNA barcodes for the identification of fish for regulatory compliance. J AOAC Int 94:201–210

    Google Scholar 

  • Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P (2008) Identifying Canadian freshwater fishes through DNA barcodes. PLoS One 3:e2490

    Google Scholar 

  • Hubert N, Wibowo A, Busson F, Caruso D, Sulandari S, Nafiqoh N, Pouyaud L, Rüber L, Avarre J-C, Herder F (2015) DNA barcoding Indonesian freshwater fishes: challenges and prospects. DNA Barcodes 3:144–169

    Google Scholar 

  • Jefri E, Zamani NP, Subhan B, Madduppa HH (2015) Molecular phylogeny inferred from mitochondrial DNA of the grouper Epinephelus spp in Indonesia collected from local fish market Biodiversitas Journal of Biological Diversity:16

  • Johnson WE, O’Brien SJ (1997) Phylogenetic reconstruction of the Felidae using 16S rRNA and NADH-5 mitochondrial genes. J Mol Evol 44:S98–S116

    Google Scholar 

  • Kohno H, Ordonio-Aguilar RS, Ohno A, Taki Y (1997) Why is grouper larval rearing difficult?: an approach from the development of the feeding apparatus in early stage larvae of the grouper, Epinephelus coioides. Ichthyol Res 44:267–274

    Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Google Scholar 

  • Lakra W, Verma M, Goswami M, Lal KK, Mohindra V, Punia P, Gopalakrishnan A, Singh K, Ward RD, Hebert P (2011) DNA barcoding Indian marine fishes. Mol Ecol Resour 11:60–71

    Google Scholar 

  • Lebonah D, Dileep A, Chandrasekhar K, Sreevani S, Sreedevi B, Pramoda Kumari J (2014) DNA barcoding on bacteria: a review. Advances in Biology 2014

  • Lourie SA, Vincent AC (2004) A marine fish follows Wallace's line: the phylogeography of the three-spot seahorse (Hippocampus trimaculatus, Syngnathidae, Teleostei) in Southeast Asia. J Biogeogr 31:1975–1985

    Google Scholar 

  • Lowe-Mcconnell R (1969) Speciation in tropical freshwater fishes. Biol J Linn Soc 1:51–75

    Google Scholar 

  • Macey JR, Papenfuss TJ, Kuehl JV, Fourcade HM, Boore JL (2004) Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol Phylogenet Evol 33:22–31

    Google Scholar 

  • Madduppa HH, Timm J, Kochzius M (2014) Interspecific, spatial and temporal variability of self-recruitment in anemonefishes. PLoS One 9:e90648

    Google Scholar 

  • Meyer CP, Paulay G (2005) DNA barcoding: error rates based on comprehensive sampling. PLoS Biol 3:e422

    Google Scholar 

  • Minamoto T, Uchii K, Takahara T, Kitayoshi T, Tsuji S, Yamanaka H, Doi H (2017) Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio. Mol Ecol Resour 17:324–333

    Google Scholar 

  • Mitchell JK, Hellberg RS (2016) Use of the mitochondrial control region as a potential DNA mini-barcoding target for the identification of canned tuna species. Food Anal Methods 9:2711–2720

    Google Scholar 

  • Mitcheson D, Sadovy Y, Liu M (2008) Functional hermaphroditism in teleosts. Fish Fish 9:1–43

    Google Scholar 

  • Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R Soc Open Sci 2:150088

    Google Scholar 

  • Morris AV, Roberts CM, Hawkins JP (2000) The threatened status of groupers (Epinephelinae). Biodivers Conserv 9:919–942

    Google Scholar 

  • Muchlisin ZA, Thomy Z, Fadli N, Sarong MA, Siti-Azizah MN (2013) DNA barcoding of freshwater fishes from Lake Laut Tawar, Aceh Province. Indonesia Acta ichthyologica et piscatoria 43

  • Pavan-KUMAR A, Gireesh-Babu P, Babu PS, Jaiswar A, Krishna VH, Prasasd KP, Chaudhari A, Raje S, Chakraborty S, Krishna G (2014) Molecular phylogeny of elasmobranchs inferred from mitochondrial and nuclear markers. Mol Biol Rep 41:447–457

    Google Scholar 

  • Pepe T, Trotta M, DI Marco I, Anastasio A, Bautista JM, Cortesi ML (2007) Fish species identification in surimi-based products. J Agric Food Chem 55:3681–3685

    Google Scholar 

  • Prehadi, P., Sembiring, A., Kurniasih, E. M., Rahmad, R., Arafat, D., Subhan, B. & Madduppa, H. H. 2014. DNA barcoding and phylogenetic reconstruction of shark species landed in Muncar fisheries landing site in comparison with Southern Java fishing port. Biodiversitas Journal of Biological Diversity, 16

  • Puebla O (2009) Ecological speciation in marine v. freshwater fishes. J Fish Biol 75:960–996

    Google Scholar 

  • Rocha L, Bowen B (2008) Speciation in coral-reef fishes. J Fish Biol 72:1101–1121

    Google Scholar 

  • Roy D, Docker M, Hehanussa P, Heath D, Haffner G (2004) Genetic and morphological data supporting the hypothesis of adaptive radiation in the endemic fish of Lake Matano. J Evol Biol 17:1268–1276

    Google Scholar 

  • Sadovy de Mitcheson Y, Craig MT, Bertoncini AA, Carpenter KE, Cheung WW, Choat JH, Cornish AS, Fennessy ST, Ferreira BP, Heemstra PC (2013) Fishing groupers towards extinction: a global assessment of threats and extinction risks in a billion dollar fishery. Fish Fish 14:119–136

    Google Scholar 

  • Seehausen O, Wagner CE (2014) Speciation in freshwater fishes. Annu Rev Ecol Evol Syst 45:621–651

    Google Scholar 

  • Sembiring A, Pertiwi NPD, Mahardini A, Wulandari R, Kurniasih EM, Kuncoro AW, Cahyani ND, Anggoro AW, Ulfa M, Madduppa H (2015) DNA barcoding reveals targeted fisheries for endangered sharks in Indonesia. Fish Res 164:130–134

    Google Scholar 

  • Sevilla RG, Diez A, Norén M, Mouchel O, Jérôme M, Verrez-Bagnis V, van Pelt H, Favre-krey L, Krey G, Consortium TF (2007) Primers and polymerase chain reaction conditions for DNA barcoding teleost fish based on the mitochondrial cytochrome b and nuclear rhodopsin genes. Mol Ecol Notes 7:730–734

    Google Scholar 

  • Sharp GD (1996) Oceanography of the Indonesian archipelago and adjacent areas. The Fish Resources of Western Indonesia ICLARM Stud Rev, Baseline Studies of Biodiversity, p 321

    Google Scholar 

  • Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E (2012a) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One 7:e41732

    Google Scholar 

  • Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E (2012b) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573

    Google Scholar 

  • Wafar M, Venkataraman K, Ingole B, Khan SA, Lokabharathi P (2011) State of knowledge of coastal and marine biodiversity of Indian Ocean countries. PLoS One 6:e14613

    Google Scholar 

  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London B: Biological Sciences 360:1847–1857

    Google Scholar 

  • Wilcox TM, Mckelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS One 8:e59520

    Google Scholar 

  • Winterbottom R, Hanner RH, Burridge M, Zur M (2014) A cornucopia of cryptic species-a DNA barcode analysis of the gobiid fish genus Trimma (Percomorpha, Gobiiformes). ZooKeys 79

  • Zhang J-B, Hanner R (2011) DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochem Syst Ecol 39:31–42

    Google Scholar 

Download references

Acknowledgments

We would like to thank the graduate students of Molecular Physiology Laboratory, Pukyong National University, Busan, Korea for their helpful suggestions during this study. We grateful for the Indonesian Endowment Fund for Education (LPDP) scholarship under Beasiswa Unggulan Dosen Indonesia-Luar Negeri (BUDI-LN) batch I 2016 and also BK21 PKNU support in the partial experiment. Besides that, for the great survey along Java and Bali Island, we would like to thank our several colleagues, Ricky, and Suciyono (Gresik, Malang, Banyuwangi, and Bali), Senin at Pelabuhan Ratu survey, and Alfie and Raka at Bali Survey.

Author information

Authors and Affiliations

  1. Interdisciplinary Program of Biomedical, Mechanical, and Electrical Engineering, Pukyong National University, Busan, 48513, Republic of Korea

    Sapto Andriyono, Md. Jobaidul Alam & Hyun-Woo Kim

  2. Departmen of Marine Science, Fisheries and Marine Faculty, UNAIR C Campus Jl. Mulyorejo Surabaya 60115. Universitas Airlangga, Surabaya, East Java, 60115, Indonesia

    Sapto Andriyono

  3. Department of Marine Biology, Pukyong National University, Busan, 48513, Republic of Korea

    Hyun-Woo Kim

Authors
  1. Sapto Andriyono
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Md. Jobaidul Alam
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hyun-Woo Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

SA: conducted survey, whole experiment, data analysis and write manuscript; HWK: design primer experiment, data analysis, and writing manuscript; MJA: experiment and write the manuscript.

Corresponding author

Correspondence to Sapto Andriyono.

Ethics declarations

Conflict of Interest

No competing interests were disclosed.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Andriyono, S., Alam, M.J. & Kim, HW. The Jawa and Bali Island Marine Fish Molecular Identification to Improve 12S rRNA-tRNA Valin-16S rRNA Partial Region Sequences on the GenBank Database. Thalassas 36, 343–356 (2020). https://doi.org/10.1007/s41208-020-00196-x

Download citation

  • Received:

  • Revised:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s41208-020-00196-x

Keywords

Search

Navigation